1,904 Matching Annotations
  1. Oct 2026
    1. The long clinical history of a 45-year-old woman started at 22 years of age when she had surgery for a right adrenal pheochromocytoma. Two years later, a pancreaticoduodenectomy was performed to remove a pancreatic mass which turned out to be a pancreatic neuroendocrine tumor. After a long period of relative wellness, 21 years after the surgical resection of her primary pancreatic neuroendocrine tumor, abdominal lymph node metastases of pancreatic neuroendocrine origin occurred. In fact, three abdominal nodules were removed by laparoscopic surgery, and the histological examination showed well-differentiated neuroendocrine tumors with similar immunohistochemical characteristics and Ki67 below 1%.

      PatientID: N/A (case)

      KindredID: 1

      Case: F, 45Y0M, Italian

      DiseaseAssertion: Assumed VHL

      FamilyInfo: Genetic analysis was performed on the patients relatives, including her daughter. Her 55Y0M brother had the same mutation but no clinical signs of VHL disease.

      CasePresentingHPOs: HP:0006748; HP:0030405 (adrenal pheochromocytoma, pancreatic neuroendocrine tumour)

      CaseHPOFreeText: At 22Y0M, she had surgery for a right adrenal pheochromocytoma. Two years later, a pancreatic oduodenectomy was performed to remove a pancreatic neuroendocrine tumor. 21 years later, abdominal lymph node metastases of the pancreatic neuroendocrine that was removed 21 years prior had occurred. Three abdominal nodules that were found to be neuroendocrine tumours immunohistochemical characteristics were removed. The patient’s clinical history suggested a hereditary endocrine syndrome.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.T157I (c.470C>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223223, https://www.ncbi.nlm.nih.gov/clinvar/variation/223223/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense variant; transition

      CivicName: T157I (c.470C>T)

      MultipleGeneVariants: N/A

    1. c.499C>T p.Arg167Trp

      PatientID: II:4 (proband 5’s sister 2)

      KindredID: 5

      Case: F, 34Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: Her father and two sisters presented with this same mutation. The father had RCC diagnosed at 54Y. The one sister (II:3) had had pancreatic tumors at 36Y and hemangioblastomas at 38Y. The brother (II:1) appeared to be non-affected, while the other sister (II:2) had hemangioblastoma, renal cell carcinoma, pancreatic cysts, and Papillary cystadenoma of the epididymis diagnosed at 37Y; and pheochromocytoma at 39Y

      CasePresentingHPOs: HP:0009711 (retinal capillary angiomas)

      CaseHPOFreeText: had retinal angiomas at 34Y

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.R167W (c.499C>T)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: 2218 (https://www.ncbi.nlm.nih.gov/clinvar/variation/2218/)

      CAID: N/A

      gnomAD: 0.000007954 https://gnomad.broadinstitute.org/variant/3-10191506-C-T

      VariantEvidence: N/A

      MutationType: missense_variant; transition

      CivicName: R167W (c.499C>T)

      MultipleGeneVariants: N/A

    2. 1Deletion

      PatientID: II:2

      KindredID: 8

      Case: F, 43Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: a 3 generational family found with 5 phenotypically affected members, two of which were confirmed with the exon 1 deletion. This patient and her son were tested to be found with the deletion of exon 1. Her son was found with retinal angiomas at 17Y, pancreatic cysts and epididymal/ovarian cystadenoma at 19Y, and hemangioblastomas at 23Y. Her two sisters and father all had hemangioblastomas; and father also had RCC, however the father and one sister were deceased; and the other sister was not available to provide a DNA sample.

      CasePresentingHPOs: HP:0009711; HP:0010797 (retinal capillary hemangioma, hemangioblastoma)

      CaseHPOFreeText: patient was found with retinal hemangioblastomas at 35Y and hemangioblastomas at 43Y

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: exon 1 deletion

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: exon_loss_variant

      CivicName: exon 1 deletion

      MultipleGeneVariants: N/A

    1. PatientID: 93 (First cousin once removed)

      KindredID: 18

      Case: M, 31Y0M, Ethnicity Unknown

      DiseaseAssertion: Assumed VHL

      FamilyInfo: 11 members of this family tested positive for the c.712C>T/c.499C>T germline variant of the VHL gene. 14 members of this family were assumed to carry this variant due to family history/personal medical history. Members of this family range from asymptomatic to multi-organ involvement (pheochromocytoma, pancreatic and renal cysts/tumors and hemangioblastomas). The family was previously reported in PMID 3942913.

      CasePresentingHPOs: HP:0002666 (Pheochromocytoma)

      CaseHPOFreeText: This patient presented with pheochromocytoma (31Y). Patient died at 31Y.

      CaseNotHPOs: HP:0005584; HP:0000077; HP:0001732; HP:0009711; HP:0010797 (Renal cell carcinoma, Abnormality of the kidney, Abnormality of the pancreas, Retinal capillary hemangioma, Hemangioblastoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 3942913 (some members of this family are previously reported (phenotypes only) but unable to match patients across papers with confidence)

      SupplementalData: Supplementary Table 1.

      Variant: N/A

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: Authors state that the c.712C>T germline familial variant of the VHL gene in this patient is “inferred from the family”. No genetic testing was done on this patient to confirm this. Being that this familial variant is out of bound with respect to the NM_000551.3 reference sequence, it was concluded that this variant is noted in the Latif et al. (1993) reference and was translated to c.499C>T (NM_000551.3).

      MutationType: N/A

      CivicName: N/A

      MultipleGeneVariants: N/A

    2. PatientID: 5 (Aunt)

      KindredID: 17

      Case: F, 38Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: 6 members of this family tested positive for the c.496_506del germline variant of the VHL gene. ID 4 presented with CNS hemangioblastoma, retinal angioma and renal and pancreatic abnormalities. ID 1, 25 and 8 were asymptomatic.ID 22 presented with CNS hemangioblastoma. 2 members were assumed to have the variant but were not genetically confirmed (ID 20 and ID 11). ID 11 and 20 presented with CNS hemangioblastoma.

      CasePresentingHPOs: HP:0009711 (Retinal capillary hemangioma)

      CaseHPOFreeText: This patient presented with retinal angioma (16Y).

      CaseNotHPOs: HP:0005584; HP:0002666; HP:0010797; HP:0000077; HP:0001732 (Renal cell carcinoma, Pheochromocytoma, Hemangioblastoma, Abnormality of the kidney, Abnormality of the pancreas)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Supplementary Table 1.

      Variant: p.V166Sfs*4 (c.496_506del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223229, https://www.ncbi.nlm.nih.gov/clinvar/variation/223229/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: It is unclear from the publication if this variant is reported according to legacy (AF010238.1) or NM_000551.3 reference sequence. Clinical notes from the case confirm the reference sequence to be NM_000551.3.

      MutationType: deletion; minus_2_frameshift_variant

      CivicName: V166SFS*4 (c.496_506del)

      MultipleGeneVariants: N/A

    1. 55 16 c.307C>G p.Pro103Ala x Familial Parents No

      PatientID: 55

      KindredID: 55

      Case: Sex Unknown, 16Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: Variant was transmitted from a parent (both parents were analyzed) but it is unclear which parent was positive for the variant.

      CasePresentingHPOs: HP:0002666 (Pheochromocytoma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0000107; HP:0006770; HP:0010797; HP:0001732; HP:0009711 (Renal cyst, Clear cell renal cell carcinoma, Hemangioblastoma, Abnormality of the pancreas, Retinal capillary hemangioma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Table S1, S2 and S3

      Variant: p.P103A (c.307C>G)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 219823, https://www.ncbi.nlm.nih.gov/clinvar/variation/219823/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transversion

      CivicName: P103A (c.307C>G)

      MultipleGeneVariants: N/A

    1. 16 different families

      PatientID: 3

      KindredID: 5

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: Patient’s father is presented with renal cell carcinoma, renal cysts, adrenal pheochromocytoma, spinal hemangioblastoma, pancreatic cysts, endolymphatic sac tumor and salivary gland neoplasm at age 19Y0M. This patient is 1 of 3 carrier children of this mutation, without any further phenotypic information.

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.G93R (c.277G>C)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223174, https://www.ncbi.nlm.nih.gov/clinvar/variation/223174

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant, transversion

      CivicName: G93R (c.277G>C)

      MultipleGeneVariants: N/A

    1. 350MaleIYesAGLOH (G)AGLOH (G)

      PatientID: 3

      KindredID: 3

      Case: M, 50Y0M, Taiwanese (East-Asian)

      DiseaseAssertion: renal cell carcinoma

      FamilyInfo: N/A

      CohortInfo: 8 of 19 patients presenting with clear cell renal cell carcinoma were found to be heterozygous for the germline variant rs1642742 in VHL (c.*294G>A). All but one of these patients (7/8) also presented with the germline variant rs779805 (c.-195G>A) in VHL.

      CasePresentingHPOs: HP:0006770 (clear cell renal cell carcinoma)

      CaseHPOFreeText: He had stage I clear cell renal cell carcinoma

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 21982469

      SupplementalData: Yes - Additional file 1: Figure S1

      Variant: c.*294G>A

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 342407 https://www.ncbi.nlm.nih.gov/clinvar/variation/342407/

      CAID: N/A

      gnomAD: 0.5911 https://gnomad.broadinstitute.org/variant/3-10191943-G-A

      VariantEvidence: Heterozygous for both, he also presented with the germline variant c.-195G>A in VHL. LOH (G) of both mutations was found in the tumor tissue as well

      MutationType: 3_prime_UTR_variant

      CivicName: c.-195G>A AND c.*294G>A

      MultipleGeneVariants: Germline, VHL, c.-195G>A

    1. proband’s mother (52 years)

      PatientID: None

      KindredID: 1

      Case: F, 52Y0M, Danish

      DiseaseAssertion: Breast carcinoma

      FamilyInfo: The patient had three sons all of whom carried the VHL mutation. Two of the sons were asymptomatic and one had renal cell carcinoma. The affected son also had a P2P mutation and he had a child who was found to have the VHL mutation (P2P). The patient's mother had the mutation but was also asymptomatic. See Figure 1 for family pedigree.

      CasePresentingHPOs: HP:0003002 (Breast carcinoma)

      CaseHPOFreeText: The patient had breast cancer at age 34.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.P81S (c.241C>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2233 https://www.ncbi.nlm.nih.gov/clinvar/variation/2233/

      CAID: N/A

      gnomAD: 0.0002179 https://gnomad.broadinstitute.org/variant/3-10183772-C-T

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName:P81S (c.241C>T)

      MultipleGeneVariants: N/A

    1. We identified deletions ranging from 0.5 kb to 250 kb affecting part of or the entire VHL and flanking genes in 54 families.

      GroupID: 15

      DiseaseAssertion: VHL

      GroupSize: N/A GroupNumberMales: N/A GroupNumberFemales: N/A GroupEthnicity: N/A GroupAgeRange: N/A

      GroupInfo: 54 VHL deletion families from the Freiburg registry were selected in order to assist in the correlation of VHL deletions to clinical phenotypes.

      GroupPresentingHPOs: HP:0005584; HP:0000107; HP:0009711; HP:0010797; HP:0009713; HP:0001737; HP:0030424 (Renal cell carcinoma, Renal cyst, Retinal capillary hemangioma, Hemangioblastoma, Spinal hemangioblastoma, Pancreatic cysts, Epididymal cyst)

      GroupHPOFreeText: # of affected individuals: Renal cell carcinoma (1), Renal cyst (1), Retinal capillary hemangioma (1), Hemangioblastoma/brain/cerebellum (1), Spinal hemangioblastoma (1), Pancreatic cysts (1), Epididymal cyst (1)

      GroupNotHPOs: N/A

      GroupNotHPOFreeText: N/A

      GroupPreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Supplemental Table 2, Table 1, Table 3

      Variant: Exon 2 Deletion (c.341-?-463+?del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: exon_loss_variant

      CivicName: Exon 2 Deletion

      MultipleGeneVariants: N/A

    1. This case concerns a 35-year-old woman referred to our Gastroenterology Department with long-standing dyspepsia and pancreatic cysts detected by ultrasound examination. There were no other symptoms, such as abdominal pain, weight loss, visual or hearing changes, headache or urinary complaints. The past medical and family histories were not of significance. There were no abnormal findings on examination.The patient underwent an abdominal computed tomography (CT) scan (Figure ​(Figure1),1), which showed an enlargement of the pancreas, especially in the cephalic region, with heterogeneous density due to the presence of multiple hypodense nodules dispersed throughout the parenchyma. The majority of these lesions were small, but one larger contrast-enhancing lesion of 22 mm was present in the uncinate process.Open in a separate windowFigure 1Computed tomography abdominal scan. A: Small cystic lesions dispersed throughout the pancreas; B: The largest lesion.Given the findings of the CT scan, we performed an abdominal magnetic resonance imaging (MRI) (Figure ​(Figure2),2), which revealed several cysts that had a high signal intensity on T2 weighted images.Open in a separate windowFigure 2Magnetic resonance imaging. Cyst lesions are bright on T2-weighted images.The patient underwent endosonography that confirmed the presence of multiple simple cysts throughout the entirety of the pancreas. The majority of the cysts were less than 1 cm in diameter, but two cysts were larger than 1 cm. One of the larger cysts was 16 mm in diameter and was located at the isthmus-body transition. This cyst and did not communicate with the main pancreatic duct and was aspirated. The content had a serous appearance, and cytological analysis revealed amorphous material, few erythrocytes and inflammatory cells (Figure ​(Figure33).Open in a separate windowFigure 3Endosonography. A, B show a large cyst of 16 mm in diameter without communication or dilatation of the pancreatic duct; C: Demonstrates aspiration of the cyst; D: Demonstrates its appearance after total aspiration.The largest cyst was 23 mm in diameter and was located in the head of the pancreas. The cyst had a honeycomb appearance characteristic of serous cystadenomas (Figure ​(Figure4A).4A). The cytology did not show evidence of cellular atypia (Figure ​(Figure4B).4B). The carninoembryonic antigen was < 0.6 ng/dL, and the amylase in the cystic content was 135 U/L.Open in a separate windowFigure 4The largest cyst was 23 mm in diameter and was located in the head of the pancreas. A: Endosonography. Cyst with a honeycomb appearance; B: Cytology (papanicolaou stain, × 100). Benign pancreatic cysts.The endosonography also showed cysts in the left kidney and in the spleen (Figure ​(Figure5).5). The findings described were compatible with simple cysts and pancreatic serous cystadenomas and provided an indication for genetic testing for VHL. The sequencing of the VHL gene revealed one pathogenic heterozygous mutation in exon 1 (c.269A > T), confirming the diagnosis of VHL disease.Open in a separate windowFigure 5Endosonography. A: A cyst in the renal cortex; B: A cyst in the spleen.The patient underwent a MRI of the brain and entire spine and no hemangioblastomas were detected. The abdominal MRI scan excluded renal carcinoma. The plasma and urinary catecholamines and the urinary vanilmandelic acid were normal, excluding pheocromocytoma. The patient was also referred for examination of the retina and ear, nose and throat, including audiometry. There were no abnormal findings, which excluded angiomas of the retina and endolymphatic sac tumors, respectively.

      PatientID: None

      KindredID: 1

      Case: F, 35Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: Her family was genetically tested, and the same mutation was found in her 7 year-old daughter. Assumed de novo.

      CasePresentingHPOs: HP:0410281; HP:0001737; HP:0005562; HP:0030423 (Dyspepsia, Pancreatic cysts, Multiple renal cysts, Splenic cyst)

      CaseHPOFreeText: Admitted with long-standing dyspepsia and pancreatic cysts detected by ultrasound examination. There were no other symptoms, such as abdominal pain, weight loss, visual or hearing changes, headache or urinary complaints. The past medical and family histories were not of significance. There were no abnormal findings on examination.CT scan showed an enlargement of the pancreas, especially in the cephalic region, with heterogeneous density due to the presence of multiple hypodense nodules dispersed throughout the parenchyma. Abdominal MRI revealed several cysts. Endosonography that confirmed the presence of multiple simple cysts throughout the entirety of the pancreas as well as cysts in the left kidney and in the spleen. The findings described were compatible with simple cysts and pancreatic serous cystadenomas.

      CaseNotHPOs: HP:0006880; HP:0009711; HP:0009713; HP:0005584; HP:0002666; HP:0030393 (Cerebellar hemangioblastoma, Retinal capillary hemangioma, Spinal hemangioblastoma, Renal cell carcinoma, Pheochromocytoma, Endolymphatic sac tumor)

      CaseNotHPOFreeText: MRI of the brain and entire spine and no hemangioblastomas were detected. Abdominal MRI scan excluded renal carcinoma.The plasma and urinary catecholamines and the urinary vanilmandelic acid were normal, excluding pheochromocytoma. Examination of the retina and ear, nose and throat, including audiometry excluded angiomas of the retina and endolymphatic sac tumors, respectively.

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.N90I (c.269A>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223172, https://www.ncbi.nlm.nih.gov/clinvar/variation/223172/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transversion

      CivicName: N90I (c.269A>T)

      MultipleGeneVariants: N/A

    1. PatientID: 187

      KindredID: 72

      Case: M, 67Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: The proband, patient 72, has multiple family members with the same mutation. Her father (patient 73) had a CNS hemangioblastoma at 65, renal cell carcinioma at 54, and multiple pancreatic cysts/tumors at 67. Her sister 2 (second sister) had multiple pancreatic cysts/tumors at 36, and a CNS hemangioblastoma at 39. Her sister 3 had multiple pancreatic cysts/tumors at 32, and a retinal angioma at 34. The proband's sister 1 had a CNS hemangioblastoma at 22, but passed away before they could be diagnosed/ confirmed with the mutation.

      CasePresentingHPOs: HP:0010797; HP:0005584; HP:0001732; HP:0001737 (Hemangioblastoma, Renal cell carcinoma, Abnormality of the pancreas, Pancreatic cysts)

      CaseHPOFreeText: The patient presented with a CNS hemangioblastoma at 65, renal cell carcinoma at 54, and multiple pancreatic cysts/tumors at 67.

      CaseNotHPOs: HP:0009711; HP:0002666 (Retinal capillary hemangioma, Pheochromocytoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: This patient was also published in a later paper by Wang et al., 2018 (PMID: 29330336).

      SupplementalData: Patient and family genotype-phenotype information is listed in Supplementary Table 1.

      Variant: p.R167W (c.499C>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2218; https://www.ncbi.nlm.nih.gov/clinvar/variation/2218/

      CAID: N/A

      gnomAD: 0.000007954; https://gnomad.broadinstitute.org/variant/3-10191506-C-T?dataset=gnomad_r2_1

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: R167W (c.499C>T)

      MultipleGeneVariants: N/A

    2. PatientID: 272

      KindredID: 106

      Case: F, 51Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: The proband, patient 272, has a daughter and a father who both passed away before diagnosis/ before they could undergo genetic testing. The proband's daughter (patient 273) had a CNS hemangioblastoma at age 13, and the proband's father (patient 274) had a CNS hemangioblastoma at age 30.

      CasePresentingHPOs: HP:0001737; HP:0001732; HP:0010797 HP:0009711; HP:0005584 (Pancreatic cysts, Abnormality of the pancreas, Hemangioblastoma, Retinal capillary hemangioma, Renal cell carcinoma)

      CaseHPOFreeText: The proband presented with a retinal angioma at 49, and at 51 presented with a CNS hemangioblastoma, renal cell carcinoma, and multiple pancreatic cysts/tumors.

      CaseNotHPOs: HP:0002666 (Pheochromocytoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: This cohort was also published in a later paper by Wang et al., 2018 (PMID: 29330336).

      SupplementalData: Patient and family genotype-phenotype information is listed in Supplementary Table 1.

