Case#: Case 2

DiseaseAssertion: APDS

FamilyInfo: no familial history of PID

CaseHPOFreeText: belongs to a family in which two siblings were reported as suffering from a CSR-D (data from the affected sister P7 “see Tables E1 and E2”). From the age of 5 months, he suffered recurrent upper (recurrent acute otitis media) and lower respiratory tract infections complicated by bronchiectasis, chronic non-infectious diarrhea with malabsorption syndrom and failure to thrive. Other infections were also noticed, including pericarditis caused by Echo virus infection and recurrent synovitis. The diagnosis of CSR-D was made, according to his familial history and IgG substitution was started. At 6 and 8 years of age, he displayed episodes of massive enlargement of lymph nodes (cervical and mesenteric) with no malignant feature at biopsy. Serum Ig levels revealed an increase of IgM (4.5g/L at 5 years and 13g/L at 11 years) and a decrease of IgG (<1.9g/L) and IgA (0.41 g/L). At 11 years of age, he had a new episode of cervical lymph nodes enlargement which led to the diagnosis of Hodgkin disease, histological type nodular sclerosis, stage III with localization to cervical, mediastinum, retroperitoneum and spleen (EBV status was unknown and could not be studied retrospectively) (Figure 1 g-i). Patient received chemotherapy and radiotherapy with irradiation of regions above and below diaphragma, which induced complete remission. He is now well on IgG substitution and prophylactic antibiotherapy with a follow-up of more than 10 years.

CasePreviousTesting: None. Genotyping only done at position c.3061 of PIK3CD

GenotypingMethod: We genotyped the PIK3CD gene at position c.3061G as described previously (1) in a cohort of 139 patients with immunological phenotype of Ig CSR-D. We found 8 new APDS patients with the E1021K heterozygous mutation in the PIK3CD gene

Variant: E1021K

CAID: CA145460

gnomAD: absent in gnomAD v2.1.1

SupplementalData: Clinical features of patients 3-8 in supplementary

Case#: 15-year-old boy

DiseaseAssertion: SHORT syndrome and Immunodeficiency 36

FamilyInfo: Table2 Father is wild type, mother was unavailable for testing. Consanguinity was reported at Table 4. No affected family members Table4.

CasePresentingHPOs: HP:0001511(Intrauterine growth retardation) HP:0004322(Short stature) HP:0000325(Triangular face) HP:0010751(Dimple chin) HP:0000684(Delayed eruption of teeth) HP:0000347(micrognathia) HP:0100750(Atelectasis) HP:0004469(chronic bronchitis) HP:0002110(bronchiectasis) HP:0002720(Decreased circulating IgA level) HP:0011342(Mild global developmental delay) HP:0004279(short hands) HP:0000954(Single transverse palmar crease) HP:0002205(Recurrent respiratory infections)

CaseHPOFreeText:

CaseNotHPOs: Height -5.5 to -6.1 SDS

CaseNotHPOFreeText: N/A

CasePreviousTesting: CMA and MS-MLPA for chromosomes 6,14,20 was performed.

GenotypingMethod: Whole-exome sequencing was performed on the patient’s whole blood sample.

PreviouslyPublished: No

Variant: NM_001242466.2:c.68G > A p.Arg23Gln

ClinVar: 1361868

CAID: CA3290343

gnomAD: 0.00005439 https://gnomad.broadinstitute.org/variant/5-67589169-G-A

Case#: 20-year-old Spanish man

DiseaseAssertion: Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation

FamilyInfo: Maternally inherited CTLA4 variant and paternally inherited CLEC7A variant. Patient's mother had been diagnosed with mild sarcoidosis, dysphagia with eosinophilic infiltrates of esophagus, low IgM, and decreased percentages of memory B cells.

CasePresentingHPOs: HP:0100651 (Type I diabetes mellitus) HP:0001045 (Vitiligo) HP:0001047 (Atopic dermatitis) HP:0002205 (Recurrent respiratory infections) HP:0001541 (Ascites) HP:0002014 (Diarrhea) HP:0410151 (Eosinophilic infiltration of the esophagus) HP:0410147 (Eosinophilic infiltration in the stomach mucosa) HP:0033351 (Candida esophagitis) HP:0100806 (Sepsis) HP:0032061 (Hypereosinophilia) HP:0032064 (Gastrointestinal eosinophilia)

CaseHPOFreeText: Type 1 diabetes was diagnosed at 15 months old. Patient has a history of severe enteritis. Investigations, which were undertaken due to hypereosinophilia and eosinophilic infiltration, revealed a clonal γδ T cell band, characterized as reactive, with subsequent exclusion of FIP1L1-FDGFRA and PDGFRB rearrangements, as well as any abnormal karyotype. Sepsis was due to Salmonella typhi and Clostridium difficile infection.

Article provides functional evidence of CLEC7A variant affecting phenotype of this patient. Their data suggest that partial loss of DECTIN-1 in a patient with CTLA-4h may enhance IDAIL penetrance and confer additional unique phenotypes, with persistent marked hypereosinophilia as the most remarkable uncommon clinical manifestation.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Whole-genome sequencing was performed on the patient's whole blood sample. The variants were confirmed with Sanger sequencing. Presence of a somatic CTLA4 variant was ruled out with high-coverage WGS of sorted peripheral T cells.

GenotypingMethod: Whole-genome sequencing was performed on the patient's whole blood sample. The variants were confirmed with Sanger sequencing. Presence of a somatic CTLA4 variant was ruled out with high-coverage WGS of sorted peripheral T cells.

