Case#: P1

DiseaseAssertion: APDS1

FamilyInfo: Chinese

CaseHPOFreeText:

CasePreviousTesting: WES

Variant: E1021K

HGVS: NM_005026.5(PIK3CD):c.3061G>A (p.Glu1021Lys)

ClinVar: 88675

CAID: CA145460

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

Case#: P2

DiseaseAssertion: APDS1

FamilyInfo: Chinese

CaseHPOFreeText: Upper respiratory infection, Recurrent respiratory tract infections (1 m), pulmonary artery hypertension, bronchiectasis (16 y), Lymphadenomegaly, splenomegaly, hepatomegaly, Thrombocytopenia, Pericardial effusion, kidney injury, hypoalbuminemia, failure to thrive, anti-infection prophylaxis, IVIG, glucocorticoid, mTOR inhibitor.

CasePreviousTesting: WES

Variant: E1021K

HGVS: NM_005026.5(PIK3CD):c.3061G>A (p.Glu1021Lys)

ClinVar: 88675

CAID: CA145460

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

Case#: P3

DiseaseAssertion: APDS1

FamilyInfo: Chinese

CaseHPOFreeText: Pneumonia, Recurrent respiratory tract infections (6 m), bronchiectasis (7 y), Lymphadenomegaly, splenomegaly, hepatomegaly, Pericardial effusion, warts, proteinuria, hypoalbuminemia, intracranial hypertension, convulsion, failure to thrive, nasosinusitis, mastoiditis, brain atrophy, anti-infection prophylaxis, IVIG, glucocorticoid, mTOR inhibitor.

CasePreviousTesting: WES

Variant: E1021K

HGVS: NM_005026.5(PIK3CD):c.3061G>A (p.Glu1021Lys)

ClinVar: 88675

CAID: CA145460

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

Case#: P4

DiseaseAssertion: APDS1

FamilyInfo: Chinese

CaseHPOFreeText: Splenomegaly, Recurrent respiratory tract infections (9 y), Lymphadenomegaly, splenomegaly, SLE, lupus nephritis, AIHA, Flat warts, urinary tract infection, failure to thrive, anti-infection prophylaxis, IVIG, glucocorticoid, mTOR inhibitor.

CasePreviousTesting: WES

Variant: E1021K

HGVS: NM_005026.5(PIK3CD):c.3061G>A (p.Glu1021Lys)

ClinVar: 88675

CAID: CA145460

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

Case#: P10

DiseaseAssertion: APDS1

FamilyInfo: Chinese

CaseHPOFreeText: Purpura, Recurrent respiratory tract infections, bronchiectasis (9 y), Chronic diarrhea, colitis, ileitis, gastritis, Lymphadenomegaly, splenomegaly, hepatomegaly, ITP, Mastoiditis, anti-infection prophylaxis, IVIG, glucocorticoid, mTOR inhibitor.

CasePreviousTesting: WES

Variant: E1025G

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

ClinVar: 422410

CAID: CA16617216

gnomAD: absent from gnomad v4.1.0

Case#: P17

DiseaseAssertion: APDS1

FamilyInfo: Chinese

CaseHPOFreeText: Upper respiratory infection, Recurrent respiratory tract infections (1.5 y), bronchiectasis (7 y), otitis media, hearing loss, Lymphadenomegaly, splenomegaly, hepatomegaly, ILD, Kidney stones, oblique inguinal hernia, failure to thrive, mastoiditis, anti-infection prophylaxis, IVIG, glucocorticoid, mTOR inhibitor.

CasePreviousTesting: WES

Variant: E525G

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

ClinVar: 582515

CAID: CA338303813

gnomAD: absent from gnomad v4.1.0

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#: 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#: 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