      Variant: Exon 2 Deletion (c.341-?_463+?del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: exon_loss_variant

      CivicName: Exon 2 Deletion

      MultipleGeneVariants: N/A

    1. VHL-14c.463 + 1G > ASplicing mutation[4]noA2+–+–+Ovarian

      PatientID: VHL-14

      KindredID: 14

      Case: Sex Unknown, Age Unknown, Italian

      DiseaseAssertion: VHL

      FamilyInfo: None.

      CohortInfo: Forty-three index cases were referred to the Service of Medical Genetics, Genova, for germline mutation analysis in the VHL gene between 1995 and 2008.

      CasePresentingHPOs: HP:0010797, HP:0001737, HP:0009711, HP:0000138 (hemangioblastoma, pancreatic cysts, retinal capillary hemangioma, ovarian cyst)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0005584, HP:0002666 (Renal cell carcinoma, pheochromocytoma )

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: c.463+1G>A

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 526679 https://www.ncbi.nlm.nih.gov/clinvar/variation/526679/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: splice_site_variant

      CivicName: c.463+1G>A

      MultipleGeneVariants: N/A

    2. VHL-23c.341 − ?_642 + ?Del ex2 + 3[11]noA2+–+––Renal

      PatientID: VHL-23

      KindredID: 23

      Case: Sex Unknown, Age Unknown, Italian

      DiseaseAssertion: VHL

      FamilyInfo: No family history of VHL.

      CohortInfo: Forty-three index cases were referred to the Service of Medical Genetics, Genova, for germline mutation analysis in the VHL gene between 1995 and 2008.

      CasePresentingHPOs: HP:0010797; HP:0000107; HP:0001732 (Hemangioblastoma, Renal cyst, Abnormality of the pancreas)

      CaseHPOFreeText: CNS hemangioblastoma and clinical classification: A2.

      CaseNotHPOs: HP:0002666; HP:0005584; HP:0009711 (Pheochromocytoma, Renal cell carcinoma, Retinal capillary hemangioma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: Exon 2-3 Deletion (c.341-?_642+?del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: exon_loss_variant

      CivicName: Null (c.341-?_642+?del)

      MultipleGeneVariants: N/A

    1. VHL1c.242C>Tp.Pro81Leu1RCB c

      PatientID: N/A

      KindredID: 2

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: paraganglioma

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0002668 (paraganglioma)

      CaseHPOFreeText: Paraganglioma of the head and neck region (HNPGL): Right carotid body; nonsecreting paraganglioma

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: MAX, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.P81L (c.242C>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 36899 https://www.ncbi.nlm.nih.gov/clinvar/variation/36899

      CAID: N/A

      gnomAD: 0.000004349 https://gnomad.broadinstitute.org/variant/3-10183773-C-T

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: P81L (c.242C>T)

      MultipleGeneVariants: N/A

    1. PatientID: IV-12

      KindredID: 1

      Case: M, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: Family’s roots were traced to the German town of Leipzig in Saxony, from whence the original 11 siblings had immigrated to America around 1670. The following report is a 2011 updated pedigree on the previously reported Tisherman kindred. At the time of this study, 43/49 patients have undergone mutational analysis revealing the VHL familial mutation (Y112H) and 35/49 patients have clinical VHL manifestations. Phenotypic cumulative lifetime risk was 71% for Pheo/PGL, 15% for hemangioblastoma, 33% for retinal angioma, 3% for renal cell carcinoma, and 3% for pancreatic cysts. 6 members of the family (all deceased; 4 males, 2 females) had suspected VHL and 2 (males) of these were suspected to have had Pheo/PGL.

      CasePresentingHPOs: HP:0002666; HP:0002668 (Pheochromocytoma, Paraganglioma)

      CaseHPOFreeText: Phenotype noted as: Pheo/PGL (unclear which of the two or if both apply to this patient).

      CaseNotHPOs: HP:0005584; HP:0009711 (Renal cell carcinoma, Retinal capillary hemangioma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 9201016; 8239848 (no genetic information; only phenotypes)

      SupplementalData: N/A

      Variant: p.Y112H (c.334T>C)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2222, https://www.ncbi.nlm.nih.gov/clinvar/variation/2222/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: Y112H (c.334T>C)

      MultipleGeneVariants: N/A

    1. A previously healthy 10-year-old girl presented with occasional routine blood pressure measurements by her pediatrician above the 99th percentile for her age, sex, and height. She had noted mild hand edema over the previous days and reported recent nocturia. She was taking no medications. Family history was unremarkable. The physical examination was without significant findings other than an elevated blood pressure of 139/113 mm Hg. Urine tests showed boderline moderate albuminuria (albumin-creatinine ratio of 50 mg/g). There was no hematuria.On ultrasound, kidney size and parenchyma were unremarkable but an increased flow rate of the left renal artery in color duplex sonography was detected (systolic flow rate: right, 100 cm/s; left, 300 cm/s [age-adjusted normal values range from 72 to 104 cm/s]) (Fig 1A and B). No additional finding was reported. Magnetic resonance (MR) angiography of the kidney vessels was performed (Fig 2A) and antihypertensive therapy was initiated.

      PatientID: N/A

      KindredID: 1

      Case: F, 10Y0M, Ethnicity Unknown

      DiseaseAssertion: Assumed VHL

      FamilyInfo: No family history, authors indicate that the variant occurred de novo.

      CasePresentingHPOs: HP:0007514; HP:0000017; HP:0004421; HP:0012594; HP:0002666; HP:0001920 (Edema of the dorsum of hands; Nocturia; Elevated systolic blood pressure; Moderate albuminuria; Pheochromocytoma; Renal artery stenosis)

      CaseHPOFreeText: Patient presented with occasional high routine blood pressure at 10Y0M. She noted mild hand edema over the past days and reported recent nocturia. Physical examination appeared normal other than elevated blood pressure of 139/113 mm Hg. Urine tests showed moderate albuminuria (albumin-creatinine ratio of 50 mg/g), as well as high levels of noradrenaline and normetanephrine, suggestive of benign pheochromocytoma. Ultrasound showed normal kidney size and parenchyma, but color duplex sonography revealed increased flow rate of the left renal artery. This finding suggests renal artery stenosis. Magnetic Resonance Angiography of the kidney vessels showed a solid tumor that had cystic features. Tumor resection normalized blood pressure and pathologic examination of the removed tumor confirmed pheochromocytoma. Patient was diagnosed with secondary hypertension due to compression of renal vessels and catecholamine production by vHL-associated pheochromocytoma. Antihypertensive therapy with phenoxybenzamine as α blockade was initiated, along with subsequent expansion of the therapy with a β-blocker. Authors mention that the patient is in complete remission with no other manifestations of VHL disease and is receiving close follow-up.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.G104V (c.311G>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223183, https://www.ncbi.nlm.nih.gov/clinvar/variation//223183/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transversion

      CivicName: G104V (c.311G>T)

      MultipleGeneVariants: N/A

    1. simultaneously analysed with his daughter's DNA who had a heterozygous p.(R161*) VHL mutation.

      PatientID: None

      KindredID: 8

      Case: F, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: Asymptomatic

      FamilyInfo: Her father harboured the same VHL mutation and presented with bilateral renal cell carcinoma.

      CasePresentingHPOs: N/A

      CaseHPOFreeText: The patient had bilateral renal cell carcinoma at age 48.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.R161* (c.481C>T)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: 2217 https://www.ncbi.nlm.nih.gov/clinvar/variation/2217/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: She had a heterozygous p.R161* mutation.

      MutationType: stop_gained

      CivicName: R161* (c.481C>T)

      MultipleGeneVariants: N/A

    1. Case presentationA 35-year-old woman with VHL underwent total pancreatectomy and right nephrectomy for pancreatic SCN and renal cell carcinoma, respectively. At the 4th year follow-up examination after the resection, contrast-enhanced computed tomography (CT) and gadolinium ethoxybenzyl diethylenetriamine penta-acetic acid (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) showed arterially hyper-enhanced neoplastic lesions in the segment VI and VIII of the liver. Partial resections of the liver were performed 53 months after the initial surgery. At the 6th month follow-up examination from the second surgery, one and two tumors located in the liver segment III, and VIII, respectively, were detected by contrast-enhanced CT and Gd-EOB-DTPA-enhanced MRI. Anterior segmentectomy and partial resection of the segment III were performed 66 months after the initial surgery and 13 months after the second, respectively. The tumors were pathologically diagnosed as liver metastases of pancreatic SCN synonymous with serous cystadenocarcinoma. She remains disease-free without recurrence 6.5 years after the last operation.

      PatientID: 1

      KindredID: 1

      Case: F, 47Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: No family history.

      CasePresentingHPOs: HP:0006880; HP:0002894; HP:0005584 (Cerebellar Hemangioblastoma; neoplasm of the pancreas; renal cell carcinoma)

      CaseHPOFreeText: At 35-year old, the female patient was diagnosed with VHL due to clinical presentation of pancreatic serous cystic neoplasm and renal cell carcinoma, and cerebellar hemangioblastomas that were surgically removed at age 21. The patient had underwent total pancreatectomy and right nephrectomy for pancreatic serous cystic neoplasm (SCN) and renal cell carcinoma (RCC), respectively. 4 years later, tumors in the liver were detected by CT scan and radiographically diagnosed as metasta-ses of the pancreatic SCN or RCC. Again, morphology and immunohistochemical findings of the resected tumors again were similar to the primary pancreatic SCN, thus diagnosed as multiple metachronous liver metastases of pancreatic SCN. As of 47Y, the patient has remained disease-free without any recurrence after the third operation.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 21673464

      SupplementalData: N/A

      Variant: p.N78I (c.233A>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223169 https://www.ncbi.nlm.nih.gov/clinvar/variation/223169/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: N78I (c.233A>T)

      MultipleGeneVariants: N/A

    1. not only showed loss of the open-reading frame, but more extended deletions by using c11 and P1 demonstrating complete loss of the VHL gene sequence (>35 kb, but <90 kb)

      PatientID: 2

      KindredID: 2

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: Hemangioblastoma

      FamilyInfo: None

      CasePresentingHPOs: HP:0010797 (Hemangioblastoma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: deletion (deletion on chromosome 3 (>35kb, <90kb) resulting in complete loss of VHL gene)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: germline deletion on chromosome 3 (>35kb, <90kb) resulting in complete loss of VHL gene. Hemangioblastoma from this patient shows a missense mutation R200W(c.598C>T) in the second copy of VHL gene.

      MutationType: deletion

      CivicName: Deletion AND R200W (c.598C>T)

      MultipleGeneVariants: Somatic, VHL, c.598C>T (p.Arg200Trp)

    1. PatientsThe Chinese family study included five-generations comprising of 38 living family members, of whom nine were affected [Figure 1]. All living members were examined clinically. The clinical and radiographic images were published with the consent of the patient. The study was approved by the research Ethics Committees of Xi’an Jiaotong University School of Medicine. Written informed consents were obtained from all participants.Open in a separate windowFigure 1Haplotypes of the Chinese family affected by Von Hippel-Lindau (VHL). The open and filled blackened symbols indicated unaffected and affected individuals, respectively. The squares and circles symbolized the males and females, respectively. The proband, IV-3, was indicated by an arrow. The haplotyping was conducted using three polymorphic microsatellite markers. The marker order was determined from the Marshfield map and the UCSC Human Genome database (February 2009). The dark boxes symbolized haplotypes that cosegregated with the affected individuals and suggested linkage of VHL to disease in this family. The boxes with slash symbolized the dead family members.

      PatientID: III:1

      KindredID: 1

      Case: M, Age Unknown (deceased), Chinese

      DiseaseAssertion: VHL

      FamilyInfo: A 5-generation family with VHL in 15 members. Both second generation children (presumed), 5 third generation, and 8 further generation individuals were affected and haplotyping was conducted using three polymorphic microsatellite markers. All of the 5th generation children (9 total at time of publication) had been sequenced and haplotyped as unaffected.

      CasePresentingHPOs: N/A

      CaseHPOFreeText: unknown phenotype, however they were said to be affected

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.R167W (c.499C>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2218, https://www.ncbi.nlm.nih.gov/clinvar/variation/2218/

      CAID: N/A

      gnomAD: 0.000007954, https://gnomad.broadinstitute.org/variant/3-10191506-C-T?dataset=gnomad_r2_1

      VariantEvidence: Death before genetic diagnostic, however presumed by authors due to extensive family history (See pedigree).

      MutationType: missense_variant;transition

      CivicName: R167W (c.499C>T)

      MultipleGeneVariants: N/A

    1. VHL p.Val166Phe

      Twelve patients with hereditary non-SDHx head and neck paragangliomas were analyzed. Eleven of the 12 patients were found to carry germline mutations in the VHL gene. Blood was used for molecular genetic analyses and the NM_000551.2 reference sequence was used. The paper includes 3 additional VHL patients: case 22, 23, 27. Case 22 is a male who was found to harbour the p.V166F (c.496G>T) mutation of the VHL gene. He presented with a head/neck paraganglioma, as well as pheochromocytoma and CNS hemangioblastoma. Negative family history was described.

    1. PatientID: 16

      KindredID: F01

      Case: F, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: A total of 12 members of this family (F01) had a complete deletion of the VHL gene. Five of these patients (16, 18, 21, 33, 43) presented with clinical features of VHL. This family was previously published except for patients 43 and 48 which were newly diagnosed with VHL disease in the current study.

      CasePresentingHPOs: HP:0010797 (Hemangioblastoma)

      CaseHPOFreeText: CNS hemangioblastoma.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 17537157

      SupplementalData: Figure 2.

      Variant: Complete Deletion

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: Deletion of ~250.9kb resulted in deletion of the VHL gene.

      MutationType: deletion

      CivicName: Deletion

      MultipleGeneVariants: N/A

    1. 1 (100)

      GroupID: 8

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: VHL

      CohortInfo: a retrospective cohort study from an eye centre in Germany involved 148 VHL patients and their genetic data involved in retinal capillary hemangiomas.

      CasePresentingHPOs: HP:0009711 (retinal capillary hemangioma)

      CaseHPOFreeText: This individual patient was the only one discussed with a splice c.464-2A>G mutation. Other VHL manifestations were discussed but not per- variant.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Yes - Supplementary Table S1

      Variant: c.464-2A>G

      LegacyVariant: N/A

      GroupProblemVariantFreeText: N/A

      ClinVarID: 223222 https://www.ncbi.nlm.nih.gov/clinvar/variation/223222/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: splice_site_variant

      CivicName: spice site (c.464-2A>G)

      MultipleGeneVariants: N/A

    1. 1HbCb age 18, Hbs age 19,Hbs age 31Renal cysts 

      PatientID: 1

      KindredID: 1

      Case: M, 31Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: Mother with the same variant and presented with breast cancer at age 46 and cerebellar hemangioblastoma and renal cell carcinoma both at age 54. Maternal grandfather (id: 3) presented with cerebellar hemangioblastoma at age 65. Maternal great-uncle (id: 4) presented with prostate cancer at age 65. Maternal great-grandfather (id: 5) presented with cerebellar hemangioblastomas at age 69. Maternal grandmother and sister did not have the mutation. His maternal grandfather was not tested. No family history of retinal capillary hemangiomas or pheochromocytoma.

      CasePresentingHPOs: HP:0006880; HP:0009713; HP:0005562 (Cerebellar hemangioblastoma, Spinal hemangioblastoma, Multiple renal cysts)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0002666; HP:0009711 (Pheochromocytoma, Retinal capillary hemangioma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Figure 1 (pedigree) and Table 1 (phenotype and age of onset data).

      Variant: Exon 1 Deletion (c.1-?_340+?del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: exon_loss_variant

      CivicName: Exon 1 Deletion

      MultipleGeneVariants: Germline, FANCD2, Partial Deletion

    1. In our study, group 5 represented the c.262T > C p.Trp88Arg mutation that included 21 patients from 2 families (Figure 4 and Table 3). Variability was observed in the mean age at onset for CHB and RCC, which were 41.1 ± 9.1 (range = 29–62) and 37.4 ± 12.9 (range = 23–65), respectively.

      PatientID: 4

      KindredID: 2 (group ID 5)

      Case: F, 31Y0M, Chinese

      DiseaseAssertion: asymptomatic

      CohortInfo: Clinical characteristics of 258 patients from 80 unrelated Chinese families were reported in this study. Grouped by the 21 mutations found, 2 families with 21 members total were described, and phenotypic information was given for this group.

      FamilyInfo: In family 2, 4 members were described in a 3 generation family. The proband’s mother, uncle, and grandfather were also present with the VHL mutation. See Fig 4 for family pedigree; Table 3 for details.

      CasePresentingHPOs: N/A

      CaseHPOFreeText: No characteristics were described

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.W88R (c.262T>C)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 496053 https://www.ncbi.nlm.nih.gov/clinvar/variation/496053/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: W88R (c.262T>C)

      MultipleGeneVariants: N/A

    1. 2

      PatientID: Unknown

      KindredID: 2

      Case: Sex Unknown, 53Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: This is the proband. 5 members of this family were found to have the mutation and pheochromocytoma. Other declared diseases in this family are: paraganglioma, hemangioblastoma, lung metastases and spinal hemangioblastoma but the presenting patient is unclear.Relationship between these family members is unclear.

      CohortInfo: Patients with the diagnosis of familial or sporadic PHEO and their relatives.

      CasePresentingHPOs: HP:0002666 (Pheochromocytoma)

      CaseHPOFreeText: Follow-up 18 years later but it is unclear if this pertained to all affected family members.

      CaseNotHPOs: HP:0005584 (Renal cell carcinoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Table 1

      Variant: p.P138= (c.414A>G)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223206, https://www.ncbi.nlm.nih.gov/clinvar/variation/223206/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: P138= (c.414A>G)

      MultipleGeneVariants: N/A

    2. unilateral PHEOs (Fig. 1a): her father (II:1) at age 73, her 34-year-old brother (III:2)

      PatientID: III:2

      KindredID: 1

      Case: M, 34Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: Look to proband (III:3) for extensive family info.

      CohortInfo: Patients with the diagnosis of familial or sporadic PHEO and their relatives.

      CasePresentingHPOs: HP:0002666; HP:0000107 (Pheochromocytoma, Renal cyst)

      CaseHPOFreeText: Unilateral pheochromocytoma diagnosed at age 34.

      CaseNotHPOs: HP:0005584 (Renal cell carcinoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Figure 1

      Variant: p.P138= (c.414A>G)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223206, https://www.ncbi.nlm.nih.gov/clinvar/variation/223206/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: P138= (c.414A>G)

      MultipleGeneVariants: N/A

    1. In four families, partial deletions of one or more exons were detected by Southern blot analysis

      PatientID: 9

      KindredID: A

      Case: F, Age unknown, Turkish

      DiseaseAssertion: assumed VHL

      FamilyInfo: 5 family members are grouped with this deletion (ages 16-37Y; mean 31Y). VHL was clinically diagnosed in, at minimum, the proband. See Fig. 2 for family pedigree. The father and one uncle were not tested for the DNA deletion however it is assumed by the authors due to the segregation observed.

      CasePresentingHPOs: HP:0010797 (hemangioblastoma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0009711; HP:0002666; HP:0005584 (retinal capillary hemangioma; pheochromocytoma; renal cell carcinoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: Deletion of exons 1 and 2

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: HindIII and revealed an aberrant banding pattern in three affected family members (1, 2, and 9)

      MutationType: exon_loss_variant

      CivicName: exon 1-2 deletion

      MultipleGeneVariants: N/A

    1. Twelve (75%) of 16 gene carriers were found to have ocular hemangioblastomas(Figure 1 and Figure 2), and 7 of these had bilateral disease (Table 1). The mean number of angiomas was 3.3. However, 1 individual had 22 angiomas, most of which were in an area of previous exudative retinal detachment (see the "Comment" section) (Table 2). Exclusion of this individual resulted in a mean number of angiomas of 2.1. Six eyes had optic disc angiomas (Figure 2). Six of the 19 eyes with ocular hemangioblastomas had visual acuity less than 20/40. Two patients had no light perception in one or both eyes. The average age at diagnosis of ocular angiomatosis was 37 years.