PreviouslyPublished: No

Variant: NM_005214.5:c.208C>T p.Arg70Trp

ClinVar: 161114

CAID: CA173999

gnomAD: 0.000001313 https://gnomad.broadinstitute.org/variant/2-203870684-C-T?dataset=gnomad_r4

Variant: NM_197947.3:c.547C>T p.Leu183Phe

ClinVar: 717363

CAID: CA6443934

gnomAD: 0.01719 https://gnomad.broadinstitute.org/variant/12-10123309-G-A?dataset=gnomad_r4

SupplementalData: Detailed clinical info and and immunological test results can be found in Supplementary Materials.f

CTLA4 Alteration and Neurologic Manifestations: A New Family with Large Phenotypic Variability and Literature Review

Case#: III:3, female, 45 years old, Italian

DiseaseAssertion: Celiac disease/IBD with immunodeficiency (CVID) and CNS demyelination

FamilyInfo: non-consanguineous Italian parents, history of autoimmune disorders (Hashimoto thyroiditis, psoriasiform dermatitis, celiac disease and rheumatoid arthritis), see Figure 1 CasePresentingHPOs: HP:0002028, HP:0002721, HPO:0001888, HPO:0008897, HP000:6515, HP:0002110, HP:0011108, HP:0001878, HP:0001973, HP:0031688, HP:0007185, HP:0002140, HP:0001081, HP:0011097, HP:0001945, HP:0007305, HP:0000238, HP:0200063, HP:0004313, HP:0000939, HP:0030252

CasePreviousTesting: whole-exome sequencing on the proband and parental DNA samples (trio-WES) from peripheral blood

GenotypingMethod: Reads aligned against GRCh38/hg38, variant calling using in-house pipeline according to international guidelines, variants with a frequency of <5% in gnomAD v4.1.0 and an in-house database, virtual panel of 564 genes related to primary immunodeficiency and inflammatory bowel disease (PanelApp version 7.21), CNVs detected with Control-FREEC and EXCAVATOR tools

**Variant: ** NM_005214.5:c.436G>A; p.Gly146Arg

ClinVar: VCV000849622.11

gnomAD: 0.000001696 https://gnomad.broadinstitute.org/variant/2-203870912-G-A?dataset=gnomad_r4

Case#: 10-month‐old Japanese female

DiseaseAssertion: Patients are asserted to have “SHORT syndrome” and “harbor either a common or a previously unknown mutation in PIK3R1 as well as provide an in silico functional analysis of the mutant proteins.”

FamilyInfo: Her father has SHORT syndrome, with the same variant of PIK3R1, NM_181523.3:c.1957A>T, further described in Case 4. Her paternal grandmother "also manifests some facial characteristics of SHORT syndrome as well as a hearing impairment."

CasePresentingHPOs: HP:0001511, HP:0011220, HP:0000325, HP:0000430, HP:0004322, HP:0000490, HP:0000684, HP:0000331, HP:0000963, HP:0007392

CaseHPOFreeText: Born at 37 weeks of gestation with a birth length of 40.0 cm (−2.9 SD relative to the average for this gestational age) and birth weight of 1,676 g (−3.1 SD relative to the average for this gestational age) (Table 1). Her height and weight were 60.3 cm (−4.0 SD relative to the average for her age) and 4.01 kg (−7.6 SD relative to the average for her age), respectively, at the time of evaluation for the present study. Her fasting plasma glucose, serum IRI concentrations, and serum C‐peptide were 83 mg/dL, 2.6 μIU/mL, and 1.34 ng/mL, respectively, with an HbA1c level of 4.6%. Her HOMA‐IR was 0.53, and her HOMA‐β was 46.8%.

CaseNotHPOs: HP:0000819, HP:0000855, HP:0001382, HP:0000023, HP:0000558, HP:0000400, HP:0000369, HP:0000233, HP:0002714, HP:0005328, HP:0000540, HP:0000483, HP:0000545, HP:0000593, HP:0000501, HP:0100578, HP:0001249, HP:0000750, HP:0000365

CaseNotHPOFreeText: Readily visible veins

CasePreviousTesting: NR

GenotypingMethod: Initially, comprehensive sequencing analysis was conducted on all 22 exons of the INSR gene using the Sanger sequencing method, confirming the absence of pathogenic variants. Subsequently, sequencing was extended to encompass all 16 exons of the PIK3R1 gene.

PreviouslyPublished: No

Variant: NM_181523.3:c.1957A>T

ClinVar: 3767319

gnomAD: NR

SupplementalData: Table 1, Figure 1c,d

Case#: 33-year‐old Japanese male

DiseaseAssertion: Patients are asserted to have “SHORT syndrome” and “harbor either a common or a previously unknown mutation in PIK3R1 as well as provide an in silico functional analysis of the mutant proteins.”

FamilyInfo: His daughter has SHORT syndrome, with the same variant of PIK3R1, NM_181523.3:c.1957A>T, further described in Case 3. His mother also manifests some facial characteristics of SHORT syndrome as well as a hearing impairment.

CasePresentingHPOs: HP:0008619, HP:0000365, HP:0000501, HP:0000819, HP:0001511, HP:0004322, HP:0000023, HP:0000490, HP:0000558, HP:0000325, HP:0011220, HP:0000430, HP:0000331, HP:0000400, HP:0005328, HP:0100578

CaseHPOFreeText: He was born at 36 weeks of gestation with a birth weight of 1,970 g. Weight at time of diagnosis was 44.2 kg (-2.4 SD), height 154 cm (-3.00SD) , body mass index 18.6 kg/m2 (-1.5 SD). He had been treated with a DPP‐IV (dipeptidyl peptidase‐IV) inhibitor and an SGLT2 inhibitor and manifesting an HbA1c level of 7.4% at the time of the current evaluation. His blood glucose and serum IRI levels at baseline and at 30, 60, 90, and 120 min after the glucose load were 130, 220, 238, 243, and 252 mg/dL and 8.0, 15.5, 25.6, 27.1, and 24.6 μIU/mL, respectively. His HOMA‐IR, HOMA‐β, and insulinogenic index were 2.57, 43.0%, and 0.083, respectively.

