Case#: P18, Female, German, 32.2 years old at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: Mildly affected based on a CHAI score of 11.11%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.416A>G (p.Tyr139Cys)

ClinVar ID: 623475

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P17, Male, Belgian, 40 years at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.407C>T (p.Pro136Leu)

ClinVar ID: 1711524

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P16, male, german, age: n/a, alive at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 45.83%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.392T>C (p.Val131Ala)

ClinVar ID: 624171

gnomAD: Not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P02, Female, the age of clinical and genetic diagnosis: Unknown, Finnish, alive at the time of article's publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NC_000002.12:g.203868053T>A

ClinVar ID:

CAID: CA350138070

gnomAD: not found in any gnomAD version.

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P15, female, age: n/a, ethnicity: n/a, alive at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.384C>G (p.Ile128Met)

ClinVar ID: 662956

gnomAD: 0.000006814

https://gnomad.broadinstitute.org/variant/2-203870860-C-G?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P01, Female, clinical diagnosis at the age of 45, genetic diagnosis at the age of 56, German, alive at the time of article's publication

DiseaseAssertion: Patient is classified as "Mildly affected" based on a CHAI score of 10.42%.

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.109+1G>T

ClinVar ID: 161113

gnomAD: This variant was not found in any gnomAD version.

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P14, Female, Czech, 36 years old at the time of genetic diagnosis, daed at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: unregistered variant - without the bp change we can't confidently assert this variant at this time but it is possible it is CA2953901753

ClinVar ID: n/a

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P05, Male, age: n/a, ethnicity:n/a, alive at the time of publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: <br /> NM_005214.5(CTLA4):c.208C>T (p.Arg70Trp)

ClinVar ID: 161114

gnomAD: 6.195e-7 https://gnomad.broadinstitute.org/variant/2-203870684-C-T?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: Case 1, 19 year old male, Romanian

DiseaseAssertion: APDS

FamilyInfo: non-consanguineous parents, Sanger sequencing on the patient and his family members (the father's DNA was unavailable) revealed the E1021K substitution only in the patient, with no history of the disease in the family (Fig. 1A).

CaseHPOFreeText: recurrent respiratory infections, chronic hepatosplenomegaly and nonmalignant lymphadenopathy, acute pericarditis, bronchiolitis, recurrent episodes of upper and lower respiratory tract infections, suppurative otitis media from the 2nd year of life and a severe episode of haemolytic anemia, persistent lymphopenia with decreased naïve CD4 T cells, dysgammaglobulinaemia with an increase of IgM and absence of specific response to anti-pneumococcal vaccination

CasePreviousTesting: WES

GenotypingMethod: WES followed by Sanger

Variant: G > A mutation at the position c.3061 of the PIK3CD gene with E1021K substitution

CAID: CA145460

gnomAD: absent in gnomAD v2.1.1

Case#: 2 year old female

DiseaseAssertion: APDS (She was diagnosed with polymorphous B-cell lymphoproliferative disorder)

FamilyInfo: no family history suggestive of an immunodeficiency

CaseHPOFreeText: referred by pulmonary to clinical immunology for evaluation of her recurrent pneumonias and bronchiectasis. Work-up at that time revealed IgA < 6 (34–305 mg/dL), IgG 30 (572–1,474 mg/dL), IgM 1190 (31–208 mg/dL). In addition to low levels of IgG and IgA but elevated IgM levels, immune evaluation revealed T and B cell lymphopenia −827 (876–3,394 CU MM) and 28 (200–1,259/CU MM), respectively. Her CD4 count was 331 (412–2,095/CU MM) and CD8 count was 481 (236–995/CU MM). She had a normal response to lymphocyte mitogen and antigen stimulation. Due to these results and her clinical history, she was started on intravenous immunoglobulin replacement which helped decrease her incidence of infections. As she grew older she began to have increased hospitalizations for hemolytic anemia and recurrent pneumonias and sinusitis. She also developed lymphadenopathy and splenomegaly. She received rituximab with resultant improvement in her counts and decrease in size of her lymphadenopathy and hepatosplenomegaly. She was also started on trimethoprim/sufamethoxazole prophylaxis to help prevent infections, and though she continued to have intermittent respiratory infections the amount was improved. In addition to asymmetrical cervical lymphadenopathy and parotid gland enlargement Figures 2A,B, a CT neck/chest/abdomen and pelvis done at that time showed mediastinal, hilar, abdominal, and pelvic lymphadenopathy, impressive retroperitoneal lymphadenopathy, hepatosplenomegaly, and cecum and terminal ileum thickening Figures 2C,D.