      Family history of several kindreds in Iowa have been linked together as one pedigree originating from a common ancestor who immigrated to Iowa from Baden-Baden Germany in 1832. SSCP analysis disclosed 16 family members with same mutation (legacy notation c.505T>C converted to NM_000551.3 c.292T>C). This mutation is identical to other families who trace their lineage to the Black Forest region of Germany (Brauch et al., 1995). None of the members had renal cell carcinoma. Patient #1: pheochromocytoma (11 years old) ; b/l retinal angioma (11 years old), diagnosed at 22 years. Patient #2: diagnosed at 24 years with the mutation. Patient #3: diagnosed at 39 years with the mutation. Patient #4: b/l pheochromocytoma (24 years) ; b/l retinal angioma (19 years) ; CNS hemangioblastoma (29 years); diagnosed 34 years. Patient #5: b/l pheochromocytoma (20 years); b/l retinal angioma (20 years); diagnosed at 35 years. Patient #6: pheochromocytoma (49 years); retinal angioma (49 years); diagnosed at 60 years. Patient #7: retinal angioma (41 years); diagnosed 42 years. Patient #8: retinal angioma (58 years); diagnosed 59 years. Patient #9: pheochromocytoma (29 years); b/l retinal angioma (29 years); diagnosed 30 years. Patient #10: pheochromocytoma (13 years); diagnosed at 23 years. Patient #11: pheochromocytoma (45 years); retinal angioma (45 years); diagnosed 50 years. Patient #12: pheochromocytoma (9 years); b/l retinal angioma (37 years); diagnosed at 38 years. Patient #13: pheochromocytoma (69 years); retinal angioma (54 years); CNS hemangioblastoma (29 years); diagnosed 70 years. Patient #14: b/l retinal angioma (56 years); CNS hemangioblastoma (56 years); diagnosed 59 years. _atient #15; b/l pheochromocytoma (23 years); diagnosed at 29 years. Patient #16: b/l pheochromocytoma (53 years) ; b/l retinal angioma (20 years); hemangioblastoma (46 years); diagnosed at 62 years.

    1. p.Leu188Val

      PatientID: 1

      KindredID: A

      Case: M, 61Y0M, Ethnicity Unknown

      DiseaseAssertion: assumed VHL

      FamilyInfo: Positive: the patient’s sister also presented with the germline c.562C>G mutation, and metastatic lobular breast carcinoma. In a family pedigree, 10 additional members affected with cancer were displayed. This included both of their parents: father with lung cancer, mother with skin cancer, additional sister with breast cancer, brother with melanoma. Lastly, his two sons presented with skin cancer, however no description of their genotyping. See Fig. 3.

      CasePresentingHPOs: HP:0006770; HP:0001028 (Clear cell renal cell carcinoma, hemangioma)

      CaseHPOFreeText: He presented in 2012 (52Y) with worsening lower abdominal discomfort (CT scan revealed a right renal solid mass of renal cell carcinoma). A right renal nephrectomy was done, confirming ccRCC. 4 years later, new lung nodules and an enhancing lesion in the L1 vertebral body was found (metastatic ccRCC). Additionally, in 2020, a pancreatic lesion present on his scans was presumed to be a metastatic RCC lesion (consistent with an atypical hemangioma).

      CaseNotHPOs: HP:0002666; HP:0009711 (Pheochromocytoma, retinal capillary hemangioblastoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: MAX/NF1/RET/SDHA/SHDB/SHDC/SDHD/SDHAF2/TMEM127 [133 genes evaluated by germline testing - Invitae]

      PreviouslyPublished: N/A

      SupplementalData: Yes

      Variant: p.L188V (c.562C>G)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: In 2013, somatic next generation sequencing (NGS) testing using a panel of 447 cancer genes (OncoPanel, BWH Pathology, MA, USA) was performed on the resected renal specimen. This revealed the following variants: VHL p.Leu188Val (c.562C>G), CHEK2 p.Val395Leu (c.1183G>C), VHL p.Ala149Thr (c.445G>A) variant, and several copy number losses including a large single-copy deletion in 3p. 6 years later, germline testing revealed a heterozygous germline VHL p.Leu188Val variant, a CHEK2 and ERCC4 mutation.

      ClinVarID: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

      CAID: N/A

      gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

      VariantEvidence: N/A

      MutationType: missense_variant;transversion

      CivicName: L188V (c.562C>G)

      MultipleGeneVariants: Somatic, VHL, c.445G>A (p.Ala149Thr)

    1. PatientID: V322

      KindredID: V322

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: Asymptomatic

      FamilyInfo: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.R167Q (c.500G>A)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2216 https://www.ncbi.nlm.nih.gov/clinvar/variation/2216/

      CAID: N/A

      gnomAD: 0.000003977 https://gnomad.broadinstitute.org/variant/3-10191507-G-A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: R167Q (c.500G>A)

      MultipleGeneVariants: N/A

    2. PatientID: V3

      KindredID: V3

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText:N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 8956040

      SupplementalData: N/A

      Variant: p.R161* (c.481C>T)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: 2217 https://www.ncbi.nlm.nih.gov/clinvar/variation/2217/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: stop_gained

      CivicName: R161* (c.481C>T)

      MultipleGeneVariants: N/A

    1. PatientID: 14

      KindredID: 5

      Case: Sex Unknown, 40Y0M, Indian

      DiseaseAssertion: VHL

      FamilyInfo: 2 other members of this family presented with the same variant. Patient 13 (Gen 2) presented with bilateral pheochromocytoma. Patient 12 (Gen 2) presented with bilateral pheochromocytoma and sympathetic paraganglioma.

      CohortInfo: This retrospective study was conducted at Department of Endocrinology of a tertiary care health centre in Western India. Patients presented to our institute between 2008 and 2016 were included in the study. During the study period a total of 33 patients were suspected to have VHL syndrome based on clinical features among whom 31 patients were found to have mutation in VHL gene. All patients are of Asian Indian descent.

      CasePresentingHPOs: HP:0002666 (Pheochromocytoma)

      CaseHPOFreeText: Bilateral pheochromocytoma and sympathetic paraganglioma.

      CaseNotHPOs: HP:0009711; HP:0010797; HP:0001737; HP:0005584; HP:0030405; HP:0002668 (Retinal capillary hemangioma, Hemangioblastoma, Pancreatic cysts, Renal cell carcinoma, Pancreatic endocrine tumor, Paraganglioma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.L198P (c.593T>C)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223235, https://www.ncbi.nlm.nih.gov/clinvar/variation/223235/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: L198P (c.593T>C)

      MultipleGeneVariants: N/A

    1. PMID: 19399650

      ArticleReferenceSequence: Not specified – Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3

      GenotypingMethod: Primers were selected and polymerase chain reactions (PCR) for every amplicon were established - PCR was carried out on a Eppendorf Mastercycler; WAVE-analysis hetero-duplex.

      SamplingMethod: frozen tumor tissue; and whole blood leukocytes

    1. The second, H125Y – previously unreported – was associated with the presence of a right pneumogastric nerve PGL diagnosed at 49 years.

      PatientID: N/A

      KindredID: 2

      Case: Sex Unknown, 49Y0M, Ethnicity Unknown

      DiseaseAssertion: Paraganglioma

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0002668 (Paraganglioma)

      CaseHPOFreeText: right pneumogastric nerve paraganglioma

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: SDHD/SDHB/SDHC

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.H125Y (c.373C>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVar: 411970 https://www.ncbi.nlm.nih.gov/clinvar/variation/411970/

      CAID: N/A

      gnomAD: 0.00001193 https://gnomad.broadinstitute.org/variant/3-10188230-C-T

      VariantEvidence: N/A

      MutationType: missense_transition

      CivicName: H125Y (c.373C>T)

      MultipleGeneVariants: N/A

    1. Somatostatin receptor expression was investigated in vitro by immunohistochemistry in pancreatic tumor sections. On the basis of in vivo and in vitro findings, octreotide long-acting release treatment followed by 90Y-1,4,7,10-Tetraazacyclododecane-N, N′, N′’, N‴-tetraacetic acid (DOTA0)-Tyr3-octreotide led to a lack of progression in this patient although this result is a possibility which needs to be proved by further investigation and longer follow-up. The results of this study suggest that [111In-DTPA0] octreotide scintigraphy may be helpful in the routine work-up of VHL patients for diagnostic and therapeutic purposes.

      ArticleReferenceSequence: Not specified – Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3

      GenotypingMethod: N/A (not stated)

      SamplingMethod: tissue resection (paraffin-embedded sections of the pancreatic islet cell tumors)

    1. PatientID: Carrier 1 (sister to proband 1)

      KindredID: 1

      Case: F, 29Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: The family with PCCs includes 56 members of 4 generations, and is from Gansu Province. Among them, 7 extended over 3 generations were diagnosed as PCCs. One died before admission and another died due to a cardiovascular incident. Five were initially evaluated; evaluation included medical history, physical examination, abdominal ultrasonography, CT or MRI and laboratory tests. All 5 probands of this family underwent surgical resection. The tumors were benign under pathological examinations. There were no recurrence and malignant transformation over the period of up to 23-year follow-up. Twenty members, including 5 live patients and 15 direct relatives, accepted genetic examination.

      CasePresentingHPOs: HP:0002666 (Pheochromocytoma)

      CaseHPOFreeText: Bilateral PCC diagnosed at 17Y and did not have any other clinical presentations. Stated as having VHL type IIC.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.H125P (c.374A>C)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 223201, https://www.ncbi.nlm.nih.gov/clinvar/variation/223201/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transversion

      CivicName: H125P (c.374A>C)

      MultipleGeneVariants: N/A

    1. rs617500716128464c.4120C > T28p.R1374C110.0000242A/M

      Case:n.a.

      DiseaseAssertion:VWD 2A/M

      FamilyInfo:n.a.

      ParentalGenotype(s):n.a.

      CasePresentingHPOs:n.a.

      CaseHPOFreeRext:n.a.

      CaseNOTHPOs:n.a.

      CaseNOTHPOFreeText:n.a.

      CasePreviousTesting:n.a.

      GenotypingMethod: n.a.

      PreviouslyPublished: If applicable. n.a.

      Gene:VWF

      Variant: c.4120C > T

      HGVS: NM_000552.5:c.4120C>T

      ClinVarID:n.a.

      CAID:n.a.

      gnomAD:n.a.

    2. rs617493956128641c.3943C > T28p.R1315C20.0000242A/M

      Case: n.a.

      DiseaseAssertion: VWD 2A/M

      FamilyInfo:n.a.

      ParentalGenotype(s):n.a.

      CasePresentingHPOs:n.a.

      CaseHPOFreeRext:n.a.

      CaseNOTHPOs:n.a.

      CaseNOTHPOFreeText:n.a.

      CasePreviousTesting:n.a.

      GenotypingMethod:n.a.

      PreviouslyPublished: If applicable. n.a.

      Gene:VWF

      Variant:NM_000552.5(VWF):c.3943C>T (p.Arg1315Cys)

      HGVS:NM_000552.5:c.3943C>T

      ClinVarID:100310

      CAID:n.a.

      gnomAD:n.a.

    1. 2-years-old male

      Case: 2 year old male at the time of genetic diagnosis, initially presenting with abnormal gait

      DiseaseAssertion: Clinical exome sequencing showed the recurrent VWA1 founder mutation

      FamilyInfo: no family history of neurological or musculoskeletal conditions

      CasePresentingHPOs: HP:0001288 (abnormal gait), HP:0002359 (frequent falls), HP:0003701 (proximal muscle weakness)

      CaseHPOFreeText: Gower's sign

      Gene: VWA1

      Variant: c.62_71dup (p.Gly25ArgfsTer74) (maternally inherited)

      HGVS: NM_022834.5:c.62_71dup

      ClinVar: 830327

      gnomad: does not exist in database

      MultipleGeneVariants: novel paternally inherited missense variant, c.212T>C (p.Leu71Pro)

    1. DiseaseAssertion: Hypertrophic Cardiomyopathy

      VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.

      VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.

      VariantAddInfo: Seen in one HCM probands

      Variant: NM_000257.4(MYH7):c.715G>A (p.Asp239Asn)

      ClinVar: 43100 https://www.ncbi.nlm.nih.gov/clinvar/variation/43100/

      gnomAD: 0.00002891, http://gnomad.broadinstitute.org/variant/14-23900811-C-T

    2. DiseaseAssertion: Hypertrophic Cardiomyopathy

      VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.

      VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.

      VariantAddInfo: Seen in three HCM probands

      Variant: NM_000257.4(MYH7):c.2681A>G (p.Glu894Gly)

      ClinVarID: 42922 https://www.ncbi.nlm.nih.gov/clinvar/variation/42922/

      gnomAD: Not in gnomAD

    3. DiseaseAssertion: None

      VariantPreviousTesting: Some combination of ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, ABCC9, CTF1, DES, EMD, LDB3, LMNA, MYH6, RBM20, SGCD, TAZ, TCAP, TTN, VCL, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, TTR, DSC2, DSG2, DSP, JUP, PKP2, RYR2, TMEM43, CASQ2 and RYR2 were tested via NGS.

      VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.

      Variant: NM_000257.4(MYH7):c.4399C>G (p.Leu1467Val)

      ClinVar: 43015 https://www.ncbi.nlm.nih.gov/clinvar/variation/43015/

      gnomAD: 0.001111, http://gnomad.broadinstitute.org/variant/14-23886482-G-C

    4. DiseaseAssertion: Hypertrophic Cardiomyopathy

      VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.

      VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.

      VariantAddInfo: Seen in two HCM probands

      Variant: NM_000257.4(MYH7):c.1988G>A (p.Arg663His)

      ClinVarID: 42875 https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/

      gnomAD: 0.00003097, http://gnomad.broadinstitute.org/variant/14-23896042-C-T

    5. DiseaseAssertion: Hypertrophic Cardiomyopathy

      VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.

      VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.

      VariantAddInfo: Seen in one proband

      Variant: NM_000257.4(MYH7):c.1063G>A (p.Ala355Thr)

      ClinVarID: 42820 https://www.ncbi.nlm.nih.gov/clinvar/variation/42820/

      gnomAD: Not in gnomAD

    6. DiseaseAssertion: Hypertrophic Cardiomyopathy

      VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.

      VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.

      VariantAddInfo: Seen in two HCM probands

      Variant: NM_000257.4(MYH7):c.2722C>G (p.Leu908Val)

      ClinVar: 14097 https://www.ncbi.nlm.nih.gov/clinvar/variation/14097/

      gnomAD: 0.00006482, http://gnomad.broadinstitute.org/variant/14-23893316-G-C

    7. DiseaseAssertion: None

      VariantPreviousTesting: Some combination of ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, ABCC9, CTF1, DES, EMD, LDB3, LMNA, MYH6, RBM20, SGCD, TAZ, TCAP, TTN, VCL, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, TTR, DSC2, DSG2, DSP, JUP, PKP2, RYR2, TMEM43, CASQ2 and RYR2 were tested via NGS.

      VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.

      Variant: NM_000257.4(MYH7):c.3803G>A (p.Arg1268His)

      ClinVar: 42975 https://www.ncbi.nlm.nih.gov/clinvar/variation/42975/

      gnomAD: 0.0009786, http://gnomad.broadinstitute.org/variant/14-23888742-C-T

    1. index case

      Case#: index case, III.4, female, 52 yrs,

      DiseaseAssertion: HCM

      FamilyInfo: Yes, III.3, IV.3 and IV.4 also diagnosed

      CasePresentingHPOs: Cafe-au-lait spot, freckling, neurofibromas, heart murmur, left ventricular hypertrophy (HP:0000957, HP:0001480, HP:0001067, HP:0030148, HP:0001712)

      CaseHPOFreeText: 20 mm IVS, 56% EF, 50 mmHg LVOTO, NSVT (VA)

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: No AV, no ICD

      CasePreviousTesting: N/A

      CaseGenotypingMethod: ECG, cardiac magnetic resonance, physical examination, NGS tech

      Variant: NM_000257.4(MYH7):c.1357C>T (p.Arg453Cys)

      ClinVar: 14089 https://www.ncbi.nlm.nih.gov/clinvar/variation/14089/

      CAID: N/A

      gnomAD: absent

      MultipleGeneVariants:

      (1) NF1 Variant:

      Variant: NM_000267.3(NF1):c.6709C>T (p.Arg2237Ter)

      ClinVar: 230389 https://www.ncbi.nlm.nih.gov/clinvar/variation/230389/

      CAID: N/A

      gnomAD: absent

    1. HCM147

      CaseHCM147: 31 yrs report, Vietnam, Asian

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: Family history of Sudden Cardiac Death and Hypertrophic Cardiomyopathy, Has a 9 year old daughter with the same variant but no symptoms

      CasePresentingHPOs: HP:0100749, HP:0006698, HP:0031295 (Chest pain, Dilatation of the ventricular cavity, Left atrial enlargement)

      HPOsFreeText: Maximal LV thickness 32 mm

      CaseNotHPOs: HP:0005110, HP:0001297, HP:0004756 (Atrial fibrillation, Stroke, Ventricular tachycardia)

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: The gene panel included 10 sarcomeric genes (MYH7, MYBPC3, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1, TNNC1, MYH6), 9 genes encoding Z-disk components and Ca2+ homeostasis factors (LDB3, CSRP3, TCAP, VCL, ACTN2, MYOZ2, NEXN, JPH2, PLN), and 4 genes involved in HCM phenocopies (GLA, LAMP2, PRKAG2, TTR), All probands had left ventricular wall thickness >= 15 mm and no other diseases that can cause secondary hypertrophy

      CaseGenotypingMethod: The coding region, flanking sequences, and untranslated regions of each gene were enriched by LC-PCR, amplified, and sequenced on the Illumina MiSeq or MiniSeq platform. Identified variants were then filtered for pathogenicity and confirmed by Sanger sequencing.

      Variant: NM_000257.4(MYH7):c.2156G>A (p.Arg719Gln)

      ClinVar: 14107 https://www.ncbi.nlm.nih.gov/clinvar/variation/14107/

      gnomAD: Not in gnomAD

    1. 9

      CaseIX: Brazil, Caucasian

      DiseaseAssertion: Hypertrophic cardiomyopathy

      FamilyInfo: Family history of HCM

      CasePresentingHPOs: HP:0001712, HP:0001639 (Left ventricular hypertrophy, Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: Only MYH7, MYBPC3, and TNNT2 were tested.

      CaseGenotypingMethod: DNA was extracted from peripheral blood and the above genes were subject to PCR amplification and directly sequenced. The resulting sequences were compared with the reference and filtered for pathogenicity.