CaseNotHPOs: HP:0000855, HP:0001382, HP:0000684, HP:0000369, HP:0000233, HP:0002714, HP:0000540, HP:0000483, HP:0000545, HP:0000593, HP:0000963, HP:0007392, HP:0001249, HP:0000750

CaseNotHPOFreeText: Readily visible veins

CasePreviousTesting: NR

GenotypingMethod: Initially, comprehensive sequencing analysis was conducted on all 22 exons of the INSR gene using the Sanger sequencing method, confirming the absence of pathogenic variants. Subsequently, sequencing was extended to encompass all 16 exons of the PIK3R1 gene.

PreviouslyPublished: No

Variant: NM_181523.3:c.1957A>T

ClinVar: 3767319

gnomAD: NR

SupplementalData: Table 1, Figure 1e,f

Case#: 33-year-old Chinese adult female

DiseaseAssertion: Patient is asserted to have “SHORT syndrome due to a PIK3R1 gene variant (c.1945C > T).”

FamilyInfo: Both parents were healthy and non-consanguineous. Her father was 167 cm tall and her mother was 160 cm tall. The patient had a younger brother, aged 29, who was 175 cm tall and weighed 60 kg.

CasePresentingHPOs: HP:0000684, HP:0000750, HP:0040270, HP:0000855, HP:0004322, HP:0001382, HP:0000858, HP:0000558, HP:0011220, HP:0000430, HP:0000331, HP:0000233, HP:0000369, HP:0005328, HP:0007392, HP:0000963, HP:0100578, HP:0001952, HP:0000819, HP:0000147, HP:0000325

CaseHPOFreeText: Patient has a spontaneous full-term vaginal delivery without birth trauma or asphyxia. At birth, the patient weighed 2000 g (< 3rd percentile), though her length was unknown. Her first primary tooth emerged at 9 months and her ability to say “mom” and “dad” developed at 10 months. Throughout childhood, the patient consistently lagged in growth and development compared with their peers. At 5 years of age, her height was only 99.7 cm (−3 SD) and her weight 11.5 kg(< 3rd percentile). By age 9, her height was 116.5 cm (−3 SD) and her weight was 15.0 kg(< 3rd percentile). Her test results revealed a fasting blood glucose (FBG) level of 5.48 mmol/L and 2-hour postprandial blood glucose level of 8.04 mmol/L. Notably, her postprandial 2-hour insulin level exceeded the upper detection limit (> 2152.5 pmol/L), while her postprandial 2-hour C-peptide level was 0.4 nmol/L. Her glycosylated hemoglobin (HbA1c) was 5.78%. Consequently, she was prescribed long-term voglibose monotherapy. The patient exhibited distinctive facial features. The patient also exhibited visible veins and had polycystic ovarian syndrome. Height: 147.50 cm, Weight: 37.50 kg, BMI: 17.24 kg/m2, Lean mass: 23.90 kg, Fat mass: 9.30 kg, VFA: 35.3 cm2, Total cholesterol: 4.20 mmol/L, HDL-c: 1.09 mmol/L, LDL-c: 2.92 mmol/L, Triglyceride: 1.47 mmol/L, Calcium: 2.19 mmol/L, Phosphorous: 1.25 mmol/L, 25-hydroxyvitamin D3: 14.5 ng/ml, TSH: 1.97 mIU/L, Free T4: 11.47 pmol/L, Total testosterone: 1.47 nmol/L

CaseNotHPOs: HP:0001249, HP:0000956, HP:0002240, HP:0001397,<br /> HP:0000501, HP:0000488, HP:0009830

CaseNotHPOFreeText: Elevated plasma triglycerides, ocular hypotension, diabetic kidney disease, lower extremity arterial disease. The patient exhibited no lipid dysregulation, with fat mass and visceral fat area falling below the normal range, accompanied by a reduction in lean body mass.

CasePreviousTesting: NR

GenotypingMethod: Whole-exome sequencing

PreviouslyPublished: No

Variant: NM_181523.3:c.1945C>T

ClinVar: 60763

gnomAD: NR

SupplementalData: Table 1, 2, 3, 4

Case#: III.7, an 18-year-old female patient

DiseaseAssertion: immune thrombopenia, autoimmune hemolytic anemia, and Evans syndrome with infections early-onset herpes zoster and chronic Epstein-Barr virus

FamilyInfo: Table 1

CasePresentingHPOs: HP:0001433, HP:0002716

CaseHPOFreeText: severe necrotic dermohypodermitis of left leg caused by Pseudomonas aeruginosa, hypogammaglobulinemia

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: II.1, 61-years-old male (deceased)

DiseaseAssertion: Hashimoto disease

Variant: c.379T >G variant in CTLA4

CasePresentingHPOs: HP:0034954

CaseHPOFreeText: Anti-AChR antibodies without myasthenia gravis, unilateral uveitis, Staphylococcus aureus pneumoniae, Candida kefyr pneumoniae, Erythroderma, autoimmune alopecia, diffuse interstitial lung disease

Case#: II.4, 56-year-old male relative, age of onset 44

DiseaseAssertion: Spondylarthritis

Variant: c.379T >G variant in CTLA4

Case#: III.3, a diseased 31-year-old male relative, age of onset 7

DiseaseAssertion: Evans syndrome (ITP and AIHA)

CaseHPOFreeText: Lymphadenopathy, colic and renal nonclonal proliferation, Extensive chicken pox, viral encephalitis, EBV chronic viremia including inside tissues, Ear, nose and throat infections, pneumoniae, multiple Clostridium difficile colitis infections, Interstitial pneumopathy, Epilepsy, transverse myelitis C2 and T12, ADEM, Transplantation for interstitial fibrosis, late rejection with nonmalignant lymphoproliferation and EBV replication, Portal hypertension with diffuse nodular hyperplasia