CasePreviousTesting: Genetic testing revealed no mutation in AID, UNG, CD40, or CD40L but later gene sequencing discovered a dominant activating mutation in PIK3CD–c.3061G > A (p.Glu1021Lys).

GenotypingMethod:

Variant: PIK3CD–c.3061G > A (p.Glu1021Lys).

CAID: CA145460

gnomAD: absent in gnomAD v2.1.1

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

Case#: Family_A_Patient_A.II.9, male, onset at or before the age of 17, death at age 37 years, ethnicity not specified

DiseaseAssertion: Patients are asserted to have "CTLA4 haploinsufficiency" or impaired ligand binding by CTLA4 resulting in "a complex syndrome with features of both autoimmunity and immunodeficiency".

FamilyInfo: The Family A pedigree is shown in Figure 1a and includes 39 members and 11 genotype-positive members, of whom 5 are affected.

CasePresentingHPOs: HP:0010444 (Pulmonary insufficiency), HP:0004313 (Decreased circulating antibody level), HP:0001744 (Splenomegaly), HP:0011108 (Recurrent sinusitis), HP:0002837 (Recurrent bronchitis), HP:0000787 (Nephrolithiasis), HP:0032262 (Pulmonary tuberculosis), HP:0032271 (Extrapulmonary tuberculosis), HP:0006532 (Recurrent pneumonia), HP:0025419 (Pulmonary pneumatocele), HP:0030875 (Abnormality of pulmonary circulation), HP:0010976 (B lymphocytopenia), HP:0004313 (Decreased circulating antibody level), HP:0002720 (Decreased circulating IgA level), HP:0002850 (Decreased circulating total IgM)

CaseHPOFreeText: Diagnosis at age 17 was accompanied by hypogammaglobulinemia and splenomegaly. Death at age 37 was due to pulmonary insufficiency. The patient had pulmonary hypertension and clubbing. Lobectomy and lung transplant were performed. Laboratory values included very low B cells and NK cells.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Genotyping was performed at the genome-wide level (whole exome sequencing), and additional linkage analysis was performed in this family.

GenotypingMethod: Genotyping was performed by whole exome sequencing as well as genetic linkage analysis with microsatellite markers, linking the disease locus to the D2S1384 marker on chromosome 2 (close to CTLA4).

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

Variant: The patient harbors the NM_005214.5(CTLA4):c.105C>A (p.Cys35Ter) variant in the heterozygous state.

ClinVar: 161112

CAID: N/A (Not required, as there is already a ClinVar ID for this variant)

gnomAD: This variant was not found in gnomAD v.2.1.1.

SupplementalData: Yes, the description of the patient is located in the Supplementary Notes, while the clinical phenotypes and laboratory measurements are found in Tables S1 and S2.

[[AD_VCEP_Annotation_Protocol_Updated.pdf]]

Case#: 42 Chinese APDS1 patients (27 males and 15 females)

DiseaseAssertion: activated PI3Kδ syndrome 1(APDS1)

FamilyInfo: 42 patients from 41 different families in China (P3 and P11 were from one family)

CasePresentingHPOs: HP:0002205(Recurrent respiratory infections) HP:0002110(Bronchiectasis) HP:00027168(Lymphadenopathy) HP:0001744(Splenomegaly) HP:0002240(Hepatomegaly) HP:0002960(Autoimmunity) HP:0003496(Increased circulating IgM level) HP:0004315(Decreased circulating IgG level) HP:0003237(Increased circulating IgG level) HP:0003212(Increased circulating IgE level) HP:0002720(Decreased circulating IgA level) HP:0040218(Reduced natural killer cell count) HP:0005403(T lymphocytopenia) HP:0005407(Decreased proportion of CD4-positive helper T cells)

CaseHPOFreeText: Table 1 contains information of 42 patients. Immunological phenotype of cohort is summarized in Table 2.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Whole-exome sequencing

GenotypingMethod: Whole-exome sequencing

PreviouslyPublished: No

Variant: NM_005026.5:c.3061G>A p.E1021K

ClinVar: 88675

CAID: CA577192

gnomAD: 8.475e-7 https://gnomad.broadinstitute.org/variant/1-9726972-G-A?dataset=gnomad_r4

Variant: NM_005026.5(PIK3CD):c.3074A>G p.Glu1025Gly

ClinVar: 422410

CAID: CA16617216

gnomAD: Variant is not present in gnomAD data

Variant: NM_005026.5(PIK3CD):c.1574A>G (p.Glu525Gly)