      Variant: NM_000257.3:c.788T>C (p.Ile263Thr)

      ClinVar: 43106 https://www.ncbi.nlm.nih.gov/clinvar/variation/43106/

      gnomAD: European (Non-Finnish) 8.792e-6, Overall 3.977e-6 https://gnomad.broadinstitute.org/variant/14-23900635-A-G

    1. WPW381

      Case#: WPW381

      DiseaseAssertion: WPW, LY non compaction cardiomyopathy

      FamilyInfo: inherited

      CasePresentingHPOs: Wolff-Parkinson-White syndrome, Left ventricular noncompaction cardiomyopathy (HP:0001716, HP:0011664)

      CaseHPOFreeText: 0 ARIC, 0 THou, 8.12e-6 gnomAD, 8.24e-6 Exac, 0 esp6500, 34 CADD_phred, 0 pLI,

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      CaseGenotypingMethod: ECG, exome sequencing, gene analysis, burden analysis,

      Variant: NM_000257.4(MYH7):c.728G>A (p.Arg243His)

      ClinVar: 14126 https://www.ncbi.nlm.nih.gov/clinvar/variation/14126/

      CAID: N/A

      gnomAD: 0.00002891 Latino/Admixed American https://gnomad.broadinstitute.org/variant/14-23894525-C-T

    1. Case404: Female, 0.083 years onset, Japan, Asian

      DiseaseAssertion: Left ventricular noncompaction

      CasePresentingHPOs: HP:0030682, HP:0025169 (Left ventricular noncompaction, Left ventricular systolic dysfunction)

      HPOsFreeText: Left Ventricular Ejection Fraction at 48.9%, LVDD-Z score at 0.0408

      CaseNotHPOs: HP:0011675, HP:0001635 (Arrhythmia, Heart failure)

      NotHPOsFreeText: Congenital heart disease with significant hemodynamic changes

      CaseAddInfo: No family history


      CasePreviousTesting: Genes tested include the 8 sarcomere genes as well as 65 more listed in Table S1.

      CaseGenotypingMethod: Genomic DNA was extracted from whole blood from each of the probands. Next Generation Sequencing of 73 genes related to cardiac function was performed, incorporating PCR amplification, and any variants found were subjected to filtering for frequency and pathogenicity. Any variants suggested to be pathogenic were confirmed by Sanger sequencing afterwards.


      Variant: NM_000257.3:c.67C>T (p.Arg23Trp)

      ClinVar: 181295 https://www.ncbi.nlm.nih.gov/clinvar/variation/181295/

      gnomAD: European (Finnish) 7.961e-5, Overall 2.475e-5 https://gnomad.broadinstitute.org/variant/14-23902875-G-A

    2. Case391: Female, 0.83 years onset, Japan, Asian

      DiseaseAssertion: Left ventricular noncompaction

      CasePresentingHPOs: HP:0030682, HP:0025169, HP:0001635 (Left ventricular noncompaction, Left ventricular systolic dysfunction, Heart failure)

      HPOsFreeText: Left Ventricular Ejection Fraction at 38%, LVDD-Z score at 2.6785

      CaseNotHPOs: HP:0011675 (Arrhythmia)

      NotHPOsFreeText: Congenital heart disease with significant hemodynamic changes

      CaseAddInfo: No family history


      CasePreviousTesting: Genes tested include the 8 sarcomere genes as well as 65 more listed in Table S1.

      CaseGenotypingMethod: Genomic DNA was extracted from whole blood from each of the probands. Next Generation Sequencing of 73 genes related to cardiac function was performed, incorporating PCR amplification, and any variants found were subjected to filtering for frequency and pathogenicity. Any variants suggested to be pathogenic were confirmed by Sanger sequencing afterwards.


      Variant: NM_000257.3:c.5401G>A (p.Glu1801Lys)

      ClinVar: 43069 https://www.ncbi.nlm.nih.gov/clinvar/variation/43069/

      gnomAD: Not in gnomAD

    3. Case362: Female, 0.0833 years onset, Japan, Asian

      DiseaseAssertion: Left ventricular noncompaction

      CasePresentingHPOs: HP:0030682, HP:0025169 (Left ventricular noncompaction, Left ventricular systolic dysfunction)

      HPOsFreeText: Left Ventricular Ejection Fraction at 40%, LVDD-Z score at -0.823

      CaseNotHPOs: HP:0011675, HP:0001635 (Arrhythmia, Heart failure)

      NotHPOsFreeText: Congenital heart disease with significant hemodynamic changes

      CaseAddInfo: No family history


      CasePreviousTesting: Genes tested include the 8 sarcomere genes as well as 65 more listed in Table S1.

      CaseGenotypingMethod: Genomic DNA was extracted from whole blood from each of the probands. Next Generation Sequencing of 73 genes related to cardiac function was performed, incorporating PCR amplification, and any variants found were subjected to filtering for frequency and pathogenicity. Any variants suggested to be pathogenic were confirmed by Sanger sequencing afterwards.


      Variant: NM_000257.3:c.689T>C (p.Phe230Ser)

      ClinVar: 263543 https://www.ncbi.nlm.nih.gov/clinvar/variation/263543/

      gnomAD: Not in gnomAD

    1. 12

      Case: Patient 12, male, 7yo

      CasePresentingHPOs: HP:0030682 (left ventricular noncompaction)

      HPOsFreeText: CK = 1400U/l

      CaseNotHPOs:

      NotHPOsFreeText: no muscle symptoms, no respiratory or cardiac involvement

      FamilyInfo: family history, pedigree in figure 1

      DiseaseEntity: no assertion

      InheritancePattern: no assertion

      CasePreviousTesting: see below

      CaseGenotypingMethod: 9 cases underwent targeted Sanger sequencing of MYH7, 12 cases underwent Motorplex analysis (NGS of 93 myopathy-related genes - PMID:25214167), all MYH7 variants confirmed via Sanger sequencing, segregation analysis performed on available family members, which cases received which sequencing technique is not specified

      Variant: NM_000257.4(MYH7):c.5401G>A (p.Glu1801Lys)

      ClinVar: 43069, https://www.ncbi.nlm.nih.gov/clinvar/variation/43069/

      gnomAD: absent

    2. 21

      Case: Patient 21, female, 40yo, symptom onset in adulthood

      CasePresentingHPOs: HP:0009027, HP:0002460, HP:0003458, HP:0025115 (foot drop, distal muscle weakness, EMG: myopathic abnormalities, hyalin bodies)

      HPOsFreeText: CK = 500 U/l

      CaseNotHPOs: HP:0002650 (scoliosis)

      NotHPOsFreeText: no respiratory or cardiac involvement

      FamilyInfo: no family history

      DiseaseEntity: no assertion

      InheritancePattern: no assertion

      CasePreviousTesting: see below

      CaseGenotypingMethod: 9 cases underwent targeted Sanger sequencing of MYH7, 12 cases underwent Motorplex analysis (NGS of 93 myopathy-related genes - PMID:25214167), all MYH7 variants confirmed via Sanger sequencing, segregation analysis performed on available family members, which cases received which sequencing technique is not specified

      Variant: NM_000257.4(MYH7):c.1322C>T (p.Thr441Met)

      ClinVar: 14122, https://www.ncbi.nlm.nih.gov/clinvar/variation/14122/

      gnomAD: 0.0002227, https://gnomad.broadinstitute.org/variant/14-23898249-G-A?dataset=gnomad_r2_1

    1. Case: Australian

      DiseaseAssertion: HCM

      CaseHPOFreeText: maximum left ventricular wall thickness of ≥15 mm

      CasePreviousTesting: electrocardiography, echocardiography, Full testing (MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1)

      CaseGenotypingMethod: DNA isolated from peripheral blood or buccal swabs, PCR, Sanger sequencing, segregation analysis, haplotype analysis of MYBPC3 and MYH7

      Variant: NM_000257.3(MYH7):c.427C>T (p.Arg143Trp)

      ClinVar: 164401, https://www.ncbi.nlm.nih.gov/clinvar/variation/164401/

      gnomAD: 0.00002784, https://gnomad.broadinstitute.org/variant/14-23901923-G-A

    2. Supplementary Data, Table 2

      Case: Australian

      DiseaseAssertion: HCM

      CaseHPOFreeText: maximum left ventricular wall thickness of ≥15 mm

      CasePreviousTesting: electrocardiography, echocardiography, Full testing (MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1)

      CaseGenotypingMethod: DNA isolated from peripheral blood or buccal swabs, PCR, Sanger sequencing, segregation analysis, haplotype analysis of MYBPC3 and MYH7

      Variant: NM_000257.3(MYH7):c.1207C>T (p.Arg403Trp)

      ClinVar: 14102, https://www.ncbi.nlm.nih.gov/clinvar/variation/14102/

      gnomAD: n/a

    1. Supplementary Data: S2 Table

      Case 198: Spanish, 56, Male

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1

      CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes

      Variant: NM_000257.3(MYH7):c.2167C>T (p.Arg723Cys)

      ClinVar: 14095, https://www.ncbi.nlm.nih.gov/clinvar/variation/14095/

      gnomAD: 0.00001194, https://gnomad.broadinstitute.org/variant/14-23895023-G-A

    2. Supplementary Data: S2 Table

      Case 9: Spanish, 13yo, Female

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1

      CaseGenotypingMethod: genomic DNA obtained from blood or saliva, PCR, Sanger Sequencing

      Variant: NM_000257.3(MYH7):c.4124A>G (p.Tyr1375Cys)

      ClinVar: 164293, https://www.ncbi.nlm.nih.gov/clinvar/variation/164293/

      gnomAD: n/a

    3. Supplementary Data: S2 Table

      Case 65: Spanish, 35yo, Male

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1

      CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes

      Variant: NM_000257.3(MYH7):c.715G>A (p.Asp239Asn)

      ClinVar: 43100, https://www.ncbi.nlm.nih.gov/clinvar/variation/43100/

      gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23900811-C-T

      MultipleGeneVariants:

      (1) MYBPC3 Variant:

      Variant: NM_000256.3(MYBPC3):c.3676C>T (p.Arg1226Cys)

      ClinVar: 42731, https://www.ncbi.nlm.nih.gov/clinvar/variation/42731/

      gnomAD: 0.00004815, https://gnomad.broadinstitute.org/variant/11-47353761-G-A

      (2) TTN Variant:

      Variant: NM_001267550.2(TTN):c.49175C>A (p.Ala16392Glu)

      ClinVar: 405004, https://www.ncbi.nlm.nih.gov/clinvar/variation/405004/

      gnomAD: 0.000004042, https://gnomad.broadinstitute.org/variant/2-179478949-G-T

    4. Supplementary Data: S2 Table

      Case 251: Spanish, 55yo, Female

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1

      CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes

      Variant: NM_000257.3(MYH7):c.3610G>C (p.Gly1204Arg)

      ClinVar: 42966, https://www.ncbi.nlm.nih.gov/clinvar/variation/42966/

      gnomAD: 0.000004008, https://gnomad.broadinstitute.org/variant/14-23889170-C-G

    5. Supplementary Data: S2 Table

      Case 10: Spanish, 69yo, Male

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1

      CaseGenotypingMethod: genomic DNA obtained from blood or saliva, PCR, Sanger Sequencing

      Variant: NM_000257.3(MYH7):c.4377G>T (p.Lys1459Asn)

      ClinVar: 43012, https://www.ncbi.nlm.nih.gov/clinvar/variation/43012/

      gnomAD: 0.0002937, https://gnomad.broadinstitute.org/variant/14-23886504-C-A

    6. Supplementary Data: S2 Table

      Case 130: Spanish, 14yo, Male

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1

      CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes

      Variant: NM_000257.3(MYH7):c.2167C>G (p.Arg723Gly)

      ClinVar: 42885, https://www.ncbi.nlm.nih.gov/clinvar/variation/42885/

      gnomAD: n/a

      MultipleGeneVariants:

      (1) TCAP Variant:

      Variant: NM_003673.3(TCAP):c.97C>T (p.Arg33Trp)

      ClinVar: 282451, https://www.ncbi.nlm.nih.gov/clinvar/variation/282451/

      gnomAD: 0.00007092, https://gnomad.broadinstitute.org/variant/17-37821709-C-T

    7. Supplementary Data: S2 Table

      Case 67: Spanish, 40yo, Male

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1

      CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes

      Variant: NM_000257.3(MYH7):c.2389G>A (p.Ala797Thr)

      ClinVar: 42901, https://www.ncbi.nlm.nih.gov/clinvar/variation/42901/

      gnomAD: 0.00002386, https://gnomad.broadinstitute.org/variant/14-23894525-C-T

      MultipleGeneVariants:

      (1) TTN Variant:

      Variant: NM_133378.4(TTN):c.4396T>C (p.Phe1466Leu)

      ClinVar: 166320, https://www.ncbi.nlm.nih.gov/clinvar/variation/166320/

      gnomAD: 0.0006871, https://gnomad.broadinstitute.org/variant/2-179642515-A-G

    1. Supplementary Data: Online Table 2a

      Case:

      CasePreviousTesting: Full sarcomere testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CRYAB, CSRP3, DES, DMD, DSC2, DSG2, DSP, EMD, GLA, JPH2, JUP, LAMA4, LAMP2, LMNA, MYH6, MYPN, MYOZ1, MYOZ2, PKP2, PLN, PRKAG2, RBM20, RYR2, SCN5A, SGCD, TAZ, TCAP, TMEM43, TNNC1, TTN, VCL and LDB3)

      CaseGenotypingMethod: DNA isolated from peripheral blood, targeted enrichment, next-gen sequencing with panel of 46 genes

      Variant: NM_000257.3(MYH7):c.2710C>T (p.Arg904Cys)

      ClinVar: 164316, https://www.ncbi.nlm.nih.gov/clinvar/variation/164316/

      gnomAD: 0.000003977, https://gnomad.broadinstitute.org/variant/14-23893328-G-A

    2. Supplementary Data: Online Table 1a

      Case:

      CasePresentingHPOs: HP:0001629 (Ebstein anomaly)

      CasePreviousTesting: Full sarcomere testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CRYAB, CSRP3, DES, DMD, DSC2, DSG2, DSP, EMD, GLA, JPH2, JUP, LAMA4, LAMP2, LMNA, MYH6, MYPN, MYOZ1, MYOZ2, PKP2, PLN, PRKAG2, RBM20, RYR2, SCN5A, SGCD, TAZ, TCAP, TMEM43, TNNC1, TTN, VCL and LDB3)

      CaseGenotypingMethod: DNA isolated from peripheral blood, targeted enrichment, next-gen sequencing with panel of 46 genes

      Variant: NM_000257.3(MYH7):c.689T>C (p.Phe230Ser)

      ClinVar: 263543, https://www.ncbi.nlm.nih.gov/clinvar/variation/263543/

      gnomAD: n/a

    3. Supplementary Data: Online Table 3

      Case:

      CasePreviousTesting: Full sarcomere testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CRYAB, CSRP3, DES, DMD, DSC2, DSG2, DSP, EMD, GLA, JPH2, JUP, LAMA4, LAMP2, LMNA, MYH6, MYPN, MYOZ1, MYOZ2, PKP2, PLN, PRKAG2, RBM20, RYR2, SCN5A, SGCD, TAZ, TCAP, TMEM43, TNNC1, TTN, VCL and LDB3)

      CaseGenotypingMethod: DNA isolated from peripheral blood, targeted enrichment, next-gen sequencing with panel of 46 genes

      Variant: NM_000257.3(MYH7):c.345C>T (p.Tyr115=)

      ClinVar: 42962, https://www.ncbi.nlm.nih.gov/clinvar/variation/42962/

      gnomAD: 0.0001061, https://gnomad.broadinstitute.org/variant/14-23902293-G-A

    1. Supplementary Data table 1

      Case:

      DiseaseAssertion: hypertrophic cardiomyopathy

      CaseHPOFreeText: maximal wall thickness (MWT) ≥15 mm

      CasePreviousTesting: Full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (TNNC1, CSRP3, TCAP, ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CAV3, CRYAB, CTNNA3, DES, DSC2, DSG2, DSP, EMD, FHL1, GLA, JPH2, JUP, LAMA4, LAMP2, LDB3, LMNA, MIB1, MYH6, MYOZ2, MYPN, NEXN, PKP2, PLN, PRDM16, PRKAG2, RBM20, SCN5A, TAZ, TMEM43, TNNC1, TTN, TTR, VCL), electrocardiography

      CaseGenotypingMethod: direct sequencing of all coding intron-exon boundaries of 12 genes (prior to 2012), next-generation sequencing (post 2012)

      Variant: NM_000257.3(MYH7):c.1532T>C (p.Ile511Thr)

      ClinVar: 42848, https://www.ncbi.nlm.nih.gov/clinvar/variation/42848/

      gnomAD: n/a

    2. Supplementary Data table 1

      Case:

      DiseaseAssertion: hypertrophic cardiomyopathy

      CaseHPOFreeText: maximal wall thickness (MWT) ≥15 mm

      CasePreviousTesting: Full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (TNNC1, CSRP3, TCAP, ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CAV3, CRYAB, CTNNA3, DES, DSC2, DSG2, DSP, EMD, FHL1, GLA, JPH2, JUP, LAMA4, LAMP2, LDB3, LMNA, MIB1, MYH6, MYOZ2, MYPN, NEXN, PKP2, PLN, PRDM16, PRKAG2, RBM20, SCN5A, TAZ, TMEM43, TNNC1, TTN, TTR, VCL), electrocardiography

      CaseGenotypingMethod: direct sequencing of all coding intron-exon boundaries of 12 genes (prior to 2012), next-generation sequencing (post 2012)

      Variant: NM_000257.3(MYH7):c.727C>T (p.Arg243Cys)

      ClinVar: 43101, https://www.ncbi.nlm.nih.gov/clinvar/variation/43101/

      gnomAD: 0.00003184, https://gnomad.broadinstitute.org/variant/14-23900799-G-A

    1. CaseMYH7-29: N/A

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: 1 other proband shares this genotype

      CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.

      Variant: NM_000257.3:c.1988G>A (p.Arg663His)

      ClinVar: 42875 https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/

      gnomAD: European (Non-Finnish) 3.097e-5, Overall 1.414e-5 https://gnomad.broadinstitute.org/variant/14-23896042-C-T

    2. CaseMYH7-12: N/A

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: 1 other proband shares this genotype

      CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.

      Variant: NM_000257.3:c.1358G>A (p.Arg453His)

      ClinVar: 42838 https://www.ncbi.nlm.nih.gov/clinvar/variation/42838/

      gnomAD: Not in gnomAD

    3. CaseMYH7-10: N/A

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: 3 other probands share this genotype

      CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.

      Variant: NM_000257.3:c.2779G>A (p.Glu927Lys)

      ClinVar: 42932 https://www.ncbi.nlm.nih.gov/clinvar/variation/42932/

      gnomAD: Not in gnomAD

    4. CaseMYH7-21: N/A

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: 5 other probands share this genotype

      CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.

      Variant: NM_000257.3:c.2722C>G (p.Leu908Val)

      ClinVar: 14097 https://www.ncbi.nlm.nih.gov/clinvar/variation/14097/

      gnomAD: European (Non-Finnish) 6.482e-5, Overall 3.185e-5 https://gnomad.broadinstitute.org/variant/14-23893316-G-C

    5. CaseMYH7-4: N/A

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.

      Variant: NM_000257.3:c.2156G>A (p.Arg719Gln)

      ClinVar: 140107 https://www.ncbi.nlm.nih.gov/clinvar/variation/14107/

      gnomAD: Not in gnomAD

    6. CaseMYH7-19: N/A

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: 2 other probands share this genotype

      CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.