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: III.4, a 34-year-old female relative, unknown age of onset

DiseaseAssertion: Hashimoto disease

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: IV.2, a 15 year old male realtive, unknown age of onset

CaseHPOFreeText: Ear, nose and throat infections; Dermatitis

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case# III.6, 27-year-old male relative, unknown age of onset

CaseHPOFreeText: Infectious mononucleosis, severe CMV infectious (nonautoimmune thrombocytopenia, splenomegaly, lymphadenopathy and hepatitis), Toxoplasma gondii infection, Dermatitis

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: II.3, a 59 year old female, age of onset 58

DiseaseAssertion: Inflammatory polyarthritis

FamilyInfo: Table 1

CaseHPOFreeText: presented with lymphoid proliferation, central nervous system inflammation (transverse myelitis and extensive disseminated encephalomyelitis), epilepsy, chronic kidney disease with one transplantation (benign polyclonal B-cell infiltration, interstitial fibrosis), interstitial pneumopathy, splenomegaly, hepatic abnormality with diffuse nodular hyperplasia, rectocolitis, extensive varicella zoster virus infection (VZV), viral encephalitis without documentation, Epstein–Barr virus (EBV) chronic viremia, Clostridium difficile severe colitis

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: 20-year-old male, Race: White (ancestry unavailable) DiseaseAssertion: The patient is asserted to have "CTLA4 haploinsufficiency" manifesting as aplastic anemia. FamilyInfo: Patient's father has disease variant Case PresentingHPOs: HP:0012378 (Fatigue), HP:0001962 (Palpitations), HP:0002875 (Exertional dyspnea), HP:0001903 (Anemia), HP:0001873 (Thrombocytopenia), HP:0002608 (Celiac disease), HP:0000608 (Macular degeneration), HP:0001876 (pancytopenia), HP:0001915 (aplastic anemia), CaseHPOFreeText: ** Diagnosis at age 20 when patient presented with persistent and profound incapacitating fatigue. Bone marrow biopsy was consistent to aplastic anemia. Table 1 summarizes presenting labs and flow cytometry results. Patient was first treated with high-dose IVIG, cyclosporine, and systemic corticosteroids. He initially responded well, but 6 months into therapy he developed renal impairment and was transitioned to sirolimus. His aplastic anemia relapsed. Patient underwent haploidentical (sibling, variant negative) hematopoietic stem cell transplantation, which was curative. CaseNotHPOs: HP:4000129 (Recent blood transfusion), CaseNotHPOFreeText: N/A CasePreviousTesting: The following studies were negative: Bone marrow chromosome analysis; FISH hybridization for BCR/ABL1, monosomy 5, monosomy 7, trisomy 8, and 20q deletion; myelodysplastic syndrome mutation sequencing. GenotypingMethod: A primary immunodeficiency NGS panel was run (gene content not specified) and identified a paternally inherited heterozygous missense variant in CTLA4. Variant: The patient is heterozygous for the NM_005214.5(CTLA4):c.385T>A (p.Cys129Ser). ClinVar: 1414930 CAID: N/A gnomAD**: This variant was not found in gnomAD v.4.1.0

Case#: 15-year-old Chinese boy

DiseaseAssertion: Patient was diagnosed with systemic lupus erythematosus (SLE) at a young age and was recently found to carry heterozygous mutations in PIK3CD. Diagnoses: Activated PI3Kδ syndrome

FamilyInfo: Family history revealed that his mother died of gastric cancer. Whole exome sequencing was performed in patient and in his father, when he was at the age of 15 and the PIK3CD gene was found to exhibit good coverage.

CasePresentingHPOs: HP:0002725, HP:0005425, HP:0032218, HP:0002716, HP:0000093, HP:0020072, HP:0000790, HP:0001882, HP:0001903, HP:0003493, HP:0025289, HP:0001744, HP:0004322, HP:0550004, HP:0001873, HP:0003565, HP:0011227, HP:0020026, HP:0032230, HP:0002110, HP:6001383, HP:0033726, HP:0033493, HP:0012574

CaseHPOFreeText: Serum level of complements was low, such as C3, C4, and CH50. Serum level of IgM and IgE was elevated, but IgG and IgA was normal. Lung CT scan showed partial consolidation of left upper lung with bronchiectasis and left upper bronchial stenosis. Renal biopsy was also done because of persistent hematuria and proteinuria, and it displayed moderately increased mesangial matrix and mesangial hypercellularity under the light microscope; subepithelial deposits was noted, and some mesangial changes may be present as seen in electron microscopy. Immunofluorescence was positive for C1q, C3, IgG, IgM, and Fb (Fig. 2). The patient was given oral prednisolone and hydroxychloroquine combined with mycophenolate mofetil. Six months later, the level of complement was restored to normal, hematuria and proteinuria disappeared, and liver function returned to normal. He was currently receiving intravenous immunoglobulin in association with hydroxychloroquine, low-dose prednisolone, and mycophenolate mofetil, with a good efficacy.

CasePreviousTesting: NR

GenotypingMethod: Whole exome sequencing, Sanger sequencing

PreviouslyPublished: No

Variant: NM_005026.5:c.3061G>A

ClinVar: 88675

gnomAD: chr1-9726972-G-A

SupplementalData: Figure 1, 2, 3

Case#: Patient 1 (P1) is a 24-year-old Chinese female.

DiseaseAssertion: Patients are asserted to have "CTLA4 haploinsufficiency (CTLA-4 h).

FamilyInfo: The patient's father carries the same CTLA4 variant as the patient but has been asymptomatic. No other family history reported.