ClinVar: 582515

CAID: CA338303813

gnomAD: Variant is not present in gnomAD data

Variant: NM_005026.5(PIK3CD):c.1570T>A p.Tyr524Asn

ClinVar: Not present in ClinVar

CAID: CA338303802

gnomAD: Variant is not present in gnomAD data

Case#: Grammatikos_2021_Case 1, female, 35 y.o. (onset) 51 y.o. (report), origin not reported

DiseaseAssertion: CTLA4 haploinsufficiency

FamilyInfo: affected younger daughter (case 2), affected son (case 3). 2 brothers of case 1 were affected by Evans syndrome. Another brother was affected by unexplained lymphadenopathy. Deceased brother passed due to eft ventricular fibrosis at age 40. Case 1 also had a niece with recurrent cutaneous ulceration and was a LRBA mutation carrier. The eldest daughter of case 1 developed AML (age 14).

CasePresentingHPOs: HP:0001903, HP:0002716, HP:0001945,HP:0003326, HP:0002829, HP:0031457, HP:0033608, HP:0002110, HP:0001744, HP:0033805, HP:0040312, HP:0002840, HP:0002113, HP:0005479, HP:0010976, HP:0025379, HP:0002922, HP:0001974, HP:0032289, HP:0002321, HP:0002013, HP:0001250, HP:0012534, HP:0001260, HP:0001310 (anaemia, lymphadenopathy, fevers, myalgia, arthralgia, scattered opacification, nodules in lung, bronchiectasis, splenomegaly, non-necrotising granulomas, arthritis of left temporomandibular joint, granulomatous lymphadenitis, migratory infiltrates, decreased IgE, low b-cell count, increased TPO antibodies, increased protein CSF, increased WBC, IgG oligoclonoal pattern, vertigo, vomiting, seizures, right-facial dysesthesia, dysarthria, right-sided dysmetria)

CaseHPOFreeText: mass of 1.4 cm resolving spontaneously behind tibialis posterior tendon. MRI revealed mass in the right middle cerebellar peduncle with surrounding edema. Cellular infiltration by CD4:CD* T cells, plasma cells, microglia (2:1 ratio). Neutrophilic infiltrate of the lymphatic system, EBV-related lymphoprliferation, bile salt malabsorption

CaseNotHPOs: HP:0031693, HP:0005344, HP:0003116 (serum EBV, abnormal carotid ultrasound, abnormal echocardiogram)

CaseNotHPOFreeText: presence of inflammatory markers

CasePreviousTesting: 194 genes associated with immune deficiency, next-gen sequencing. Heterozygous VUS found in LRBA.

GenotypingMethod: confirmation of CTLA4 c.81dup by Sanger sequencing

PreviouslyPublished: not reported

Variant: Heterozygous NM_005214.4(CTLA4):c.81_82insT (p.Leu28fs), Heterozygous NM_006726.4(LRBA):c.6424T>C (p.Phe2142Leu)

ClinVarID: 644629, 1038663

CAID: CA645516071, CA358607456

gnomAD: not found, not found

SupplementalData: Figure S1 shows extensive family history

Case#: Case 1, male

DiseaseAssertion: APDS

FamilyInfo: consanguineous Pakistani parents. During the preparation of this manuscript, two kindreds with loss-of-function (LOF) variants in PIK3CD were published, all of whom had hypogammaglobulinemia and recurrent sinopulmonary infections (Table E1).3,4

CaseHPOFreeText: The patient received the attenuated Bacillus Calmette-Guérin, polio, and measles vaccines without sequelae and was healthy until six years of age, when he presented with chronic diarrhea and polyarticular arthritis affecting his knees and ankles. He was empirically treated with steroids for two months, leading to complete resolution of his symptoms. Over the subsequent five years, he had episodes of colitis treated with prednisone, sulfasalazine, and methotrexate for presumed inflammatory bowel disease. Due to worsening colitis, he underwent an upper endoscopy and colonoscopy that revealed candida esophagitis as well as increased intraepithelial lymphocytes and moderate villous blunting in the duodenum. His laboratory evaluation was notable for leukocytosis, neutrophilia, mild monocytosis, and thrombocytosis (Table 1). He had normal numbers of T, B, and NK cells and normal percentages of T and B cell subsets. His serum levels of IgG and IgA were decreased. Ca2+ flux in response to anti-CD3 crosslinking on T cells was decreased (Fig. 1A), although proliferation to anti-CD3+CD28 stimulation was robust (Table 1). The patient was treated with immunoglobulin replacement therapy, antifungal prophylaxis, and prophylactic antibiotics, but died at the age of 14 years due to a severe pneumonia and sepsis shortly after the mutation was identified.