      Variant: NM_000257.3:c.4066G>A (p.Glu1356Lys)

      ClinVar: 164294 https://www.ncbi.nlm.nih.gov/clinvar/variation/164294/

      gnomAD: Not in gnomAD

    1. Supplementary Data Table S3

      Case: 349

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant: NM_000257.4(MYH7):c.4472C>G (p.Ser1491Cys)

      ClinVar: 43020 https://www.ncbi.nlm.nih.gov/clinvar/variation/43020/

      gnomAD: 0.01265, https://gnomad.broadinstitute.org/variant/14-23886409-G-C

      MultipleGeneVariants:

      (1) MYH6 Variant

      Variant: NM_002471.3(MYH6):c.1763A>C (p.Asp588Ala)

      ClinVar: 155811 https://www.ncbi.nlm.nih.gov/clinvar/variation/155811/

      gnomAD: 0.003074, https://gnomad.broadinstitute.org/variant/14-23868065-T-G

      (2) MYH6 Variant

      Variant: NM_002471.3(MYH6):c.5491G>A (p.Glu1831Lys)

      ClinVar: 196975 https://www.ncbi.nlm.nih.gov/clinvar/variation/196975/

      gnomAD: 0.0003008, https://gnomad.broadinstitute.org/variant/14-23853725-C-T

      (3) RBM20 Variant

      Variant: NM_001134363.3(RBM20):c.1958C>T (p.Thr653Ile)

      ClinVar: 180045 https://www.ncbi.nlm.nih.gov/clinvar/variation/180045/

      gnomAD: 0.0007430, https://gnomad.broadinstitute.org/variant/10-112572113-C-T

      (4) TMPO Variant

      Variant: NM_003276.2(TMPO):c.821G>A (p.Arg274Lys)

      ClinVar: 44673 https://www.ncbi.nlm.nih.gov/clinvar/variation/44673/

      gnomAD: 0.005407, https://gnomad.broadinstitute.org/variant/12-98926856-G-A

    2. Supplementary Data Table S3

      Case: 18

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant: NM_000257.4(MYH7):c.2770G>A (p.Glu924Lys)

      ClinVar: 14092, https://www.ncbi.nlm.nih.gov/clinvar/variation/14092/

      gnomAD: absent

      MultipleGeneVariants:

      (1) LMNA Variant

      Variant: NM_170707.4(LMNA):c.357C>T (p.Arg119=)

      ClinVar: 48062, https://www.ncbi.nlm.nih.gov/clinvar/variation/48062/

      gnomAD: 0.00424

      (2) SDHA Variant

      Variant: NM_004168.4(SDHA):c.1886A>T (p.Tyr629Phe)

      ClinVar: 224949, https://www.ncbi.nlm.nih.gov/clinvar/variation/224949/

      gnomAD: 0.1547, https://gnomad.broadinstitute.org/variant/5-254599-A-T

      (2) TTN Variant

      Variant: NM_001267550.2(TTN):c.74597_74599CAA[1] (p.Thr24867del)

      ClinVar: 165840, https://www.ncbi.nlm.nih.gov/clinvar/variation/165840/

      gnomAD: 0.001152, https://gnomad.broadinstitute.org/variant/2-179436256-ATTG-A

    3. Supplementary Data Table S3

      Case: 8

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)

      ClinVar: 155814, https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/

      gnomAD: 0.00006010, https://gnomad.broadinstitute.org/variant/14-23891476-C-T

      MultipleGeneVariants

      (1) LAMA4 Variant

      Variant: NM_001105206.3(LAMA4):c.2614C>G (p.Pro872Ala)

      ClinVar: 180391, https://www.ncbi.nlm.nih.gov/clinvar/variation/180391/

      gnomAD: 0.0004032, https://gnomad.broadinstitute.org/variant/6-112463374-G-C

    4. Supplementary Data Table S3

      Case: 110

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant1: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)

      ClinVar: 155814 https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/

      gnomAD: 0.0006368, https://gnomad.broadinstitute.org/variant/14-23891476-C-T

      Variant2: NM_000257.4(MYH7):c.4472C>G (p.Ser1491Cys)

      ClinVar: 43020 https://www.ncbi.nlm.nih.gov/clinvar/variation/43020/

      gnomAD: 0.01265, https://gnomad.broadinstitute.org/variant/14-23886409-G-C

      MultipleGeneVariants:

      (1) CRYAB Variant

      Variant as listed does not exist on any transcript

      Variant: c.331G>A (p.Gly111Ser)

      ClinVar: N/A

      gnomAD: N/A

      (2) DSP Variant

      Variant: NM_004415.4(DSP):c.4588G>T (p.Val1530Phe)

      ClinVar: 137171 https://www.ncbi.nlm.nih.gov/clinvar/variation/137171/

      gnomAD: 0.01477, https://gnomad.broadinstitute.org/variant/6-7581011-G-T

      (3) SDHA Variant

      Variant: NM_004168.4(SDHA):c.1886A>T (p.Tyr629Phe)

      ClinVar: 224949 https://www.ncbi.nlm.nih.gov/clinvar/variation/224949/

      gnomAD: 0.5249, https://gnomad.broadinstitute.org/variant/5-254599-A-T

      (4) TMPO Variant

      Variant: NM_001032283.2(TMPO):c.859G>C (p.Ala287Pro)

      ClinVar: 43693 https://www.ncbi.nlm.nih.gov/clinvar/variation/43693/

      gnomAD: 0.04732, https://gnomad.broadinstitute.org/variant/12-98938295-G-C

      (5) TTN Variant

      Variant: NM_001267550.2(TTN):c.74597_74599CAA[1] (p.Thr24867del)

      ClinVar: 165840 https://www.ncbi.nlm.nih.gov/clinvar/variation/165840/

      gnomAD: 0.003324, https://gnomad.broadinstitute.org/variant/2-179436256-ATTG-A

    5. Supplementary Data Table S3

      Case: 21

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)

      ClinVar: 155814, https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/

      gnomAD: 0.00006010, https://gnomad.broadinstitute.org/variant/14-23891476-C-T

      MultipleGeneVariants:

      (1) LDB3 Variant

      Variant: NM_007078.3(LDB3):c.295C>T (p.Pro99Ser)

      ClinVar: 178059, https://www.ncbi.nlm.nih.gov/clinvar/variation/178059/

      gnomAD: 0.0009830, https://gnomad.broadinstitute.org/variant/10-88439888-C-T

    6. Supplementary Data Table S3

      Case: 216

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant1: NM_000257.4(MYH7):c.1816G>A (p.Val606Met)

      ClinVar: 14091 https://www.ncbi.nlm.nih.gov/clinvar/variation/14091/

      gnomAD: 0.00001548, https://gnomad.broadinstitute.org/variant/14-23896866-C-T

      Variant2: NM_000257.4(MYH7):c.3853+7C>T

      ClinVar: 42977 https://www.ncbi.nlm.nih.gov/clinvar/variation/42977/

      gnomAD: 0.003956, https://gnomad.broadinstitute.org/variant/14-23888685-G-A

    7. Supplementary Data Table S3

      Case: 2

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)

      ClinVar: 155814, https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/

      gnomAD: 0.00006010, https://gnomad.broadinstitute.org/variant/14-23891476-C-T

      MultipleGeneVariants:

      (1) MYBPC3 Variant

      Variant: NM_000256.3(MYBPC3):c.440C>T (p.Pro147Leu)

      ClinVar: 181035, https://www.ncbi.nlm.nih.gov/clinvar/variation/181035/

      gnomAD: 0.0005896, https://gnomad.broadinstitute.org/variant/11-47371630-G-A

      (2) MYOZ2 Variant

      Variant: NM_016599.4(MYOZ2):c.738A>G (p.Ile246Met)

      ClinVar: 30509, https://www.ncbi.nlm.nih.gov/clinvar/variation/30509/

      gnomAD: 0.002300, https://gnomad.broadinstitute.org/variant/4-120107298-A-G

      (3) PSEN2 Variant

      Variant: NM_000447.3(PSEN2):c.211C>T (p.Arg71Trp)

      ClinVar: 192130, https://www.ncbi.nlm.nih.gov/clinvar/variation/192130/

      gnomAD: 0.003711, https://gnomad.broadinstitute.org/variant/1-227071475-C-T

      (4) SCN5A Variant

      Variant: NM_000335.4(SCN5A):c.1715C>A (p.Ala572Asp)

      ClinVar: 67683, https://www.ncbi.nlm.nih.gov/clinvar/variation/67683/

      gnomAD: 0.005175, https://gnomad.broadinstitute.org/variant/3-38645378-G-T

    8. Supplementary Data Table S3

      Case: 231

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant: NM_000257.4(MYH7):c.4472C>G (p.Ser1491Cys)

      ClinVar: 43020 https://www.ncbi.nlm.nih.gov/clinvar/variation/43020/

      gnomAD: 0.01265, https://gnomad.broadinstitute.org/variant/14-23886409-G-C

      MultipleGeneVariants:

      (1) LDB3 Variant

      Variant: NM_007078.3(LDB3):c.295C>T (p.Pro99Ser)

      ClinVar: 178059 https://www.ncbi.nlm.nih.gov/clinvar/variation/178059/

      gnomAD: 0.009200, https://gnomad.broadinstitute.org/variant/10-88439888-C-T

    9. Supplementary Data Table S3

      Case: 129

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant: NM_000257.4(MYH7):c.1987C>T (p.Arg663Cys)

      ClinVar: 42874 https://www.ncbi.nlm.nih.gov/clinvar/variation/42874/

      gnomAD: Not in gnomAD

      MultipleGeneVariants:

      (1) LAMA4 Variant

      Variant: NM_001105206.3(LAMA4):c.3239G>A (p.Arg1080Gln)

      ClinVar: 44374 https://www.ncbi.nlm.nih.gov/clinvar/variation/44374/

      gnomAD: 0.02400, https://gnomad.broadinstitute.org/variant/6-112460365-C-T

    10. Supplementary Data Table S3

      Case: 152

      DiseaseEntity: HCM

      HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

      InheritancePattern: n/a

      CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

      CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

      Variant: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)

      ClinVar: 155814 https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/

      gnomAD: 0.0006368, https://gnomad.broadinstitute.org/variant/14-23891476-C-T

      MultipleGeneVariants:

      (1) CRYAB Variant

      Variant as listed does not exist on any transcript

      Variant: c.331G>A (p.Gly111Ser)

      ClinVar: N/A

      gnomAD: N/A

      (2) DSP Variant

      Variant: NM_004415.4(DSP):c.4372C>G (p.Arg1458Gly)

      ClinVar: 44906 https://www.ncbi.nlm.nih.gov/clinvar/variation/44906/

      gnomAD: 0.003556, https://gnomad.broadinstitute.org/variant/6-7580795-C-G

    1. HCM16.1

      CaseHCM16.1: Mixed ancestry

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0000819 (Diabetes mellitus)

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: See Table 1

      CaseGenotypingMethod: DNA was extracted from the probands' blood, followed by sequencing of the coding regions and exon/intron boundaries of 15 genes associated with HCM. From there, they were amplified by PCR ampliication and variants were filtered by pathogenicity. Every unclassified variant was confirmed by Sanger sequencing afterwards.

      Variant: NM_000257.3:c.746G>A (p.Arg249Gln)

      ClinVar: 14088 https://www.ncbi.nlm.nih.gov/clinvar/variation/14088/

      gnomAD: Not in gnomAD

    1. CaseMYH7-16: Australia

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: 3 other probands have the same genotype

      CasePreviousTesting: See Table 1

      CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.

      Variant: NM_000257.3:c.2681A>G (p.Glu894Gly)

      ClinVar: 42922 https://www.ncbi.nlm.nih.gov/clinvar/variation/42922/

      gnomAD: Not in gnomAD

    2. CaseMYH7-20: Australia

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: See Table 1

      CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.

      Variant: NM_000257.3:c.2420G>A (p.Arg807His)

      ClinVar: 391904 https://www.ncbi.nlm.nih.gov/clinvar/variation/391904/

      gnomAD: Latino 5.644e-5, Overall 1.414e-5 https://gnomad.broadinstitute.org/variant/14-23894494-C-T

    3. CaseMYH7-9: Australia

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: See Table 1

      CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.

      Variant: NM_000257.3:c.4066G>A (p.Glu1356Lys)

      ClinVar: 164294 https://www.ncbi.nlm.nih.gov/clinvar/variation/164294/

      gnomAD: Not in gnomAD

    4. CaseMYH7-33: Australia

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: See Table 1

      CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.

      Variant: NM_000257.3:c.1727A>G (p.His576Arg)

      ClinVar: 177625 https://www.ncbi.nlm.nih.gov/clinvar/variation/177625/

      gnomAD: African 4.008e-5, Overall 1.768e-5 https://gnomad.broadinstitute.org/variant/14-23896955-T-C

    5. CaseMYH7-27: Australia

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: See Table 1

      CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.

      Variant: NM_000257.3:c.2156G>A (p.Arg719Gln)

      ClinVar: 14107 https://www.ncbi.nlm.nih.gov/clinvar/variation/14107/

      gnomAD: Not in gnomAD

    1. II-3

      CaseBII-3: Female, 64 years diagnosis, Italy, Caucasian

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: See Figure 1

      CasePresentingHPOs: HP:0001639, HP:0002094 (Hypertrophic cardiomyopathy, Dyspnea)

      HPOsFreeText: Max Left ventricular wall thickness of 19 mm, Left atrium diameter of 42 mm, Left ventricular ejection fraction of 64%

      CaseNotHPOs: HP:0003115, HP:0011675 (Abnormal ECG, Arrhythmia)

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: The ACM proband from Family B was genotyped for PKP2, DSP, DSC2, DSG2, JUP and CTNNA3; the HCM patient from Family B was genotyped for MYBPC3, MYH7, TNNI3 and TNNT2.

      CaseGenotypingMethod: All patients in Family B were directly sequenced according to the found variants in CTNNA3 and MYH7. These variants were filtered for pathogenicity and prevalence and classified accordingly.

      Variant: NM_000257.3:c.2631G>T (p.Met877Ile)

      ClinVar: 417718 https://www.ncbi.nlm.nih.gov/clinvar/variation/417718/

      gnomAD: Not in gnomAD

    1. Supplementary Material 4

      Case M-12: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.1988G>A (p.Arg663His)

      ClinVar: 42875, https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/

      gnomAD: 0.00001414, https://gnomad.broadinstitute.org/variant/14-23896042-C-T

    2. Supplementary Material 4

      Case M-11: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.1988G>A (p.Arg663His)

      ClinVar: 42875, https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/

      gnomAD: 0.00001414, https://gnomad.broadinstitute.org/variant/14-23896042-C-T

    3. Supplementary Material 4

      Case M-27: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.2770G>A (p.Glu924Lys)

      ClinVar: 14092, https://www.ncbi.nlm.nih.gov/clinvar/variation/14092/

      gnomAD: n/a

    4. Supplementary Material 4

      Case M-3: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.746G>A (p.Arg249Gln)

      ClinVar: 14088, https://www.ncbi.nlm.nih.gov/clinvar/variation/14088/

      gnomAD: n/a

    5. Supplementary Material 4

      Case M-5: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.1012G>A (p.Val338Met)

      Clinvar: 164381, https://www.ncbi.nlm.nih.gov/clinvar/variation/164381/

      gnomAD: n/a

    6. Supplementary Material 4

      Case M-17: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.2207T>C (p.Ile736Thr)

      ClinVar: 164342, https://www.ncbi.nlm.nih.gov/clinvar/variation/164342/

      gnomAD: n/a

    7. Supplementary Material 4

      Case M-13: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.2011C>T (p.Arg671Cys)

      ClinVar: 164350, https://www.ncbi.nlm.nih.gov/clinvar/variation/164350/

      gnomAD: n/a

    8. Supplementary Material 4

      Case M-7: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant 2: NM_000257.3(MYH7):c.1357C>T (p.Arg453Cys)

      ClinVar: 14089, https://www.ncbi.nlm.nih.gov/clinvar/variation/14089/

      gnomAD: n/a

    9. Supplementary Material 4

      Case M-24: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.2546T>C (p.Met849Thr)

      ClinVar: 42914, https://www.ncbi.nlm.nih.gov/clinvar/variation/42914/

      gnomAD: n/a

    10. Supplementary Material 4

      Case M-4: Japanese

      DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

      CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

      CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

      Variant: NM_000257.3(MYH7):c.746G>A (p.Arg249Gln)

      ClinVar: 14088, https://www.ncbi.nlm.nih.gov/clinvar/variation/14088/

      gnomAD: n/a

    1. Table V

      Case 898: Italian, 1yo at onset

      DiseaseAssertion: HCM

      FamilyInfo: family history of HCM

      CasePresentingHPOs: HP:0001712 (left ventricular hypertrophy)

      CaseHPOFreeText: LVWT = 11mm, LV ejection fraction = 70%

      CasePreviousTesting: echocardiography, Full testing (MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1), additional testing: (GLA, LAMP2, PRKAG2), additional genes added with NGS: (TNNC1, MYH6, MYOM1, MYOZ2, ANKRD1, VCL, CALR3, CAV3)

      CaseGenotypingMethod: Genomic DNA extracted from peripheral leukocytes, Sanger sequencing (73 samples), Next-gen sequencing (19 samples)

      Variant: NM_000257.3(MYH7):c.5302G>A (p.Glu1768Lys)

      ClinVar: 43059, https://www.ncbi.nlm.nih.gov/clinvar/variation/43059/

      gnomAD: n/a

    1. Table 1 and 4

      Case A13: Male, 10yo, proband (III-2)

      DiseaseAssertion: malignant HCM

      FamilyInfo: positive family history (fig 1), grandfather died at 42yo from heart disease, father died at 40yo due to sudden cardiac death, mother (A11, II-1) had no clinical symptoms, sister (A12, III-1) diagnosed at 21yo with severe HCM

      CasePresentingHPOs: HP:0100749, HP:0001279 (chest pain, syncope)

      CaseHPOFreeText: interventricular septum thickness = 21.0mm, left ventricular posterior wall thickness = 12.0mm, left atrium = 40.0mm, left ventricular ejection fraction = 48%, septal asymmetry, decreased left ventricular systolic and diastolic function

      CasePreviousTesting: 12-lead ECG, echocardiography, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing (LMNA, PRKAG2, SCN5A, MYH6)

      CaseGenotypingMethod: genomic DNA collected from peripheral whole blood samples, PCR, high-throughput sequencing using PGM Sequencing 400 kit, variants verified via Sanger Sequencing

      Variant: NM_000257.3(MYH7):c.2155C>T (p.Arg719Trp)

      ClinVar: 14104, https://www.ncbi.nlm.nih.gov/clinvar/variation/14104/

      gnomAD: 0.00003185, https://gnomad.broadinstitute.org/variant/14-23895180-G-A

      MultipleGeneVariants:

      (1) PRKAG2 Variant:

      Variant: NM_016203.3(PRKAG2):c.298G>A (p.Gly100Ser)

      ClinVar: 36697, https://www.ncbi.nlm.nih.gov/clinvar/variation/36697/

      gnomAD: 0.006770, https://gnomad.broadinstitute.org/variant/7-151478406-C-T

    1. KMP 22

      Case KMP 22: Eastern Slovakia, Male, 21yo

      DiseaseAssertion: hypertrophic cardiomyopathy

      FamilyInfo: negative family history

      CaseHPOFreeText: left ventricular ejection fraction = 60%, implantable cardioverter defibrillator

      CaseNotHPOFreeText: left ventricular outflow tract obstruction

      CasePreviousTesting: 12-lead ECG, echocardiography, partial testing (MYBPC3, MYH7, NEBL, SCN5A, TNNI3, TNNT2)

      CaseGenotypingMethod: genomic DNA collected from peripheral blood leukocytes, Sanger sequencing

      Variant: NM_000257.3(MYH7):c.2845G>A (p.Glu949Lys)

      ClinVar: 14093, https://www.ncbi.nlm.nih.gov/clinvar/variation/14093/

      gnomAD: n/a

    2. KMP 8

      Case KMP 8: Eastern Slovakia, Male, 62yo

      DiseaseAssertion: hypertrophic cardiomyopathy

      FamilyInfo: no family history

      CaseHPOFreeText: left ventricular outflow tract obstruction, left ventricular ejection fraction = 60%

      CasePreviousTesting: 12-lead ECG, echocardiography, partial testing (MYBPC3, MYH7, NEBL, SCN5A, TNNI3, TNNT2)

      CaseGenotypingMethod: genomic DNA collected from peripheral blood leukocytes, Sanger sequencing

      Variant: NM_000257.3(MYH7):c.2845G>A (p.Glu949Lys)

      ClinVar: 14093, https://www.ncbi.nlm.nih.gov/clinvar/variation/14093/

      gnomAD: n/a

    1. N16

      Case N16: Tunisia, Female, 72yo at onset, 76yo at study

      DiseaseAssertion: hypertrophic cardiomyopathy

      CasePresentingHPOs: HP:0100749 (chest pain)

      CaseHPOFreeText: left ventricular septum (LVS) ≥15 mm, septum size = 18mm

      FamilyInfo: family history sudden cardiac death

      CasePreviousTesting: Full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (FLNC, TNNC1), electrocardiogram, echocardiography

      CaseGenotypingMethod: PCR, Next-generation sequencing, identified variants confirmed via Sanger Sequencing

      Variant: NM_000257.3(MYH7):c.4909G>A (p.Ala1637Thr)

      ClinVar: 43044, https://www.ncbi.nlm.nih.gov/clinvar/variation/43044/

      gnomAD: 0.00008840, https://gnomad.broadinstitute.org/variant/14-23885257-C-T

    1. 8

      Case8: Female, 58 years report, China, Asian

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: No family history

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: Interventricular septal thickness at 17.3 mm, Left ventricular posterior wall thickness at 15.9 mm, Left ventricular end-diastolic diameter at 60.7 mm, Left ventricular septal thickness at 45.3 mm, Left ventricular ejection fraction at 50%

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: See list of sequenced genes

      CaseGenotypingMethod: Genomic DNA was isolated from whole blood of all patients and controls. Whole coding exons and exon-intron boundaries of the 19 HCM-related genes listed above were amplified and sequenced on Ion Torrent PGM. These variants were then filtered for pathogenicity and compared to the controls. Any mutations found were confirmed by conventional dideoxy sequencing and Sanger sequencing.