CasePresentingHPOs: HP:0031245 (Productive cough), HP:0002105 (Hemoptysis), HP:0001878 (Hemolytic anemia), HP:0006532 (Recurrent pneumonia), HP:0004313 (Decreased circulating immunoglobulin concentration, HP:0033608 (Pulmonary nodule), HP:0002716 (Lymphadenopathy), HP:0001596 (Alpecia),

CaseHPOFreeText: Patient first presented at age 14 with respiratory symptoms. She was hospitalized at age 16 with hemolytic anemia and recurrent pulmonary infections. Lab work showed hypogammaglobinemia. Chest CT showed scattered solid and ground-glass density nodules bilaterally in the lungs, Lung biopsy demonstrated lymphocytic infiltration and siderophages. Treatment with corticosteroids achieved temporary remission, but the patient relapsed with dose tapering. She developed Evans syndrome, alopecia, and skin lesions. Disease stabilized with weekly subcutaneous abatacept (125mg) and the interval was subsequently extended to once every 4 weeks.

CaseNotHPOs: HP:0003493 (Antinuclear antibody positivity), HP:0032230 (Cytoplasmic antineutrophil antibody positivity).

GenotypingMethod: Genotyping was performed by whole exome sequencing.

PreviouslyPublished: No prior article is known to contain information on the same proband.

Variant: The patient is heterozygous for the NM_005214.4(CTLA4):c.155G>T(p.Gly52Val) variant.

ClinVar: 1420586

gnomAD: The variant was not found in gnomAD v4.1.1.

SupplementalData: No supplemental data provided.

Case#: Patient 2 (P2) is a 23-year-old Chinese male.

DiseaseAssertion: Patients are asserted to have "CTLA4 haploinsufficiency (CTLA-4 h).

FamilyInfo: The patient's father and oldest sister are both positive for the same CTLA4 variant. Both the parents and two older sisters are asymptomatic. The TNFRSF13B variants were not found in the parents or sisters.

CasePresentingHPOs: HP:0002254 (Intermittent diarrhea), HP:4000055 (Intestinal inflammation), HP:0002582 (Atrophic gastritis), HP:0004313 (Decreased circulating immunoglobulin concentration), HP:0030167 (Antimitochondrial antibody positivity)

CaseHPOFreeText: Patient presented at 12 years old with intermittent diarrhea, predominantly mushy stools with ocassional watery stools. Colonoscopy at age 21 demonstrated histopathological evidence of acute and chronic inflammation. Gastroscopy showed chronic atrophic gastritis and duodenitis. Treatment with intravenous immunoglobulin and biweekly subcutaneous abatacept (125 mg) led to clinical improvement.

CaseNotHPOs: HP:0003493 (Antinuclear antibody positivity), HP:0032230 (Antineutrophil antibody positivity)

CasePreviousTesting: None reported.

GenotypingMethod: Genotyping was performed via whole exome sequencing.

PreviouslyPublished: No prior article is known to contain information on the same proband.

Variant1: The patient is heterozygous for the NM_005214.4 CTLA4):c.538C>T (p.Leu180Phe) variant.

CAID1: CA350139042

gnomAD1: This variant has a minor allele frequency of 0.0001370 in gnomAD v4.1.1. (https://gnomad.broadinstitute.org/variant/chr2-203871458-C-T?dataset=gnomad_r4).

Variant2: The patient is heterozygous for the NM_012452.3(TNFRSF13B):c.83G>A variant.

ClinVar2: 1063279

gnomAD2: This variant has a minor allele frequency of 0.00009130 in gnomAD v4.1.1. (https://gnomad.broadinstitute.org/variant/chr17-16952562-C-T?dataset=gnomad_r4)

Variant3: The patient is heterozygous for the NM_012452.3(TNFRSF13B):c.716C>T

ClinVar3: 471370

gnomAD3: This variant has a minor allele frequency of 0.0002962 in gnomAD v4.1.1. (https://gnomad.broadinstitute.org/variant/chr17-16939713-G-A?dataset=gnomad_r4)

SupplementalData: There is no supplemental data.

Case#: Patient 3 (P3) is a 20-year-old Chinese female.

DiseaseAssertion: Patients are asserted to have "CTLA4 haploinsufficiency (CTLA-4 h).

FamilyInfo: The patient's brother died at age 15 from pancytopenia. The patient's mother was diagnosed with large granular lymphocytic leukemia. Patient's mother (Patient 4) also harbors the same CTLA4 variant as the patient. Authors do not indicate if patient's brother had genetic testing.

CasePresentingHPOs: HP:0001744 (Splenomegaly), HP:0001369 (Arthritis), HP:0020062 (Decreased hemoglobin concentration), HP:0011873 (Abnormal platelet count), HP:0002254 (Intermittent diarrhea), HP:0001876 (Pancytopenia), HP:0020026 (Positive Coombs test)

CaseHPOFreeText: Patients symptoms onset at 9 years old with chronic eczema, Evans syndrome, and splenomegaly. Initially responded well to corticosteroids and IV Ig, but relapsed after steroid tapering. She developed polyarthritis at age 16, diagnosed as juvenile idiopathic arthritis. She also developed photosensitive rashes. She was hospitalized due to pancytopenia and heavy vaginal bleeding. Anti-kertain antibody (AKA) and antiperinuclear factor were negative. Treatment with subcutaneous abatacept injections (125mg) resolved joint pain and brought hemoglobin and platelet counts to normal range.

CaseNotHPOs: HP:0003493 (Antinuclear antibody positivity), HP:0034092 (Anti-cyclic citrullinated peptide antibody positivity), HP:0002923 (Rheumatoid factor positive),

CasePreviousTesting: None reported.