CasePreviousTesting: WES

GenotypingMethod: WES

Variant: Whole-exome sequencing of the patient revealed a novel homozygous frameshift mutation in PIK3CD (c.2558_2559delAT; p.Asp853Glyfs*20), disrupting exons 20 – 24 encoding 171 amino acids of the ATP binding site within the catalytic domain

CAID: CA2499214908

gnomAD: absent from gnomAD v2.1.1

SupplementalData:

Case#: Yap_2020_P1, male, 52, origin in Italy

DiseaseAssertion: CTLA4 haploinsufficiency

FamilyInfo: pedigree in fig 1a. unaffected brother

CasePresentingHPOs: HP:0012378, HP:0046504, HP:0100543, HP:0002028, HP:0030375, HP:0001888, HP:0002242, HP:0001369, HP:0100726 (excessive fatigue, poor libido, cognitive dysfunction, chronic diarrhea, increased memory B cells, lymphopenia, enteropathy, arthritis, Kaposi's sarcoma)

CaseHPOFreeText: diagnosed with cutaneous and nodal cKS secondary to HHV8 infection, hypersomnolence, polyarthralgia, increased DB T cells, decreased SP T cells, decreased CTLA4 expression on Tregs

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

CasePreviousTesting: negative for cKS-associated genes: IFNGR1, WAS, STIM1, or TNFRSF4

GenotypingMethod: WGS followed by Sanger sequencing

PreviouslyPublished: not reported

Variant: NM_005214.49(CTLA4):c.457G>A (p.Asp153Asn)

ClinVarID: 636389

CAID: CA350138843

gnomAD: not found

SupplementalData: n/a

note: experimental data (decreased expression in Tregs, figure 1F).

Case#: 27-month-old girl Iranian girl

DiseaseAssertion: Combined immunodeficiency.

FamilyInfo: Table2 Mother is a carrier for the variant . CasePresentingHPOs: Annotate with the HPOs presenting specifically in the proband of interest . Case#: 27-month-old girl Iranian girl

DiseaseAssertion: Combined immunodeficiency

FamilyInfo: Table2 Mother ,who has hypothyroidism and a history of frequent respiratory infections in childhood, is a carrier for the variant. Father doesn't carry the variant.

CasePresentingHPOs: HP:0001954 (Recurrent fever) HP:0001369 (Arthritis) HP:0012219 (Erythema nodosum) HP:0031936 (Delayed ability to walk) HP:0000750 (Delayed speech and language development) HP:0001698 (Pericardial effusion) HP:0002205 (Recurrent respiratory infections) HP:0002007 (Frontal bossing) HP:0004315 (Decreased circulating IgG level) HP:0033222 (Decreased CD4:CD8 ratio) HP:0001953 (Diabetic ketoacidosis) HP:0000821 (Hypothyroidism) HP:0100651 (Type I diabetes mellitus)

CaseHPOFreeText: Patient has recurrent hospitalizations. 1) 2mo fever and elevated ESR, CRP 2) 8mo massive pericardial effusion 3) 10mo recurrent pericardial effusion 4) 13 mo high-grade fever and elevated ESR, CRP 5) 18 mo high-grade fever and elevated ESR, CRP 6) 24 mo COVID-19 positive with fever 7) 28 mo COVID-19  gastrointestinal manifestations without any adverse effects.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Whole-exome sequencing was performed on the patient's whole blood sample.

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

PreviouslyPublished: No

Variant: NM_005026:c.1429G>A p.E477K

ClinVar: Was not found on ClinVar

CAID: CA577192

gnomAD: 0.0003597 https://gnomad.broadinstitute.org/variant/1-9780259-G-A

Table S1 lists two additional INSR variants identified in the proband during whole exome sequencing:

1. NM_000208.3:c.*104A>G – a 3′ UTR variant, homozygous, annotated as benign in ClinVar (rs1051690).
2. NM_000208.3:c.2666G>A (p.Arg889Gln) – a heterozygous missense variant, classified as a variant of uncertain significance in ClinVar (rs187282966).