      Variant: NM_000257.3:c.730T>C (p.Phe244Leu)

      ClinVar: 181319 https://www.ncbi.nlm.nih.gov/clinvar/variation/181319/

      gnomAD: Not in gnomAD

    1. CaseMYH7-4: Japan, Asian

      CasePresentingHPOs: HP:0001639, HP:0006685 (Hypertrophic cardiomyopathy, Endomyocardial fibrosis)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo:


      CaseGenotypingMethod: Genomic DNA was extracted from whole blood from each proband. They each had 95 genes associated with DCM, HCM, and other inherited cardiovascular diseases sequenced with a panel, including both the exons and spicing regions. Variants were then filtered for rarity and pathogenicity.


      Variant: NM_000257.3:c.2221G>C (p.Gly741Arg)

      ClinVar: 14098 https://www.ncbi.nlm.nih.gov/clinvar/variation/14098/

      gnomAD: Not in gnomAD

    1. Case14: Male, 59 years diagnosis, China, Asian

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      FamilyInfo: One sibling had recurrent syncope and HCM with ICD implantation

      CasePresentingHPOs: HP:0001639, HP:0001962, HP:0000822 (Hypertrophic cardiomyopathy, Palpitations, Hypertension)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      CasePreviousTesting: Probands were only genotyped for MYH7 and MYBPC3 in that order, stopping once a positive finding was detected.

      CaseGenotypingMethod: Genomic DNA was extracted from peripheral blood. Each gene's coding exons and flanking introns were subject to PCR amplification and sequencing. From there, any variants found were filtered for pathogenicity and low frequencies.

      Variant: NM_000257.3:c.1987C>T (p.Arg663Cys)

      ClinVar: 42874 https://www.ncbi.nlm.nih.gov/clinvar/variation/42874/

      gnomAD: Not in gnomAD

    1. Case Report

      Case: Male, born at 38 weeks gestation

      DiseaseAssertion: Hypertrophic Cardiomyopathy

      CasePresentingHPOs: HP:0030718, HP:0001667, HP:0002092, HP:0001670, HP:0200128 (enlarged right atrium, right ventricular hypertrophy, pulmonary hypertension, asymmetric septal hypertrophy, biventricular hypertrophy)

      CaseHPOFreeText: birth weight = 3.283kg, apgar scores = 8,9, asymmetric septal hypertrophy of atrioventricular septum without outflow tract obstruction or myocardial scarring, confirmed diagnosis of HCM at 6mo

      CaseNotHPOs: HP:0011611, HP:0001653, HP:0004308, HP:0005115 (aortic obstruction, mitral valve insufficiency, ventricular arrhythmia, supraventricular arrhythmia)

      FamilyInfo: Both parents and only sibling underwent genetic testing, the father and brother harbored the same variant as the patient (p.Ala1328Thr), this variant was absent in the mother. Father (36yo) and brother (5yo) had normal echocardiograms.

      CasePreviousTesting: fetal echocardiography at 32wks, postnatal echocardiography, routine cardiac follow-up at 6mo, cardiac MRI, 24hr Holter monitor, Full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (CAV3, MTTG, MTTI, MTTK, MTTQ, TNNC1, TTR, PKRAG2, LAMP2, GLA)

      CaseGenotypingMethod: blood and buccal cell samples collected from patient, coding regions and splice junctions of 18 genes were enriched with a proprietary targeted capture system by GeneDx, these then underwent NextGen sequencing, capillary sequencing used to confirm potentially pathogenic variants

      Variant: NM_000257.3(MYH7):c.3982G>A (p.Ala1328Thr)

      ClinVar: 42985, https://www.ncbi.nlm.nih.gov/clinvar/variation/42985/

      gnomAD: 0.00002154, https://gnomad.broadinstitute.org/variant/14-23887606-C-T

      InheritancePattern: autosomal dominant

    1. Pedigree 1

      Case: Pedigree 1 proband, male, 11yo at diagnosis, Iraqi‐Jewish

      CasePresentingHPOs: HP:0001639, HP:0004756, HP:0005110, HP:0002094, HP:0001712 (hypertrophic cardiomyopathy, ventricular tachycardia, atrial fibrillation, dyspnea, left ventricular hypertrophy)

      HPOsFreeText: clinical severity: moderate to asymptomatic, systolic murmur, NYHA Class II, maximal wall thickness at the anterior septum = 30 mm, resting LVOT gradient of 35 mmHg, increasing to 48 mmHg, normal LV systolic function, estimated ejection fraction (EF) of 65%, Grade II (moderate) LV diastolic dysfunction, ECH showed sinus rhythm, LV strain, inverted T waves, eptal wall thickness of 31 mm, extensive late gadolinium enhancement involving 45% of the left ventricle

      CaseNotHPOs: HP:0001279 (syncope)

      NotHPOsFreeText: skeletal involvement

      CasePreviousTesting: exact genes sequenced not specified

      CaseGenotypingMethod: Fifty‐six genes known to cause HCM were sequenced in parallel

      Variant: NM_000257.3(MYH7):c.427C>T (p.Arg143Trp)

      ClinVar: 164401, https://www.ncbi.nlm.nih.gov/clinvar/variation/164401/

      gnomAD: 0.00002784, https://gnomad.broadinstitute.org/variant/14-23901923-G-A

      FamilyInfo: mother was heterozygous for variant, she was asymptomatic, had mild nonobstructive hypertrophy, hypertension, and anterior septal thickness of 13 mm

    1. Table 5

      Case EO32: Italian

      DiseaseAssertion: HCM (early-onset)

      CasePreviousTesting: echocardiography, Full testing (MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1), additional testing: (GLA, LAMP2, PRKAG2, TNNC1, MYH6, CSPR3, PLN, TCAP, CAV3), electrocardiography

      CaseGenotypingMethod: Genomic DNA extracted from periphera whole blood, emulsion PCR, 17 HCM genes sequenced using Personal Genome Machine (PGM) IonTorrent sequencer, variants confirmed via Sanger sequencing

      Variant1: NM_000257.3(MYH7):c.1988G>A (p.Arg663His)

      ClinVar: 42875, https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/

      gnomAD: 0.00001414, https://gnomad.broadinstitute.org/variant/14-23896042-C-T

      MultipleGeneVariants:

      (1) MYPBC3 Variant:

      Variant: NM_000256.3(MYBPC3):c.3192dupC (p.Lys1065Glnfs)

      ClinVar: 42693, https://www.ncbi.nlm.nih.gov/clinvar/variation/42693/

      gnomAD: n/a

    1. CaseCM1856: Male, 15 years diagnosis, Japan, Asian

      CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001939 (Abnormality of metabolism/homeostasis)

      NotHPOsFreeText: Neuromuscular disease, Malformation syndromes

      CaseAddInfo: Positive family history of cardiomyopathy or sudden death, Proband found in Supplementary Table 2, Mother with an ECG abnormality and 2 brothers with HCM tested positive for this variant, Father with no phenotypes tested negative for this variant


      CasePreviousTesting: 8 patients with HCM and one with RCM were analyzed by NGS for the eight sarcomere-encoding genes and MYP.

      CaseGenotypingMethod: Probands were subject to PCR amplification and direct sequencing of 64 cardiomyopathy-associated genes, including the eight sarcomere-encoding genes. The variants were then filtered for rarity and tested for pathogenicity.


      Variant: NM_000257.3:c.2155C>T (p.Arg719Trp)

      ClinVar: 14104 https://www.ncbi.nlm.nih.gov/clinvar/variation/14104/

      gnomAD: European (Non-Finnish) 6.481e-5, Overall 3.185e-5 https://gnomad.broadinstitute.org/variant/14-23895180-G-A

    1. Supplementary Data: Table S3

      Case 64:

      DiseaseAssertion: left ventricular noncompaction

      CasePresentingHPOs: HP:0030682 (left ventricular noncompaction)

      CaseHPOFreeText: >7yo, able to hold breath, non compacted segment = distinct 2-layered appearance of trabeculated and compacted myocardium, NC/C ratio > 2.3:1

      CasePreviousTesting: Cardiac MRI using 17-segment model of LV segmentation, ECG, transthoracic echocardiography, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data tables S1 and S2.

      CaseGenotypingMethod: WES, variant enrichment analysis

      Variant: NM_000257.3(MYH7):c.3337-3dupC written in paper as g.23889445insG

      ClinVar: 42956, https://www.ncbi.nlm.nih.gov/clinvar/variation/42956/

      gnomAD: 0.02126, https://gnomad.broadinstitute.org/variant/14-23889445-T-TG

      MultipleGeneVariants:

      (1) - TTN Variant:

      Variant: g.179407388delC no ClinVar or CAID

    1. For GAA (Pompe disease) screening

      CaseP4-GAA: female, ethnicity = European, country origin = Italy

      CasePresentingHPOs:

      HPOsFreeText: enzyme activity = 2.22

      CaseNotHPOs: HP:0010899, HP:0010916, HP:0003236

      CaseAddInfo: homozygous

      CasePreviousTesting: initial and confirmatory DBS, biochemical tests

      CaseGenotypingMethod: mutation analyses

      Variant: NM_000152.4(GAA):c.533G>A (p.Arg178His)

      ClinVar: 554969; https://www.ncbi.nlm.nih.gov/clinvar/variation/554969/

      gnomAD: 2.646e-05, http://exac.broadinstitute.org/variant/17-78078918-G-A

    1. PD23

      Patient23: Male, Southern China

      CasePresentingHPOs:

      HPOsFreeText: IOPD

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo:

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_000152.4(GAA):c.1411_1414delGAGA (p.Glu471Profs)

      ClinVar: 188874, https://www.ncbi.nlm.nih.gov/clinvar/variation/188874/

      gnomAD: 1.688e-05, http://exac.broadinstitute.org/variant/17-78083827-CGAGA-C

      Variant2: NM_000152.4(GAA):c.2024_2026delACA (p.Asn675del)

      ClinVar: 189006, https://www.ncbi.nlm.nih.gov/clinvar/variation/189006/

      gnomAD: 2.105e-05, http://exac.broadinstitute.org/variant/17-78086806-CACA-C

    2. PD10

      Patient10: Male, Southern China

      CasePresentingHPOs:

      HPOsFreeText: IOPD

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo:

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_000152.4(GAA):c.2105G>A (p.Arg702His)

      ClinVar: 426278, https://www.ncbi.nlm.nih.gov/clinvar/variation/426278/

      gnomAD: 6.695e-05, http://exac.broadinstitute.org/variant/17-78087081-G-A

      Variant2: NM_000152.4(GAA):c.2297A>C (p.Tyr766Ser)

      ClinVar: 420102, https://www.ncbi.nlm.nih.gov/clinvar/variation/420102/

      gnomAD: 8.35e-06, http://exac.broadinstitute.org/variant/17-78090874-A-C

    3. PD11

      Patient11: Male, Southern China

      CasePresentingHPOs:

      HPOsFreeText: IOPD, survived beyond 2yo, left ventricular mass index and left ventricular posterior wall thickness decreased during ERT. Able to raise head, sit without support, stand, walk alone

      CaseNotHPOs: no significant respiratory problems during ERT

      NotHPOsFreeText:

      CaseAddInfo: homozygous, only patient to receive ERT treatment (rhGAA) every 2wks beginning at 5mo of age. ERT lasted for 90wks.

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)

      ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

      gnomAD: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A

    4. PD17

      Patient17: Female, Southern China

      CasePresentingHPOs:

      HPOsFreeText: IOPD

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo:

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)

      ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

      gnomAD: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A

      Variant2: NM_000152.4(GAA):c.2815_2816delGT (p.Val939Leufs)

      ClinVar: 371481, https://www.ncbi.nlm.nih.gov/clinvar/variation/371481/

      gnomAD: 1.653e-05, http://exac.broadinstitute.org/variant/17-78093082-CTG-C

    1. 5

      Patient5: male, Romanian

      CasePresentingHPOs: HP:0003677, HP:0003236, HP:0003325, HP:0003418, HP:0008997

      HPOsFreeText: CK > 10x increase, CK = 1500 U/L, reduced alpha-glucosidase activity

      CaseNotHPOs: HP:0002093

      CaseAddInfo: onset in middle age, enzyme activity also reduced in daughter

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_000152.4(GAA):c.2066_2070dupAGCCG (p.Ala691Serfs)

      ClinVar: 92471, https://www.ncbi.nlm.nih.gov/clinvar/variation/92471/

      gnomAD: n/a

      Variant2: NM_000152.4(GAA):c.-32-13T>G

      Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

    2. 18

      Patient18: female, White British

      CasePresentingHPOs: HP:0003677, HP:0003236, HP:0003325, HP:0003701, HP:0003458, HP:0003715, HP:0030231

      HPOsFreeText: CK > 10x increase, CK = 599 U/L. Vacuolated, degenerated, and atrophic fibers. Vacuole periphery showed abnormal immunoreactivity for desmin and p62. Z-band streaming of fibers, granular material accumulation. Treated with ERT. Normal to low alpha-glucosidase activity.

      CaseNotHPOs: HP:0002093

      NotHPOsFreeText: no evidence of glycogenosis

      CaseAddInfo: onset after 50yo

      CasePreviousTesting: same as group, muscle biopsy, NADH-tetrazolim reductase staining

      CaseGenotypingMethod: same as group

      Variant1: NM_000152.4(GAA):c.525delT (p.Glu176Argfs)

      ClinVar: 4033, https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

      gnomAD: 7.041e-05, http://exac.broadinstitute.org/variant/17-78078909-CT-C

      Variant2: NM_000152.4(GAA):c.-32-13T>G

      Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

    1. 21

      Patient21: 68yo

      CasePresentingHPOs: HP:0003325, HP:0002093, HP:0003141, HP:0001513, HP:0020038

      HPOsFreeText: GAA = 30%, BMI = 30.3, nucleo-capsular and subcortical white matter lacunes

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 30yr disease duration

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant: NM_000152.4(GAA):c.-32-13T>G

      Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

    2. 8

      Patient8: 47yo

      CasePresentingHPOs: HP:0003325, HP:0001513

      HPOsFreeText: GAA = 5%, BMI = 30.8, Normal CTA and CT

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 2yr disease duration, variants in cis

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant: NM_000152.4(GAA):c.-32-13T>G

      Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

      Variant2: NM_000152.4(GAA):c.1551+1G>C

      ClinVar: 554983, https://www.ncbi.nlm.nih.gov/clinvar/variation/554983/

      gnomAD: n/a

    3. 2

      Patient2: 76yo

      CasePresentingHPOs: HP:0003325, HP:0002093, HP:0002315, HP:0004887, HP:0000822, HP:0002870, HP:0020038

      HPOsFreeText: morning headaches, GAA = 13%, BMI = 23.6, right vertebral artery dominant, nucleo-capsular lacunes

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 33yr disease duration

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant: NM_000152.4(GAA):c.-32-13T>G

      Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

    4. 9

      Patient9: 54yo

      CasePresentingHPOs: HP:0003325, HP:0002093, HP:0002315, HP:0004887, HP:0003141, HP:0002870

      HPOsFreeText: morning headache, GAA = 7%, smoker, BMI = 23.3, normal CTA, nucleo-capsular and subcortical white matter lacunes

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 29yr disease duration, variants in cis

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant: NM_000152.4(GAA):c.-32-13T>G

      Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

      Variant2: NM_000152.4(GAA):c.1551+1G>C

      ClinVar: 554983, https://www.ncbi.nlm.nih.gov/clinvar/variation/554983/

      gnomAD: n/a

    1. c.2560C > T(p.Arg845*)

      Case14

      HPOsFreeText: See Group Phenotypes


      CasePreviousTesting: Sanger sequencing

      CaseMethod1: Sanger sequencing and PCR Amplification

      CaseMethod2: Whole Exome Sequencing (WES)

      CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.


      Variant: NM_000152.4:c.2560C>T (p.Arg854*)

      ClinVar: 4034 https://www.ncbi.nlm.nih.gov/clinvar/variation/4034/

      gnomAD: African 1.891e-3, Overall 2.090e-4 http://gnomad.broadinstitute.org/variant/17-78092070-C-T


      CaseAddInfo: Infantile Onset Pompe Disease, Patient is homozygous for this variant, 6 more patients have the same genotype

    2. c.2481+102_2646+31del (p.Gly828_Asn882del)

      Case72

      HPOsFreeText: See Group Phenotypes


      CasePreviousTesting: Sanger sequencing

      CaseMethod1: Sanger sequencing and PCR Amplification

      CaseMethod2: Whole Exome Sequencing (WES)

      CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.


      Variant1: NM_000152.4:c.2481+102_2646+31del (p.Gly828_Asn882del) (exon 18 del)

      ClinVar: 4031 https://www.ncbi.nlm.nih.gov/clinvar/variation/4031/

      gnomAD: Not in gnomAD


      Variant2: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      CaseAddInfo: Adult Late Onset Pompe Disease, 4 other patients have the same genotype

    3. c.877G > A(p.Gly293Arg)

      Case89

      HPOsFreeText: See Group Phenotypes


      CasePreviousTesting: Sanger sequencing

      CaseMethod1: Sanger sequencing and PCR Amplification

      CaseMethod2: Whole Exome Sequencing (WES)

      CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.