GenotypingMethod: Genotyping was performed via whole exome sequencing.

PreviouslyPublished: No prior article is known to contain information on the same proband.

Variant: The patient is heterozygous for the NM_005214.4 CTLA4):c.347T>A (p.Ile116Asn) variant.

ClinVar: 2430678

gnomAD: The variant was not found in gnomAD v4.1.1.

SupplementalData: There is no supplemental data.

Case#: Patient 4 (P4) is a 60-year-old Chinese woman.

DiseaseAssertion: Patients are asserted to have "CTLA4 haploinsufficiency (CTLA-4 h).

FamilyInfo: Patient's daughter is Patient 3 and harbors the same CTLA4 variant.

CasePresentingHPOs: HP:0001954 (Recurrent fever) HP:0011110 (Recurent tonsillitis), HP:0000155 (Oral ulcer), HP:0005558 (Chronic leukemia)

CaseHPOFreeText: Patient's symptoms onset in childhood with recurrent fever and tonsillitis. She experienced recurrent oral ulcers starting around age 50. She was diagnosed with large granular lymphocytic (LGL) leukemia for which she was treated with long-term corticosteroids for three years. She is currently treated with oral cyclosporine.

CaseNotHPOs: HP:0000988 (Skin rash)

CaseNotHPOFreeText: Patient denied history of rash, dry mouth, or dry eyes.

CasePreviousTesting: None reported.

GenotypingMethod: Genotyping was performed via whole exome sequencing.

PreviouslyPublished No prior article is known to contain information on the same proband.

Variant: The patient is heterozygous for the NM_005214.4 CTLA4):c.347T>A (p.Ile116Asn) variant.

ClinVar: 2430678

gnomAD: The variant was not found in gnomAD v4.1.1

SupplementalData: There is no supplemental data.

Case#: Patient 5 (P5) is a 19-year-old Chinese female.

DiseaseAssertion: Patients are asserted to have "CTLA4 haploinsufficiency (CTLA-4 h).

FamilyInfo: The patients mother, who harbors the same CTLA4 variant reported a history of chronic urticaria, alopecia areata, and intermittent diarrhea for over 10 years.

CasePresentingHPOs: HP:0001903 (Anemia), HP:0007418 (Alopecia totalis), HP:0002254 (Intermittent diarrhea), HP:0000964 (Eczematoid dermatitis), HP:0002716 (Lymphadenopathy), HP:0004818 (Paroxysmal nocturnal hemoglobinuria), HP:6000344 (Anti-intrinsic factor antibody positivity), HP:0000988 (Skin rash), HP:0004386 (Gastrointestinal inflammation), HP:0034839 (Lymphoid hyperplasia), HP:0040088 (Abnormal lymphocyte count), HP:0020062 Decreased hemoglobin concentration, HP:0025066 (Decreased mean corpuscular volume), HP:0025547 (Decreased mean corpuscular hemoglobin concentration)

CaseHPOFreeText: Patient's symptoms onset at age 10. Gastrointestinal endoscopy showed chronic inflammation and lymphoid hyperplasia. Patient has been treated with subcutaneous injections of abatacept (125mg) with notable clinical improvement. Fine white hair has started to regrow on her scalp, eyebrows, and eyelashes, and facial skin shows mild scaling.

CaseNotHPOs:

CaseNotHPOFreeText: Autoimmune screening including antinuclear antibodies were negative.

CasePreviousTesting: None reported.

GenotypingMethod: Genotyping was performed via whole exome sequencing.

PreviouslyPublished No prior article is known to contain information on the same proband.

Variant: The patient is heterozygous for the NM_005214.4 CTLA4):c.151C>T (p.Arg51Ter) variant.

ClinVar: 161109

gnomAD: The variant was not found in gnomAD v4.1.1.

SupplementalData: There is no supplemental data.

Case#: Patient 6 (P6) is an 18-year-old Chinese male.

DiseaseAssertion: Patients are asserted to have "CTLA4 haploinsufficiency (CTLA-4 h).

FamilyInfo: Patient denied family history of inborn error of immunodeficiency. The patient's father harbors the same CTLA4 variant as the patient. No symptoms are reported in the patient's father.

CasePresentingHPOs: HP:0001954 (Recurrent fever), HP:0012735 (Cough), HP:0002829 (Arthralgia), HP:0002113 (Pulmonary infiltrates), HP:0002716 (Lymphadenopathy), HP:0006532 (Recurrent pneumonia), HP:0004313 (Decreased circulating immunoglobulin concentration

CaseHPOFreeText: MRI of knees showed patchy abnormal signals in the right femoral and lateral condylar regions suggestive of bone marrow edema, with surrounding soft tissue edema. Mild joint effusion and suprapatellar bursa fluid were also noted. Treatment with avatacept was started and at the six-month follow-up the patient reported clinical improvement. He had no fever or sputum production and symptoms of lymphadenopathy and joint pain had improved.

CaseNotHPOs: HP:0001386 (Joint swelling), HP:0000988 (Skin rash), HP:0002014 (Diarrhea), HP:0003493 (Antinuclear antibody positivity), HP:0034092 (Anti-cyclic citrullinated peptide antibody positivity), HP:0002923 (Rheumatoid factor positive), HP:0032230 (Cytoplasmic antineutrophil antibody positivity)

CaseNotHPOFreeText:

CasePreviousTesting: None noted.

GenotypingMethod: Genotyping was performed via whole exome sequencing.

PreviouslyPublished No prior article is known to contain information on the same proband.

Variant: The patient is heterozygous for the NM_005214.4 CTLA4):c.436G>A(p.Gly146Arg) variant.

ClinVar: 849622

gnomAD: This variant has an allele frequency of 0.000001696 in gnomAD v4.1.1. (https://gnomad.broadinstitute.org/variant/chr2-203870912-G-A?dataset=gnomad_r4)

SupplementalData: There is no supplemental data.