Case#: P3, 9 year old girl

DiseaseAssertion: APDS

CaseHPOFreeText: presented with growth retardation since 6 months of age (currently −3 SD of height and −2.5 SD of weight). Lymphadenopathy and splenomegaly were noted at the age of 8 years, and adenoidectomy and tonsillectomy were performed. She had decreased IgA but normal IgG and IgM serum levels. Her mother had a similar clinical phenotype and died from Hodgkin lymphoma.

CasePreviousTesting: Thus, mutations known to cause APDS1 or APDS2 were searched and excluded by Sanger sequencing

GenotypingMethod: For P2 and P3, a targeted Next-Generation sequencing of a primary immunodeficiencies gene panel including PIK3CD and PIK3R1 was performed

Variant: A heterozygous G to A mutation at position 9775907 (GRCh37; NM_005026.3) in the PIK3CD gene was detected. The mutation leads to an amino acid substitution from glycine to aspartic acid at position 124 (G124D) located in the linker region between the ABD and the RBD at the N-terminal part of p110δ (Figure 1A).

CAID: CA338300460

gnomAD: absent from gnomAD v2.1.1

Case#: P2, 10 year old boy

DiseaseAssertion: APDS

CaseHPOFreeText: presented with recurrent otitis media and sinusitis since his first year of life. He had an adenoidectomy at 3 years of age. He presented with high IgM but normal IgG and IgA serum levels (Table 1). The serum levels of IgG2 (0.23; N: 0.56) and IgG4 (<0.002; N: 0.018) subclasses were low.

CasePreviousTesting: Thus, mutations known to cause APDS1 or APDS2 were searched and excluded by Sanger sequencing

GenotypingMethod: For P2 and P3, a targeted Next-Generation sequencing of a primary immunodeficiencies gene panel including PIK3CD and PIK3R1 was performed

Variant: A heterozygous G to A mutation at position 9775907 (GRCh37; NM_005026.3) in the PIK3CD gene was detected. The mutation leads to an amino acid substitution from glycine to aspartic acid at position 124 (G124D) located in the linker region between the ABD and the RBD at the N-terminal part of p110δ (Figure 1A).

CAID: CA338300460

gnomAD: absent from gnomAD v2.1.1

Case#: P1, 13 year old boy

DiseaseAssertion: APDS

FamilyInfo: no relevant family history was reported.

CaseHPOFreeText: He presented with hypogammaglobulinemia with decreased IgG and IgA but normal IgM serum levels (Table 1). Current complications include bronchiectasis, a lymphoproliferative syndrome with splenomegaly and hepatic fibrosis responsible for portal hypertension associated with gastrointestinal bleedings.

CasePreviousTesting: Thus, mutations known to cause APDS1 or APDS2 were searched and excluded by Sanger sequencing.

GenotypingMethod: Subsequently, to identify the genetic cause of the disease, whole exome sequencing was performed in P1. A heterozygous G to A mutation at position 9775698 (GRCh37; NM_005026.3) on chromosome 1, c.241 G>A in the PIK3CD gene was detected.

Variant: The variation encodes an amino acid substitution from glutamic acid to lysine at position 81 (E81K) located in the ABD at the N-terminal part of p110δ (Figure 1A). Sanger sequencing confirmed the mutation in the patient, which was not present in either parents.

CAID: CA338300169

gnomAD: absent from gnomAD v2.1.1

Case#: Patient 1, Korean, 4 year old, male

DiseaseAssertion: APDS1

CaseHPOFreeText: diagnosed with common variable immunodeficiency (CVID) was referred to our clinic for persistent lymph node enlargement, hematochezia, and increased serum immunoglobulin (Ig)M. His medical history included double barrel enterostomy and segmental resection of the small intestine, attributable to intestinal malrotation and perforation in the neonatal period. He was diagnosed with hemolytic anemia at the age of 10 months and pancytopenia at the age of 15 months, after which he received steroid treatment. At the age of 21 months, he exhibited increased IgM (304 mg/dL; normal, 43–173 mg/dL) and decreased IgG (16 mg/dL; normal, 345–1236 mg/dL) and IgA (<1 mg/dL; normal, 11–106 mg/dL). Regular immunoglobulin-replacement treatment (IGRT, 500 mg/kg every 3 weeks) was initiated for CVID. At the age of 10 months, a lymph node biopsy revealed atypical lymphoid cell proliferation. At the age of 3 years, hematochezia gradually increased, and IgG trough levels were not well maintained (average, 333 mg/dL; normal, 345–1236 mg/dL) despite IGRT (500 mg/kg every 3 weeks). Patient 1 had a head circumference of 55 cm (>95th percentile) and body weight of 15 kg (<10th percentile), as well as multiple enlarged cervical lymph nodes and splenomegaly. Complete blood count values were white blood cells (WBC), 7910/µL (normal, 6000–15000/µL); hemoglobin (Hb), 10.9 g/dL (normal, 10.5–14.0 g/dL); and platelets (PLT), 122 k/µL (normal, 150–450 k/µL). Immunological values were CD3, 68%, 2320/µL (normal: 56–75%, 1400–3700/µL); CD4, 19%, 648/µL (normal: 28–47%, 700–2200/µL); CD8, 45%, 1535/µL (normal: 16–30%, 490–1300/µL); and CD19, 10%, 341/µL (normal: 8–39%, 180–1300/µL). Serum IgG, A, and M levels were 332 mg/dL (normal, 345–1236 mg/dL), <1 mg/dL (normal, 14–159 mg/dL), and 569 mg/dL (normal, 43–207 mg/dL), respectively (Table 1). Mucosal nodular lymphoid hyperplasia visualized as cobblestone-like polyps and cytomegalovirus (CMV) was detected in a mucosal biopsy through colonoscopy. Summary of symptoms in Table 1.