      Variant1: NM_000152.4:c.877G>A (p.Gly293Arg)

      ClinVar: 4036 https://www.ncbi.nlm.nih.gov/clinvar/variation/4036/

      gnomAD: Latino 5.704e-5, Overall 1.807e-5 http://gnomad.broadinstitute.org/variant/17-78081617-G-A


      Variant2: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      CaseAddInfo: Adult Late Onset Pompe Disease

    1. Supplement Table 1)

      Patient10: 6yo

      CasePresentingHPOs: HP:0001638

      HPOsFreeText: rhGAA dosage = 40 EOW, independent walker

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: homozygous variants, 34day old at ERT

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)

      ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

      gnomAD: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A

    2. Supplement Table 1)

      Patient14: 3yo

      CasePresentingHPOs: HP:0001638

      HPOsFreeText: rhGAA dosage = 20 QW, independent walker

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: homozygous variants, 14days old at ERT start

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)

      ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

      gnomAD: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A

    1. CaseLP2-4: Female, Taiwan, Birth diagnosis

      HPOsFreeText: GAA (MS/MS) enzyme activity at 0.10 umol/hr/L, Serum CK at 66 U/L

      GenotypingMethod: GAA Gene Sequencing and PCR Amplification


      Variant1: NM_000152.4:c.752C>T (p.Ser251Leu)

      ClinVar: 325781 https://www.ncbi.nlm.nih.gov/clinvar/variation/325781/

      gnomAD: East Asian 2.760e-3, Overall 3.540e-4 http://gnomad.broadinstitute.org/variant/17-78081415-C-T


      Variant2: NM_000152.4:c.761C>T (p.Ser254Leu)

      ClinVar: 325782 https://www.ncbi.nlm.nih.gov/clinvar/variation/325782/

      gnomAD: East Asian 2.759e-3, Overall 1.947e-4 http://gnomad.broadinstitute.org/variant/17-78081424-C-T


      CaseAddInfo: Late Onset Pompe Disease, Nomenclature indicates Variants 1 and 2 are in cis and patient is homozygous for this allele, 1 other patient has the same genotype

    2. CaseOPOPD-12: Female, Taiwan, Birth diagnosis

      HPOsFreeText: GAA (MS/MS) enzyme activity at 0.68 umol/hr/L

      GenotypingMethod: GAA Gene Sequencing and PCR Amplification


      Variant1: NM_000152.4:c.752C>T (p.Ser251Leu)

      ClinVar: 325781 https://www.ncbi.nlm.nih.gov/clinvar/variation/325781/

      gnomAD: East Asian 2.760e-3, Overall 3.540e-4 http://gnomad.broadinstitute.org/variant/17-78081415-C-T


      Variant2: NM_000152.4:c.761C>T (p.Ser254Leu)

      ClinVar: 325782 https://www.ncbi.nlm.nih.gov/clinvar/variation/325782/

      gnomAD: East Asian 2.759e-3, Overall 1.947e-4 http://gnomad.broadinstitute.org/variant/17-78081424-C-T


      Variant3: NM_000152.4:c.1726G>A (p.Gly576Ser)

      ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

      gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A


      CaseAddInfo: One Pompe Mutation allele and One Pseudodeficency Mutation allele, Nomenclature shows that Variants 1 and 2 are in cis, 25 other patients share the same genotype

    3. CaseIP2-10: Male, Taiwan, Birth diagnosis

      HPOsFreeText: GAA (MS/MS) enzyme activity at 0.09 umol/hr/L, Serum CK at 483 U/L

      GenotypingMethod: GAA Gene Sequencing and PCR Amplification


      Variant: NM_000152.4:c.1935C>A (p.Asp645Glu)

      ClinVar: 4029 https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

      gnomAD: East Asian 1.729e-3, Overall 1.240e-4 http://gnomad.broadinstitute.org/variant/17-78086721-C-A


      CaseAddInfo: Infantile Onset Pompe Disease, Patient is homozygous for this variant

    4. CaseOPTPD-77: Male, Taiwan, Birth diagnosis

      HPOsFreeText: GAA (MS/MS) enzyme activity at 0.61 umol/hr/L

      GenotypingMethod: GAA Gene Sequencing and PCR Amplification


      Variant1: NM_000152.4:c.1726G>A (p.Gly576Ser)

      ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

      gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A


      Variant2: NM_000152.4:c.2014C>T (p.Arg672Trp)

      ClinVar: 188773 https://www.ncbi.nlm.nih.gov/clinvar/variation/188773/

      gnomAD: South Asian 3.355e-5, Overall 8.290e-6 http://gnomad.broadinstitute.org/variant/17-78086800-C-T


      CaseAddInfo: One Pompe Mutation allele and Two Pseudodeficency Mutation alleles, Nomenclature indicates patient is homozygous for Variant 1 and Variant 2 is in cis with one copy

    1. 17

      Case17: Female, 30 years onset, 39 years diagnosis, Italy

      HPOsFreeText: See Group Phenotypes, ERT started at 41

      GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing


      Variant1: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      Paper does not specify what kind of mutation this is. Mentions only that it is a "Loss of transcript" mutation

      Variant2: NM_000152.4:c.2331+1

      ClinVar: N/A

      gnomAD: N/A


      CaseAddInfo: Late Onset Pompe Disease

    2. 12

      Case12: Female, 48 years onset, 58 years diagnosis, Italy

      HPOsFreeText: See Group Phenotypes, ERT started at 59, GAA Activity at ~17 pmol/min/mg before ERT and ~19 after

      GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing


      Variant1: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      Variant2: NM_000152.4:c.1561G>A (p.Glu521Lys)

      ClinVar: 4022 https://www.ncbi.nlm.nih.gov/clinvar/variation/4022/

      gnomAD: South Asian 3.266e-5, Overall 3.980e-6 http://gnomad.broadinstitute.org/variant/17-78084749-G-A


      CaseAddInfo: Late Onset Pompe Disease

    1. 3.1 Description of the study population

      Patient6: IOPD Group, 13days old

      CasePresentingHPOs:

      HPOsFreeText: LDH = 767 U/L, CK = 709 U/L, ALT = 30 U/L, AST = 117 U/L, Mann-Whitney Test = 3

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo:

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)

      ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

      gnomAD: 0.0001240, https://gnomad.broadinstitute.org/variant/17-78086721-C-A

    1. LOPD-13

      CaseLOPD-13: 2 weeks diagnosis

      HPOsFreeText: GAA activity 2.6 (nmol · h−1 · mg−1), Mean percentage of normal 3.7%

      GenotypingMethod: Newborn Screening Panels


      Variant1: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      Variant2: NM_000152.4:c.2051C>T (p.Pro684Leu)

      ClinVar: 285821 https://www.ncbi.nlm.nih.gov/clinvar/variation/285821/

      gnomAD: European (Non-Finnish) 1.631e-4, Overall 8.195e-5 http://gnomad.broadinstitute.org/variant/17-78087027-C-T


      CaseAddInfo: Late Onset Pompe Disease

    2. LOPD-2

      CaseLOPD-2: 2 weeks diagnosis

      HPOsFreeText: GAA activity 3.2 (nmol · h−1 · mg−1), Mean percentage of normal 4.5%

      GenotypingMethod: Newborn Screening Panels


      Variant: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      CaseAddInfo: Late Onset Pompe Disease, Patient is homozygous for the above variant

    3. LOPD-6

      CaseLOPD-6: 32 years diagnosis

      HPOsFreeText: GAA activity 3.6 (nmol · h−1 · mg−1), Mean percentage of normal 5.1%

      CaseNotHPOs: HP:0003236 (Increased serum CK)

      GenotypingMethod: Newborn Screening Panels


      Variant: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      CaseAddInfo: Late Onset Pompe Disease, Patient is homozygous for the above variant

    4. PD/Pathogenic-5

      CasePD/Pathogenic-5: 4 weeks diagnosis

      HPOsFreeText: GAA activity 6.5 (nmol · h−1 · mg−1), Mean percentage of normal 9.1%

      GenotypingMethod: Newborn Screening Panels


      Variant1: NM_000152.4:c.1726G>A (p.Gly576Ser)

      ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

      gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A


      Variant2: NM_000152.4:c.2065G>A (p.Glu689Lys)

      ClinVar: 4030 https://www.ncbi.nlm.nih.gov/clinvar/variation/4030/

      gnomAD: East Asian 0.2355, Overall 0.05524 http://gnomad.broadinstitute.org/variant/17-78087041-G-A


      Variant3: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      CaseAddInfo: Patient has one pseudodeficency allele and one pathogenic allele, Nomenclature claims Variant 1 and 2 are in cis

    5. LOPD-5

      CaseLOPD-5: 2 weeks diagnosis

      HPOsFreeText: GAA activity 3.1 (nmol · h−1 · mg−1), Mean percentage of normal 4.4%

      GenotypingMethod: Newborn Screening Panels


      Variant: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      CaseAddInfo: Late Onset Pompe Disease, Patient is homozygous for the above variant

    6. LOPD-1

      CaseLOPD-1: 3 weeks diagnosis

      HPOsFreeText: GAA activity 3.2 (nmol · h−1 · mg−1), Mean percentage of normal 4.5%

      GenotypingMethod: Newborn Screening Panels


      Variant: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      CaseAddInfo: Late Onset Pompe Disease, Patient is homozygous for the above variant

    7. IOPD-4

      CaseIOPD-4: 3 min diagnosis

      CasePresentingHPOs: HP:0003236, HP:0001638 (Increased serum CK, Cardiomyopathy)

      HPOsFreeText: GAA activity 0.6 (nmol · h−1 · mg−1), Mean percentage of normal 0.9%

      GenotypingMethod: Newborn Screening Panels


      Variant1: NM_000152.4:c.271G>A (p.Asp91Asn)

      ClinVar: 4020 https://www.ncbi.nlm.nih.gov/clinvar/variation/4020/

      gnomAD: European (Non-Finnish) 0.03291, Overall 0.02049 http://gnomad.broadinstitute.org/variant/17-78078656-G-A


      Variant2: NM_000152.4:c.307T>G (p.Cys103Gly)

      ClinVar: 92483 https://www.ncbi.nlm.nih.gov/clinvar/variation/92483/

      gnomAD: European (non-Finnish) 7.874e-6, Overall 3.578e-6 http://gnomad.broadinstitute.org/variant/17-78078692-T-G


      Variant3: NM_000152.4:c.1000G>T (p.Gly334Cys)

      ClinVar: 284864 https://www.ncbi.nlm.nih.gov/clinvar/variation/284864/

      gnomAD: Not in gnomAD


      CaseAddInfo: Infantile Onset Pompe Disease, Nomenclature claims Variant 1 and 2 are in cis

    1. 20 mg/kg (N = 16)

      Case7HPOsFreeText: 20 mg/kg GAA treatment, GAA activity at 14 pmol/punch/hr, GAA activity at 58.3% lower limit of normal

      CaseAddInfo: Late Onset Pompe Disease


      CaseGenotypingMethod: Method not described, only that the diagnosis was "confirmed … based on 2 GAA gene mutations"


      Variant1: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 https://gnomad.broadinstitute.org/variant/17-78078341-T-G


      Variant2: NM_000152.4:c.525delT (p.Glu176Argfs)

      ClinVar: 4033 https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

      gnomAD: European (Non-Finnish) 1.880e-4, Overall 9.959e-5 https://gnomad.broadinstitute.org/variant/17-78078909-CT-C


      CaseAddInfo:

    2. 20 mg/kg (N = 16)

      Case13HPOsFreeText: 20 mg/kg GAA treatment, GAA activity at 0.5 mU/U hexosaminid, GAA activity at 17.5% lower limit of normal

      CaseAddInfo: Late Onset Pompe Disease


      CaseGenotypingMethod: Method not described, only that the diagnosis was "confirmed … based on 2 GAA gene mutations"


      Variant1: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 https://gnomad.broadinstitute.org/variant/17-78078341-T-G


      Variant2: NM_000152.4:c.2482_2646del165 (p.Gly828_Asn882del) (Exon 18 del)

      ClinVar: 4031 https://www.ncbi.nlm.nih.gov/clinvar/variation/4031/

      gnomAD: Not in gnomAD


      CaseAddInfo: Patient is heterozygous for these variants

    1. P6a

      Patient6: Female, 53yo

      CasePresentingHPOs: HP:0000822, HP:0003077, HP:0001513,

      HPOsFreeText: LOPD, smoker

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 5yr follow-up MRI, 17yr disease duration, ERT lasted for 99mo

      CasePMIDs: PMID: 25614309

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_000152.4(GAA):c.-32-13T>G

      Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

      gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

      Variant2: NM_000152.4(GAA):c.1655T>C (p.Leu552Pro)

      ClinVar: 279811, https://www.ncbi.nlm.nih.gov/clinvar/variation/279811/

      gnomAD: n/a

    1. Case6: Male, 65 years report

      HPOsFreeText: 8 years of ERT completed, 6 Minute Walking Test at 95 meters, Forced Vital Capacity at 36%

      GenotypingMethod: GAA Gene Sequencing


      Variant1: NM_000152.4:c.-32-13T>G

      ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

      gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G


      Variant2: NM_000152.4:c.2481+102_2646+31del (p.Gly828_Asn882del) (exon 18 del)

      ClinVar: 4031 https://www.ncbi.nlm.nih.gov/clinvar/variation/4031/

      gnomAD: Not in gnomAD


      CaseAddInfo: Late Onset Pompe Disease

    1. C

      Case6 14yo diagnosis, Anglo-Celtic

      CasePresentingHPOs HP:0001256, HP:0000098

      (Mild intellectual disability, Tall stature)

      HPOsFreeText Diagnosis was based on tall height and mild intellectual disability. Plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

      CaseNotHPOs HP:0001083

      (Lens dislocation)

      NotHPOsFreeText no other seqeulae

      CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. IVS8+1G>A, compound heterozygous

      ClinVar 1. 120, 2. n/a

      CAID 2. need more info

      gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. n/a

      CaseAddInfo n/a

      CasePMIDs n/a

    2. 28

      FamilyLabel Family 28

      Family28PresentingHPOs n/a

      HPOsFreeText Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Affected individuals were not responsive to the treatment, plasma homocysteine levels went unchanged. Patients were given additional oral betaine(3g twice per day) with a low protein diet.

      FamilyNotHPOs n/a

      NotHPOsFreeText no further sequelae

      CountryOrigin n/a

      Ethnicity Lebanese

      Race n/a

      Family28PreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      FamilyMethod1 PCR

      FamilyMethod2 Sanger

      FamilyGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      ProbandLabel Case 34

      Variant NM_000071.2(CBS):c.19dupC (p.Gln7Profs), homozygous

      ClinVar 371345

      gnomAD MAF=0.00005473, no homozygotes

      FamilyAddInfo n/a

      FamilyPMIDs n/a

    3. 1622ins

      the Asn541 from allele registry and mutalyzer confused me.

      However, there cannot be an Asn542 as there is no Asn542 in the refseq. Asn542 is created when you insert TGAA, that is true, but the HGVS tracks the most immediate change on the refeq which is actually the Asn541.

      It was also weird that mutalyzer and allele registry didn't take insTGAA, but only used insA. I wrote out the refseq, the refseq with TGAA inserted and the refseq with just A inserted. Sure enough, Asn541 is the most immediate change and the frameshift is the same "...LRGRP...stop" whether you insert TGAA or just A. Not too surprising since you are still in-frame after adding 3 bases, but cool to check.

      interesting!

    1. OS-127 II-1

      CaseOS-127_II-1: Male, Birth onset, Germany

      CasePresentingHPOs: HP:0001992, HP:0410145 (Organic aciduria, Decreased biotinidase activity)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001263 (Global developmental delay)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous and healthy; Proband is confirmed homozygous via parental testing

      CasePreviousTesting: GS-MS analysis identified urinary organic acids dominated by N-aceylated AAs, supported by NMR spectroscopy of urine samples with serum samples being negative; Values of excreted AAs are in Table 1; Biotinidase deficiency treated via 5 mg biotin/d

      CaseGenotypingMethod: Genomic DNA was extracted from blood samples or after EBV transformation of peripheral blood lymphocytes. Exons and exon-intron boundaries were amplified and bidirectionally sequenced.

      Variant: NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys)

      ClinVar: 18110 https://www.ncbi.nlm.nih.gov/clinvar/variation/18110/

      gnomAD: 0.004135 (4 homozygotes), https://gnomad.broadinstitute.org/variant/3-52022837-C-T

    1. K1

      CaseK1 Female, 12yr report, Bosnian

      CasePresentingHPOs HP:0001557, HP:0025116, HP:0001941, HP:0002098, HP:0003270, HP:0002013, HP:0001290, HP:0000750, HP:0011344, HP:0002069, HP:0002305, HP:0001290, HP:0002059, HP:0004881

      (Abnormal intrauterine movements, Fetal distress, Acidosis, Respiratory distress, Abdominal distension, Vomiting, Hypotonia, Speech delay, Severe GDD, Grand mal seizures, Athetosis, Hypotonia, Cerebral atrophy, Episodic hypoventilation)

      HPOsFreeText born at 42wk gestation. (neonatal, pre-treatment:) apgar score at 1min:7, 5min:8, 10min:8, acidosis, respiratory distress, abdominal distension, vomiting, onset of fits at 2d, resistant to ACD's. (18mo:) introduced to pyridoxine therapy, trial dose/route of 60mg oral, complete cessation of seizures, no apnoea or hypotonia/sleepiness, initial maintenance dose of 800mg. (infancy/childhood:) recurrence of seizures with febrile illness, hypotonia, speech delay/difficulties, severe IQ delay. 1wk after withdrawal from pyridoxine trial at 7y, grand mal seizures recurred(definite PDE).

      CaseNotHPOs HP:0000486

      (Squint)

      NotHPOsFreeText (infancy/childhood:) squint

      CasePreviousTesting Administration of pyridoxine relieved patient's seizures. plasma pipecolic acid: 12(nv<2.5μM), plasma AASA: 1.5(nv<0.2μM), urine AASA: 7.5(nv<1 mmol/mol creatinine). Blood lactate: 5.4mM and CSF lactate: 4.4mM (nv <2.5mM). (PMID:17068770:)post treatment testing: Pipecolic acid in plasma 6.7(nv 0.7-2.6mmol/liter), AASA in plasma 0.9(nv<0.2mmol/liter), urine AASA 19(nv<1mmol/molcreatinine).

      Variant NM_001182.4(ALDH7A1):c.328C>T (p.Arg110Ter), homozygous

      ClinVar 17995

      gnomAD MAF=0.0001385(Other), no homozygotes

      CaseAddInfo parental consanguinity

      CasePMIDs 10894227 (Patient 3...), 17068770 (Patient 8)

    2. family S

      FamilyLabel Family S

      FamilySPresentingHPOs HP:0002098, HP:0010818, HP:0002280

      (Respiratory distress, Generalized tonic seizures, Mega cisterna magna)

      HPOsFreeText (neonatal, pre-treatment:) respiratory distress, generalised tonic seizures. (infancy/childhood:) mega cisterna magna

      FamilyNotHPOs n/a

      CountryOrigin n/a

      Ethnicity Arabic

      Race n/a

      FamilySPreviousTesting Cessation of seizures during pyridoxine therapy

      ProbandLabel S1, Female, 15yr report

      Variant NM_001182.4(ALDH7A1):c.312+2T>A, homozygous

      ClinVar 17997

      gnomAD not in gnomAD

      FamilyAddInfo parental consanguinity

      FamilyPMIDs n/a

  2. www.nature.com www.nature.com
    1. Patient KM03

      Case#: KM03, F, neonatal (onset), Japanese

      CasePresentingHPOs: HP:0001254, HP:0002179, HP:0001276, HP:0001263 (Lethargy, Opisthotonus, Hypertonia, Global developmental delay)

      HPOsFreeText: Diagnosed at the time of newborn screening. Originally presented as classical form, but later determined to be the intermittent form.

      CaseNotHPOs:

      CasePreviousTesting: Lymphoblastoid cells from the patient showed reduced decarboxylation activity: 0.12 nmol/h per mg of protein (~9% of control). The authors previously showed by immunoblot analysis that the level of E2 protein was significantly reduced (PMID 3417306).

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Total RNA and genomic DNA prepared from lymphoblastoid cells or peripheral leukocytes. RT-PCR was performed with primers in exons 8 and 9 identified an insertion. Gnomic DNA was isolated and sequenced. Confirmed by restriction enzyme digestion.

      Variant: NM_001918.3:c.1018-550A>G (homozygous)

      ClinVar: 11946

      gnomAD: Not in gnomAD

      VariantEvidence: The predicted mRNA encoded a truncated protein with 282 amino acids, including 4 novel amino acids at the carboxyl terminus. 265bp fragment that included the 126 bp intronic region was subcloned into an exon trapping vector and transfected into COS-1 cells to confirm the splicing defect.