Case#: Patient 16 (P16) is a female child, ethnicity not specified.

DiseaseAssertion: The patient is asserted to have CTLA-4 haploinsufficiency with autoimmune infiltration (CHAI)

FamilyInfo: Sanger sequencing of other family members revealed the same CTLA4 variant in seven females across four generations, all of whom are symptomatic with autoimmunity and/or recurrent infections. See Figure 1A for pedigree.

CasePresentingHPOs: HP:0004880 (Respiratory infections in early life), HP:0003256 (Abnormality of te coagulation cascade), HP:0001954 (recurrent fever), HP:0000967 (Petechiae), HP:0002014 (Diarrea), HP:0003270 (Abdominal distention), HP:0025085 (Bloody diarrhea), HP:0001943 (Hypoglycemia), HP:0034315 (Chronic cough), HP:0000010 (Recurrent urinary tract infections), HP:0000076 (Vesicoureteral reflux)

CaseHPOFreeText: In infancy the patient was hospitalized multiple times for respiratory viral infections and an episode of transient coagulopathy. She continued to experience respiratory infections, prolonged bleeding with transient coagulopathy, and intermittent bloody diarrhea. Patient had intermittent elevated lactate. Flow cytometry demonstrated normal lymphocyte subsets and immunoglobulin concentrations were within normal limits. Soluble IL-2 receptor levels were elevated. Gastrostomy tube was placed at 26 months due to recurrent hypoglycemia and poor growth.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Whole exome sequencing performed at 18 months old reported no diagnostic variants. Mitochondrial genome analysis was normal.

GenotypingMethod: Genotyping was performed via whole exome sequencing, which initially did not identify any diagnostic variants. Research analysis of the clinical exome data identified the CTLA4 variant.

PreviouslyPublished No prior article is known to contain information on the same proband.

Variant: The patient is heterozygous for the NM_005214.5: c.654T>A (p.Tyr218*) variant.

ClinVar: 2440604

gnomAD: This variant has an allele frequency of 0.0006536 in gnomAD v4.1.1 (https://gnomad.broadinstitute.org/variant/chr3-38011318-G-A?dataset=gnomad_r4)

SupplementalData: N/A

affected individuals across two generations

Case#: 34 year-old Chinese male.

DiseaseAssertion: HAE-C1INH Type 1.

FamilyInfo: Family history of edema (mother passed away due to laryngeal edema, older sister experienced buttock swelling after prolonged sitting, maternal uncle experienced episodic abdominal pain and unilateral upper-limb swelling). Family testing for serum C4 and C1INH concentration and C1INH functional activity indicate that proband’s maternal uncle and asymptomatic daughter exhibit low values for all three of these biochemical markers, consistent with Type 1 HAE. The proband’s daughter and maternal uncle also tested positive for the variant identified in the proband. Pedigree included in figures.

ParentalTesting: Mother passed away before study. Father tested for C4 and C1INH concentration and C1INH function with all values falling in normal ranges.

CasePresentingHPOs: Edema (HP:0000969), Edema of the dorsum of hands (HP:0007514), Edema of the upper limbs (HP:0010742), Non-pitting edema (HP:6000507), Abdominal pain (HP:0002027)

CasePhenotypeFreeText: Onset at approximate age of 26. Episodes of localized edema of limbs, skin, and buttocks lasting two to three days regardless of treatment. Episodes became more frequent at age 34 and were accompanied by abdominal pain triggered by fatigue. Non-pitting edema of right hand observed on physical examination.. The proband’s C4 level was 0.02 g/L (reference range: 0.1–0.4 g/L), C1INH concentration was 0.07 g/L (reference range: 0.21–0.39 g/L), and C1INH functional activity was 4.3% (reference range: ≥68.0%).

CaseNotHPOs: N/A

CaseNotPhenotypeFreeText: N/A

CasePreviousTesting: N/A

GenotypingMethod: PCR amplification with Sanger sequencing.

Variant: NM_000062:c.1067T>A p.(Val356Glu)

LegacyVariant: N/A

ClinVar: N/A

CAID: CA380702482

gnomAD: N/A

MultipleGeneVariants: N/A

PreviouslyPublished: N/A

AdditionalInfo: N/A

GeneName: DICER1 PMID: 29762508 HGNCID: N/A Inheritance Pattern: Autosomal dominant Disease Entity: Cancer Mutation: Germline Zygosity: Heterozygosity Variant: Unregistered Family Information: 12% of children with pleuropulmonary blastomas have cystic nephromas Case: 11 year old patient with Hodgkin lymphoma with DICER1 mutation in 2016.

• Gene Name: DICER1 Syndrome (OMIM 606241, 601200)
• PMID: 34599283
• Hugo Gene Nomenclature Committee (HGNCID): N/A
• Inheritance Pattern: Autosomal Dominant
• Disease Entity: pleuropulmonary blastoma (PPB), Sertoli-Leydig cell tumor, gynandroblastoma, embryonal rhabdomyosarcomas of the cervix and other sites, multinodular goiter, differentiated and poorly differentiated thyroid carcinoma, cervical-thyroid teratoma, cystic nephroma-anaplastic sarcoma of kidney, nasal chondromesenchymal hamartoma, intestinal juvenile-like hamartomatous polyp, ciliary body medulloepithelioma, pituitary blastoma, pineoblastoma, primary central nervous system sarcoma, embryonal tumor with multilayered rosettes-like cerebellar tumor, PPB-like peritoneal sarcoma, DICER1-associated presacral malignant teratoid neoplasm and other non-neoplastic associations.
• Mutation: Germline
• Zygosity: Heterozygous
• Variant: has multiple variants associated with it
• Family Information: Germ cell tumors have been reported in family members
• Case: identified affected families w/ pleuropulmonary blastoma (PPB): germline and somatic DICER1 mutations also identified in other familial associated tumors
• CasePreviousTesting: numerous studies confirmed relationship b/t DICER1 variants in carriers and development of range neoplasms and non-neoplastic conditions