CasePreviousTesting: exome sequencing

GenotypingMethod: Diagnostic exome sequencing confirmed by Sanger

Variant: E1021K, heterozygous

CAID: CA145460

gnomAD: variant is absent in gnomAD v2.1.1

Case#: Patient 3, Korean, 13 year old, female

DiseaseAssertion: APDS1

CaseHPOFreeText: Previously diagnosed with selective IgA deficiency was reevaluated for other PIDs when she presented with multiple episodes of prolonged fever and enlargement of several lymph nodes. Patient 3 had a history of hospitalizations attributable to recurrent respiratory tract infections, cellulitis, and osteomyelitis. She was diagnosed with selective IgA deficiency at the age of 4 years at our hospital. Cervical lymph node enlargement was first noticed at the age of 6 years; hematochezia was also noted. Colon and cervical lymph node biopsies showed atypical lymphocyte proliferation with polyclonality, and persistent atypical lymphoid proliferation of the colon was observed at the age of 10 years. One colon biopsy specimen was suspicious for mucosa-associated lymphoid tissue lymphoma. The oncologists decided to observe the patient without special chemotherapy. During the follow-up period, we diagnosed and treated Patient 1 from the present case series, leading the clinicians to reevaluate Patient 3 for other PIDs. Upon reevaluation, the height and weight of Patient 3 were below the 5th percentile and development was normal. At the age of 12 years, laboratory values were WBC, 5410/µL; Hb, 8.5 g/dL; and PLT, 285k/µL. Immunological values were CD3, 391/µL (normal, 800–3500/µL); CD4, 194/µL (normal, 400–2100/µL); CD8, 190/µL (normal, 200–1200/µL); and CD19, 54/µL (normal, 200–600/µL). The CD4:CD8 ratio was 1.02. The response to phytohemagglutinin mitogen was reduced, while results from the same test performed 8 years prior were normal. Serum IgG, A, and M levels were 1920 mg/dL (normal, 639–1349 mg/dL), 3 mg/dL (normal, 70–312 mg/dL), and 1138 mg/dL (normal, 56–352 mg/dL), respectively. Hypermetabolic enlarged lymph nodes, splenomegaly, and bronchiectatic changes in the middle lobe of the right lung were observed on PET/CT. Summary of symptoms in Table 1.