      CaseAddInfo: Consanguineous, parents were heterozygous.

      CasePMIDs: 3417306

    1. Case Report

      CaseAD: Male, 5 yrs onset

      CasePresentingHPOs: HP:0000750, HP:0002572, HP:0012537, HP:0001944, HP:0001649, HP:0002789, HP:0001252, HP:0001942, HP:0001987, HP:0002919, HP:0012120 (Delayed speech and language development, Episodic vomiting, Food intolerance, Dehydration, Tachycardia, Tachypnea, Muscular hypotonia, Metabolic acidosis, Hyperammonemia, Ketonuria, Methylmalonic aciduria)

      HPOsFreeText: Frequent catabolism episodes with vomiting were noticed without decompensation

      CaseNotHPOs: HP:0001270, HP:0001919, HP:0011015 (Motor delay, Acute kidney injury, Abnormal blood glucose concentration)

      NotHPOsFreeText: Propionyl-CoA carboxylase activity was within normal ranges in fibroblasts

      CaseAddInfo: Parents are non-consanguineous with no family history, Dietary restriction and supplementation showed amelioration of symptoms

      CasePreviousTesting: Normal ECG and MRI results; Metabolic acidosis (pH = 7.08, bicarbonates = 7.3 mmol/L, normal lactic acid, PCO2 = 25 mmHg) and hyperammmoniemia (100 µmol/L) present; Large increase in plasmatic propionylcarnitine (17.5 µmol/L; N < 0.75), undetectable methylmalonylcarnitine, and high urinary excretion of 3-hydroxypropionate and methylcitrate

      CaseGenotypingMethod: Next-generation sequencing in the proband revealed a homozygous nonsense founder variant in the MCEE gene.

      Variant: NM_032601.4(MCEE):c.139C>T (p.Arg47Ter)

      ClinVar: 2343, http://www.ncbi.nlm.nih.gov/clinvar/variation/2343

      gnomAD: 0.0004884, https://gnomad.broadinstitute.org/variant/2-71351575-G-A

    1. 1

      Case# Pat1, M, Chinese, 3day onset

      CasePresentingHPOs HP:0008344, HP:0008872, HP:0001250, HP:0001276, HP:0001279, HP:0001263

      CaseNotHPOs HP:0002013

      CaseMethod1 PCR

      CaseMethod2 Direct

      CaseGenotypingMethod exons and flanking intronic regions of the BCKDHA, BCKDHB and DBT genes were amplified using PCR and sequenced

      Variant NM_000709.3:c.853+1delG ?

    1. Results

      NonPatientCell: E-Coli (DH5α)

      GeneFunction: GO:0006559

      GeneAlteration: PAH cDNA was cloned into a pMAL-c2E expression vector encoding an N-terminal MBP tag and an enterokinase cleavage site. PAH mutants were constructed using site-directed mutagenesis and confirmed using DNA sequencing. Both the wild-type and the 10 mutant vectors were transformed into E. coli DH5α via overexpresion of fusion proteins at midexponential phase. The proteins were purified and concentration was determined.

      FunctionalEvidence: Expression of the 10 mutant proteins compared to the wild-type demonstrated that several of these mutants induce protein destabilization and subsequent loss of function. Upon deconvolution analysis, five variants showed significanly distrubed oligomerization and a preponderance to misfold and form high-molecular-weight protein aggregates. Enzyme kinetic parameter analysis demonstrated moderate reduction in PAH activity and severely affected allostery in all but one mutation, indicating the strong possibility of global confirmational changes. Protein confirmation was tested by limited proteolysis with proteinase K with six out of eight tested mutants decreasing the half-life of the protein by >50% and decreased stability in five out of eight. Thermal protein denaturation was analyzed by fluorescence and demonstrated that all of the mutations led to substantial distortion of the protein's confirmation and/or loss of structural integrity compared to the wild-type, especially those in the regulatory domain. Finally, amino acid replacements were shown to disrupt local networks of amino acid interactions and alter the normal oligomeric state and therfore the function of the protein.

      FAVariant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)

      ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/

      FAVariant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

      ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

      FAVariant3: NM_000277.3(PAH):c.165T>G (p.Phe55Leu)

      ClinVar: 92734 https://www.ncbi.nlm.nih.gov/clinvar/variation/92734/

      FAVariant4: NM_000277.3(PAH):c.1249T>C (p.Tyr417His)

      ClinVar: 102579 https://www.ncbi.nlm.nih.gov/clinvar/variation/102579/

      FAVariant5: NM_000277.3(PAH):c.940C>T (p.Pro314Ser)

      ClinVar: 102905 https://www.ncbi.nlm.nih.gov/clinvar/variation/102905/

    1. 43

      Case40 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 84(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 312(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R161Q variant destroys an AciI restriction site. Thus, while the patient's DNA fragments would not be cleaved, control fragments would be cleaved. The 848del variant creates a MspI site. This would lead to cleaved patient fragments and uncleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.482G>A (p.Arg161Gln), 2. NM_000159.3(GCDH):c.848delT (p.Leu283Argfs), compound heterozygous

      ClinVar 1. 188789, 2. 370672

      gnomAD 1. MAF=0.0001384(Other), no homozygotes, 2. MAF= 0.0003331(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    2. 6, 7

      Case6 unknown sex, Spain

      CasePresentingHPOs HP:0000707

      (Neurological abnormality)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes defined as "slight," entailing minimal neurological signs and an otherwise normal life. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 500(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 461(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

      ClinVar 2083

      gnomAD MAF= 0.0004013(African), no homozygotes

      CaseAddInfo Sibling (Case 7) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 3200mmol/mol creatinine and 3-OH-glutarate was 843mmol/mol creatinine.

      CasePMIDs n/a

    3. 4, 5

      Case4 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 4135(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 752(nv 2–14 mm/mol creatinine).In patient fibroblasts, %GCD activity was <0.5.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

      ClinVar 2083

      gnomAD MAF= 0.0004013(African), no homozygotes

      CaseAddInfo Sibling(Case 5) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 2166mmol/mol creatinine and 3-OH-glutarate was 420mmol/mol creatinine.

      CasePMIDs see note on previous studies

    4. 20

      Case20 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 3571(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 232(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R132Q variant destroys an AciI site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.395G>A (p.Arg132Gln), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

      ClinVar 1. 377917, 2. 370106

      gnomAD 1. not in gnomAD, 2. MAF= 0.00005646(Latino), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    1. 5

      Case5 Female, 24yo report, USA, Lumbee

      CasePresentingHPOs HP:0001344, HP:0002540, HP:0003150

      (Nonverbal, Non-ambulatory, Glutaricaciduria)

      HPOsFreeText Urine glutaric acid was highly elevated and 3-hydroxyglutaric acid was elevated. Patient presented with acute metabolic decompensation at 2yo and feeds by mouth. Patient was diet restricted in lysine and tryptophan with per individual adjustments to maintain normal plasma amino acid levels. Treatment also included supplemental carnitine and riboflavin.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting n/a

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR and sanger sequencing was performed on exon 10 of the GCDH gene.

      Variant NM_000159.3(GCDH):c.1240G>A (p.Glu414Lys), homozygous

      ClinVar 167133

      gnomAD MAF=0.0002017(African), no homozygotes

      CaseAddInfo nonconsanguineous

      CasePMIDs n/a

    1. Case#: Patient 5, Japanese, 8 years old (report) CaseHPOs: Hyperornithinemia

      CaseHPOsFreeText: (From Hayasaka et al. 1981; PMID 7260021, Patient 2). First noted visual problems at age 5 years, glasses prescribed for myopia. Evaluation for night blindness at age 8. Best corrected visual acuity was RE 04 with correction of myopia (-8 D), LE 04 with correction of myopia (-10 D). Typical chorioretinal atrophy with scallop margins at the peripheral fundus and an abnormal reflex in the macular area. Concentric constriction of visual fields. Dark adaptation curve was monophasic. ERG was subnormal, and the electro-oculogram was flat. The ciliary processes were normal by cycloscopy. Not responsive to Vitamin B6.

      CaseNotHPOsFreeText: Normal lens

      CasePreviousTesting: Serum ornithine 12.95 mg/dl (normal 0-36-1-56). OAT activity was not detectable in cell extracts from skin fibroblasts. CaseAddInfo: No consanguinity reported CaseMethod1: PCR

      CaseMethod2: Sequence analysis

      CaseGenotypingMethod: DGGE and sequence analysis of genomic DNA was carried out to identify the variant on the other allele. Variant: NM_000274.3(OAT):c.1276C>T (p.Arg426Ter)

      ClinVar: 177

      gnomAD: Maximum population minor allele frequency = 0.00002893 (Latino); no homozygotes in any population.

    1. ee

      CaseKLC2: Male, 32 yrs death, Japan, Asian

      CasePresentingHPOs: HP:0001249, HP:0002078, HP:0000651, HP:0008353, HP:0000992 (Intellectual disability, Truncal ataxia, Diplopia, Neutral hyperaminoaciduria, Cutaneous photosensitivity)

      HPOsFreeText: Monoamino-monocarboxylic aciduria

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are first-cousin consanguineous, Max LOD score is 2.1 for family

      CasePreviousTesting: Defects in the intestinal absorption of monoamino-monocarboxylic acids determined by oral loading; Urine analyses confirmed the absence of hyperaminoaciduria in the mother (III-4), father (III-5) and the younger brother (IV-3), Brother of proband

      CaseGenotypingMethod: DNA was isolated from peripheral blood samples and from liver samples collected at autopsy. A genome-wide screen with 343 different markers was carried out and linkage analysis performed using homozygosity mapping. Both SLC6A18 and SLC6A19 were investigated for possible pathogenicity, with SLC6A19's pattern of expression supporting it as a primary candidate. Intronic primers were used to bidirectionally sequence each exon and flanking intronic regions, locating a homozygous frameshift mutation that perfectly segregated with the phenotype.

      CasePMIDs: 2582682, 11394870

      Variant: NM_001003841.3(SLC6A19):c.882_883TG1

      ClinVar: 2018 https://ww.ncbi.nlm.nih.gov/clinvar/variation/2018/

      gnomAD: 0.000008900, https://gnomad.broadinstitute.org/variant/5-1214174-CTG-C?dataset=gnomad_r2_1

    1. Patient 4

      Case4 sex unknown, Netherlands, Dutch

      CasePresentingHPOs HP:0001250, HP:0002194

      (Seizures, Delayed motor skills)

      HPOsFreeText Seizures ceased upon administration of pyridoxine. (PMID:16159904:) 1st seizure at 8do, first administered pyridoxine(and age at trial) 2mo, initial dose:100mg, maintenance dose:100mg/day, mildly affected motor skills. (PMID:17088338:) Definite="recurrent (two or more) seizures of any type that cease within seven days of the administration of oral pyridoxine (usual dose, 30 mg/ kg/day; minimum dose, 15 mg/kg/day; maximum dose, 1000 mg/kg/day) or within 30 minutes of intravenous pyridoxine (usual dose, 100 mg; minimum dose, 50 mg), that recur when pyridoxine supplementation is withdrawn, and that cease again when pyridoxine is given as above"

      CaseNotHPOs n/a

      NotHPOsFreeText intrauterine seizures

      CasePreviousTesting PDS confirmed metabolically: α‐AASA urine 4.0(nv <1mmol/mol cr), α‐AASA plasma 1.1(nv <0.2μmol/l), pipecolic acid urine 0.02(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 7.0(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk)

      Variant NM_001182.4(ALDH7A1):c.834G>A (p.Val278=)

      ClinVar 18002

      gnomAD not in gnomAD(C and not G at that position?)

      CaseAddInfo Metabolic testing of sibling(Patient 6, heterozygous for the p.Val278= variant): α‐AASA urine 0.2(nv <1mmol/mol cr), α‐AASA plasma <0.2(nv <0.2μmol/l), pipecolic acid urine 0.02(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 2.2(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk), but was not metabolically confirmed for PDS, development was also normal

      CasePMIDs 17088338 , 16159904

    1. The variant p.Y403N is located in the turn region adjacent to the alpha helix where hydrogen bond formations are more favourable (Fig. 4). The absence of this variant in 200 normal chromosomes, the clinically severe phenotypes in the two patients, the abnormal biochemical and organic acid profiles (Table 1), and the computational prediction (Figs 3 and 4 and Table 3) suggest a potential genotype–phenotype correlation for this variant.

      Variant 1: NM_002225.3:c.1207T>A

      Variant 2: NM_002225.4(IVD):c.863C>T

      VariantEvidence: This variant is located in the turn region next to the alpha helix where hydrogen bonding is favorable, this location along with the presentation of severe phenotypes and biochemical profiles in the patients harboring these variants suggests a genotype-phenotype correlation (fig. 4)

    1. Table 2

      Case11a: Male, Sweden

      CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0002804 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Arthrogryposis)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001627 (Cardiac abnormality)

      NotHPOsFreeText: N/A

      CaseAddInfo: Severe congenital myopathy, Deceased in 5 months

      CasePreviousTesting: N/A

      CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

      Variant: NM_198271.4:c.1069G>T (p.Glu357Ter)

      ClinVar: 162219 https://www.ncbi.nlm.nih.gov/clinvar/variation/162219/

      gnomAD: Not in gnomAD

    1. P17

      FamilyPY: White, United Kingdom

      FamilyPresentingHPOs: HP:0002131, HP:0001260, HP:0008003, HP:0030453 (Episodic ataxia, Dysarthria, Jerky ocular pursuit movements, Abnormal visual electrophysiology)

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0000640, HP:0000648, HP:0003390, HP:0011402, HP:0001272, HP:0002283 (Gaze-evoked nystagmus, Optic atrophy, Sensory axonal neuropathy, Demyelinating sensory neuropathy, Cerebellar atrophy, Global brain atrophy)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Blood genomic DNA was enriched and whole exome sequenced. Alightment to hg19 and variant filtering was performed with putative pathogenic variants being confirmed via Sanger sequencing.

      FamilyPreviousTesting: Underwent brain MRI and CSF examination with oligoclonal band analysis; Negative genetic testing for SCA1, 2, 3, 6, 7, 17 (now known as ATXN1, ATXN2, CACNA1A, ATXN7, and TBP, respectively), DRPLA (now known as ATN1), FA (now known as FXN) and FMR1

      FamilyAddInfo: N/A

      Variant: NM_004172.5(SLC1A3):c.1496G>A (p.Arg499Gln)

      ClinVar: 242994, https://www.ncbi.nlm.nih.gov/clinvar/variation/242994/

      gnomAD: 0.0001471, https://gnomad.broadinstitute.org/variant/5-36686238-G-A

      Affected: 3

      Segregations: 2

      AddSegregationInfo: Pedigree in Sup Data, Not enough info provided

    1. Subject C

      CaseGuC: Male, 5 days onset

      CasePresentingHPOs: HP:0200134, HP:0011153, HP:0010850, HP:0011199, HP:0001252, HP:0003487, HP:0003423, HP:0010864, HP:0011344, HP:0002188, HP:0002059 (Epileptic encephalopathy, Focal motor seizure, EEG with spike-wave complexes, EEG with generalized sharp slow waves, Muscular hypotonia, Babinski sign, Thoracolumbar kyphoscoliosis, Severe intellectual disability, Severe global developmental delay, Delayed CNS myelination, Cerebral atrophy)

      HPOsFreeText: Multiple seizure types, Bilateral T2 prolongation in caudate heads and putamina

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variant is confirmed heterozygous de novo

      CasePreviousTesting: Investigations include electroencephalography (EEG), head MRI, neurometabolic testing, and chromosome microarray; Individuals with self-limiting benign electroclinical syndromes, such as childhood absence epilepsy (onset > 4 years), were excluded; Head circumference was 44 cm at 4 months (91st percentile); Partial response to ketogenic diet and phenytoin, no response to other antiseizure medications;

      CaseGenotypingMethod: Variants within co-expressed candidate genes in Table S1 were extracted from exome sequencing data. Variants were annotated and were verified with Sanger sequencing of the proband and parents.

      Variant: NM_004171.4(SLC1A2):c.866C>G (p.Pro289Arg)

      ClinVar: 438737, https://www.ncbi.nlm.nih.gov/clinvar/variation/438737/

      gnomAD: Not in gnomAD

    1. III4/F

      Case# FIII.4, F, 19 day old diagnosis, Cyprus (Greek Cypriot)

      CasePresentingHPOs HP:0010910, HP:0010911, HP:0010913, HP:0001254, HP:0011968, HP:0001290, HP:0001276, HP:0002789, HP:0002353,

      HPOcont: Hypervalinemia, Hyperleucinemia, Hyperisoleucinemia, Lethargy, Poor feeding, Hypotonia, Hypertonia, Tachypnea, Abnormal EEG

      HPOfreetext: Reduced alloisoleucine and grunting

      CasePreviousTesting Tested blood BCAA (AIleu: 0, Ileu: 220 (NR: 26–100), Leu: 3270 (NR: 65–220), Val: 459 (NR: 90–300), urine organic acids (Increased:lactate, 2-keto-glutarate, 2-keto-isocaproic, 2-OH-isovaleric, 2-keto-isovaleric, 2-keto-3-methylvaleric, 4-OH-phenylacetate, 4-OH-phenylpyruvate and BCKD activity (0.03(NR: 0.4–3.4) (Fibroblasts))

      CaseMethod1 PCR

      CaseMethod2 Direct Sequencing

      CaseGenotypingMethod Direct sequencing repeated on proband and father for deletion varaint

      Variant (1) NM_000709.3(BCKDHA):c.632C>T (p.Thr211Met) (2) NM_000709.3:c.718delG

      ClinVar (1) 93365

      CAID (2) register link if I put that in correctly

      gnomAD (1) 0.0001163(East Asian), 0.00002043 (Overall)

      CaseAddInfo nonconsanguineous

    1. Individual 1

      Case1: Female

      CasePresentingHPOs: HP:0011343, HP:0012072, HP:0007018 (Moderate global developmental delay, Aciduria, Attention deficit hyperactivity disorder)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous, Unremarkable family history, Variants are parentally confirmed with c.2185 G>A apparently de novo

      CasePreviousTesting: At 2 yrs had elevated 2-oxoadipate (range = 10–120 mmol/mol creatinine) and 2-hydroxyadipate (range = 5–40 mmol/mol creatinine) in urine (Reference 0 mmol/mol creatinine); Elevated 2-aminoadipate (120 μmol/l); Moderate protein restriction did not influence disease course and was discontinued, Serial cranial magnetic-resonance-imaging studies showed no morphological abnormalities; Neuropsychological testing at 8 years revealed an IQ of 117; Symptoms improved after implementation of methylphenidate and at 14 is clinically normal; No mutation detected in ODC

      CaseGenotypingMethod: Whole exome sequencing was performed to identify mutations responsible for the biochemical abnormality. Exonic sequences were enriched and sequenced with data analysis being used to filter according to inheritance and low allele frequencies in controls. This narrowed down to eight different genes (ADAMTS10, AIRE, C8orf38, DHTKD1, OVOS2, CAMTA2, LPPR3, and RADIL) of which three had been associated with unrelated phenotypes and only one other had predicted pathogenic variants, DHTKD1.

      Variant1: NM_018706.7(DHTKD1):c.1A>G (p.Met1Val)

      ClinVar: 39563 https://www.ncbi.nlm.nih.gov/clinvar/variation/39563/

      gnomAD: Not in gnomAD

      Variant2: NM_018706.5(DHTKD1):c.2185G>A (p.Gly729Arg)

      ClinVar: 39564 https://www.ncbi.nlm.nih.gov/clinvar/variation/39564/

      gnomAD: 0.002748, https://gnomad.broadinstitute.org/variant/10-12154929-G-A