-Gene: DICER1 -PMID: 29343557 -Inheritance Pattern: DICER1 is inherited as an autosomal dominant condition with decreased penetrance -Disease Entity: earlier onset disease, multisite disease, 0-2 site disease, cystic lung disease, familial disease, bilateral disease, stage IA/IB, bilateral disease -mutation: germline loss-of-function mutation, missense mutation, Intronic mutations, hotspot mutation, second somatic mutation, truncating mutations, biallelic mutation -zygosity: heterozygosity -Family History: -testing should be considered for those with a family history of DICER1-associated conditions so that appropriate surveillance can be undertaken. -Individuals at 50% risk of a germline pathogenic variant based on family history who do not pursue genetic testing should follow surveillance guidelines as -if they have a DICER1 mutation unless/until genetic testing confirms that they did not inherit the familial mutation When a pulmonary cyst is identified in a young child with a pathogenic germline -DICER1 variant or family history of a DICER1-associated condition, it should be assumed to be Type I PPB until proven otherwise

Other Information: -Case: Risk for most DICER1-associated neoplasms is highest in early childhood and decreases in adulthood -affected phenotype may simply result from probabilities of generating the characteristic “loss-of-function plus hotspot” two hit typical of a DICER1 syndrome neoplasm. -Caseprevioustesting: presymptomatic testing of a minor child, should be discussed and factored into the decision process, as some individuals may choose, and have the right to choose, not to know their/their child’s genetic status. -gnomAD: n/a

FAMILY INFORMATION: FEMALE PATIENTS WITH A PERSONAL OR FAMILY HISTORY OF OVARIAN TUMORS

Case#: IV-1, male, 11 y.o, Pakistani

DiseaseAssertion: Limb-girdle muscular dystrophy (LGMD2F), sarcoglycanopathy

FamilyInfo: Consanguineous parents, both described as healthy and showing no abnormality. Three unaffected siblings were also reported: IV-2 (male, 10 y.o), IV-4 (male, 7 y.o), and IV-5 (female, 1.5 y.o). A deceased sister is included on the pedigree, but no details about this individual were reported. See Figure 1.

CasePresentingHPOs: HP:0001288, HP:0002650, HP:0003547, HP:0003749, HP:0001655

CaseHPOFreeText: Reduced weight gain noted at 3-4 y.o. Mild cardiac hypertrophy observed on cardiac review (additional echocardiography results reported in "Echocardiography" section). Additional phenotypic information reported in Supplementary Table 1.

CaseNotHPOs: HP:0009077, HP:0000703, HP:0001382, HP:0000365, HP:0001510, HP:0001249, HP:0000478, HP:0030148, HP:0011675

CaseNotHPOFreeText: Extensor muscles of the wrist, toes flexors, and hip abductors noted to be relatively normal. Additional phenotypic information reported in Supplementary Table 1.

MotorAchievement: Sat without assistance at 8 months of age, walked at 15 months of age, ran at 1.5 months of age. Never jumped or hopped. Frequent falls noted, as well as difficulty in walking and climbing stairs since 3 y.o.

CreatineKinase: 18SU (normal: 20SU for children, 10SU for adults) (see Supplementary Table 1). No assertion was made by the authors regarding whether this represents a normal or decreased CK level.

PreviousTesting: Thyroid stimulating hormone: 2.3mU/L (normal: <0.6mU/L); Serum VZV IgG: 286mlU/ml (normal: >150mlU/ml); IGF-1:186 ng/μl (normal: 102-520 ng/μl for males, 14 y.o); PRL: 202 ng/dl (normal: 42.5-414 ng/dl for males); Vitamin D: 47nmol/L (normal: 25-50 nmol/L); Free T4: 17.0 pmol/L (normal:10.8-19.0 pmol/L) (see Supplementary Table 1)

GenotypingMethod: (1) Targeted next generation sequencing of 31 genes associated with LGMD from proband genomic DNA extracted from peripheral blood sample; (2) Sanger sequencing of genomic DNA extracted from peripheral blood samples to confirm SGCD variant of interest in proband and three family members (III-3, III-4, IV-4). Variant was identified in homozygosity in the proband, in heterozygosity in each of the parents, and was not present in the unaffected sibling (IV-4).

Variant: NM_000337.5:c.289C>T (p.Arg97Ter)

CAID: CA3530549

gnomAD: Not reported

CaseAJV: 17 years diagnosis, Australia

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: Father (index case) died awaiting cardiac transplant (carried both variants). Two possibly affected relatives.

CasePresentingHPOs: HP:0001639, HP:0006536

(Hypertrophic cardiomyopathy, Obstructive lung disease)

HPOsFreeText: Maximum left ventricular hypertrophy at 17 mm, Sudden cardiac death event at 17 years, Maximal wall thickness at 22mm,

CaseNotHPOs: N/A

NotHPOsFreeText: 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.1954A>G (p.Arg652Gly)

ClinVarID:177626 https://www.ncbi.nlm.nih.gov/clinvar/variation/177626/

gnomAD: Not in gnomAD

Multiple Gene Variants:

MYBPC3 Variant

Variant: NM_000256.3:c.2980C>T (p.Leu994Phe)

ClinVarID:180992 https://www.ncbi.nlm.nih.gov/clinvar/variation/180992/

gnomAD: European (Non-Finnish) 1.624e-4, Overall 8.461e-5 https://gnomad.broadinstitute.org/variant/11-47355487-G-A