CasePreviousTesting: exome sequencing

GenotypingMethod: Diagnostic exome sequencing confirmed by Sanger

Variant: E1021K, heterozygous

CAID: CA145460

gnomAD: variant is absent in gnomAD v2.1.1

Case#: Patient 2, Korean, 4 year old, male

DiseaseAssertion: APDS1

CaseHPOFreeText: history of idiopathic thrombocytopenic purpura, Bacillus Calmette-Guérin vaccine site infection, and respiratory tract infection requiring hospitalization was referred to our clinic for enlargement of multiple lymph nodes suspicious for lymphoma. Cervical lymph node enlargement was first noticed at 31 months old. At the age of 3 years, decreased IgG (89 mg/dL) with elevated IgM (347 mg/dL) and normal IgA (16 mg/dL) were detected at a prior hospital. He received regular IGRT under the interim diagnosis of CVID; however, trough IgG levels remained below 400 mg/dL despite receiving a higher IGRT dose (800 mg/kg) every 3 weeks. Patient 2 had a head circumference of 52.8 cm (95th percentile) and body weight of 17 kg (25–50th percentile). Multiple enlarged lymph nodes in the cervical, supraclavicular, and inguinal areas were palpated, and massive splenomegaly was noted. Molloscum contagiosum was observed on his buttocks. Complete blood count results included WBC, 3300/µL; Hb, 13.1 g/dL; and PLT, 157k/µL. Immunological values were CD3, 867/µL (normal, 1578–3707/µL); CD4, 241/µL (normal, 870–2144/µL); CD8, 613/µL (normal, 472–1107/µL); and CD19, 24/µL (normal, 276–640/µL). The CD4:CD8 ratio was 0.39 (Table 1). Positron emission tomography/computed tomography (PET/CT) findings showed enlargement of multiple lymph nodes, including the bilateral cervical, supraclavicular, and inguinal areas, and abnormal uptake in the whole intestine. A colonoscopy revealed multiple nodules and masses throughout the entire length of the colon. Cervical lymph node and large intestine biopsies revealed atypical lymphocyte proliferation with polyclonality (Fig. 1A–C) (Supplementary Fig. 1A and B, only online). A colon biopsy revealed CMV, and the patient complained of diarrhea. Summary of symptoms in Table 1.

CasePreviousTesting: exome sequencing

GenotypingMethod: Diagnostic exome sequencing confirmed by Sanger

Variant: E1021K, heterozygous

CAID: CA145460

gnomAD: variant is absent in gnomAD v2.1.1

Case#: P13, Male, German, 38 years old at the time of clinical diagnosis, 40.6 yeras old at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: severly affected based on a CHAI score of 52.38%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: ENST00000295854.10:c.356T>G

ClinVar ID: not found

CAID:CA350138616

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P12, sex: n/a, age: n/a, ethnicity: n/a

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.326G>A (p.Gly109Glu)

ClinVar ID: 542071

gnomAD: 0.0002354 https://gnomad.broadinstitute.org/variant/2-203870802-G-A?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P11, Female, German, age: n/a, alive at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 18.75%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.326G>A (p.Gly109Glu)

ClinVar ID: 542071

gnomAD: 0.0002354 https://gnomad.broadinstitute.org/variant/2-203870802-G-A?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P10, Female, German, 24 years old at the time of clinical diagnosis, 25 years old at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 33.33%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.326G>A (p.Gly109Glu)

ClinVar ID: 542071

gnomAD: 0.0002354 https://gnomad.broadinstitute.org/variant/2-203870802-G-A?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P09, Male, age: n/a, ethnicity: n/a, alive at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.265T>C (p.Tyr89His)

ClinVar ID: 1391402

gnomAD: 0.000003717 https://gnomad.broadinstitute.org/variant/2-203870741-T-C?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P08, Female, Canadian, age: n/a, alive at the time of publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.257C>T (p.Ala86Val)

ClinVar ID: 661941

gnomAD: 0.00001859

https://gnomad.broadinstitute.org/variant/2-203870733-C-T?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P07, Male, German, 18 years old at the time of clinical diagnosis and 24.2 years old at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: Mildly affected based on a CHAI score of 17.65%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: <br /> NM_005214.5(CTLA4):c.224G>A (p.Arg75Gln)

ClinVar ID: 943305

gnomAD: 0.000008673

https://gnomad.broadinstitute.org/variant/2-203870700-G-A?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P06. Female, German, 52 years old at the time of clinical diagnosis, Alive at the time of publication

DiseaseAssertion: classified as "Severely affected" based on a CHAI score of 47.37%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.214A>C (p.Thr72Pro)

ClinVar ID: 546886

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P04, male, genetic diagnosis at the age of 71.4, ethnicity: N/A, Dead at the time of article's publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.160G>A (p.Ala54Thr)

ClinVar ID: 430905

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P03, Male, Age: N/A, ethnicity: N/A, Alive at the time of article's publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.155G>A (p.Gly52Asp)

ClinVar ID: 871301

gnomAD: not found in any gnomAD version.

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P22, Female, German, age: n/a , alive at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 42.86%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: ENSP00000497102.1:p.Leu163Ser

ClinVar ID:

CAID: PA2850594025

gnomAD: Not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P21, female, American, age: n/a, alive at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.467C>T (p.Pro156Leu)

ClinVar ID: 1035066

gnomAD: 0.00002292 https://gnomad.broadinstitute.org/variant/2-203871387-C-T?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P20, male, German, 22 years old at the time of clinical diagnosis, 22.7 years old at the time of genetic diagnosis, dead at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 42.11%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NP_001032720.1:p.Thr147Arg

ClinVar ID:

CAID: PA2850594024

gnomAD: Not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P19, Female, Italian, age: n/a, alive at the time of diagnosis

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: ENST00000295854.10:c.434A>G

ClinVar ID:

CAID: CA350138791

gnomAD: 6.197e-7 https://gnomad.broadinstitute.org/variant/2-203870910-A-G?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

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

Case#: 19 year old, Indian, male

DiseaseAssertion: APDS

FamilyInfo: Neither parent carried this mutation, suggesting a de novo origin.

CaseHPOFreeText: referred for the evaluation of chronic active EBV disease. The patient’s medical history revealed congenital stenosis of the left bronchus, recurrent sinopulmonary infections, and autism spectrum disorder with an IQ of 80–86. EBV seroconversion was identified at 7 years of age when the patient presented idiopathic abdominal lymphadenopathy. Furthermore, a previous laboratory examination revealed IgA deficiency and low IgG2 and IgG4 levels without an overarching diagnosis. Four months before presentation, the patient developed fatigue, fever, night sweats, hepatosplenomegaly, anemia, hepatitis, weight loss of 10 kg, and lymphadenopathy (Fig. 1). Serum EBV copy numbers were repeatedly > 1500/mL. Histology of the three lymph nodes did not reveal any evidence of malignant lymphoma, but rather a markedly positive EBV-encoded RNA (EBER). Chronically active EBV was diagnosed, and rituximab therapy of 500 mg weekly during 4 weeks was initiated. A stable condition without any additional immunosuppressive drugs was achieved for 3 months after which he developed high spiking fever, pneumonia, progressive lymphadenopathy, severe unexplained cardiomyopathy with progressive anemia, thrombocytopenia, and hyperferritinemia (Table ​(Table1).1). Malignant lymphoma was excluded and hemophagocytosis was detected in the bone marrow (Fig. 3A, B). The patient therefore fulfilled six out of eight diagnostic HLH-04 criteria (Table ​(Table2)2) [7]. His clinical status quickly deteriorated, and he developed acute respiratory distress syndrome and multiple organ failure. Salvage therapy was initiated with high-dose steroids, sirolimus, and intravenous immunoglobulin. PI3K delta inhibitors were withheld due to heart and respiratory failure. Etoposide was withheld due to leucopenia and severe sepsis with systemic infection (hospital acquired pneumonia with H. influenza, not responding to treatment). Within 1 month, the patient died from cardiac failure with refractory pulmonary edema.

CasePreviousTesting: whole exome sequencing (confirmed by Sanger sequencing)

GenotypingMethod: whole exome sequencing (confirmed by Sanger sequencing)

Variant: heterozygous c.3074A > C, p.Glu1025Gly mutation in the PIK3CD gene (NM_005026.3)

CAID: CA16617216

gnomAD: absent from gnomAD v2.1.1

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#: 2-month-old boy

DiseaseAssertion:

FamilyInfo: One healhy brother, noncontributory

CasePresentingHPOs: HP:0025104(Capillary malformation) HP:0004691(2-3 toe syndactyly) HP:0001520(Large for gestational age) HP:0001548(Overgrowth) HP:0033725(Thin corpus callosum) HP:0004315(Decreased circulating IgG level) HP:0002720(Decreased circulating IgA level)

CaseHPOFreeText: At 12 months of age two ear infections occuring four weeks apart and a bilateral eye infection.

CaseNotHPOs: HP:0012759(Neurodevelopmental abnormality) HP:0002850(Decreased circulating total IgM)

CaseNotHPOFreeText: Segmental overgrowth was not observed. Normal newborn bloodspot and hearing screen. Ophthalmology examination is normal. No no evidence for a capillary pial vascular malformation

CasePreviousTesting: Whole-exome sequencing and mtDNA testing

GenotypingMethod: Exome sequencing and mtDNA testing was performed on the patient’s blood sample and cultured fibroblast from a 3 mm punch biopsy from right lower paraspinal region.

PreviouslyPublished: No

Variant: NM_181523.2:c.1746-2A>G p.? 9% of the proband's blood cells (74 sequencing reads) and in 25% of the cultured fibroblasts (84 sequencing reads).

ClinVar: https://www.ncbi.nlm.nih.gov/clinvar/variation/1298995/ germline

CAID: CA359883172

gnomAD: Not present in gnomAD

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#: 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