Case#: Case 1

DiseaseAssertion: APDS

FamilyInfo: no familial history of PID

CaseHPOFreeText: He was referred to our hospital at the age of 2 years with recurrent bronchopulmonary infections, lymphadenopathy, hepato-splenomegaly, liver disease (elevated transaminases and portal septal fibrosis at liver biopsy). He had increased serum IgM levels (4.25g/L), normal IgG (5.7 g/L) and decreased IgA (0.65g/L) levels, compatible with the diagnosis of CSR-D. The CD40L and CD40 defects were excluded and intravenous IgG substitution was initiated. At 8 years of age, he developed a high grade diffuse large B-cell lymphoma (DLBCL, WHO classification) of biliary tract (Figure 1 a-c). In situ hybridization for Epstein Barr virus (EBV) was negative and Bcl-6 was expressed as shown by immunohistochemistry. The patient recovered after nine courses of chemotherapy (UKCCSG 9002 protocol; “see E3”). At 19 years of age, under IgG substitution, he again developed a high grade EBV(-) DLBCL of the colon, which was found to be Bcl-6 negative (Figure 1 d-f). He received CHOP (Cyclophophamide, vincristine, steroids) plus rituximab. He died from large bowel perforation and bleeding 12 days after the third course of chemotherapy.

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#: 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#: 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#: 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#: 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#: 2 year old female, Albanian

DiseaseAssertion: APDS

FamilyInfo: The patient was the first of three children from a non-consanguineous family of Albanian origin

CaseHPOFreeText: presented with recurrent otitis media, respiratory infections, persistent splenomegaly and nonmalignant lymphadenopathy. In the first year of life, she had recurrent episodes of wheezing associated with viral infections. In four occasions, she developed otitis media. Clinical evaluation at 17 months of age revealed splenomegaly suggesting Autoimmune lymphoproliferative disease (ALPS), but analysis of CD4 − /CD8 − /TCR alpha/beta + T cells was normal. In addition, bone marrow morphology and karyotype were normal. At the age of 21 months, the patient was hospitalized due to an additional episode of otitis caused by multidrug resistant Pseudomonas aeruginosa . Since then, she suffered of recurrent otorrhea, due to Haemophilus influenzae and Moraxella catarrhalis . Virological testing ( Table 1 ) revealed chronic low-level Epstein–Barr virus (EBV) viraemia characterized by EBV-DNA persistence and elevated anti-VCA IgM (total viral load ranging from negative to 506 copies/ml; VCA IgM ranging from 43 AU/ml to 186 AU/ml).

CasePreviousTesting: No genotyping ot other genes

GenotypingMethod: Genetic analysis of PIK3CD by Sanger sequencing revealed a heterozygous G > A mutation at the position c.3061 resulting in E1021K substitution

Variant: heterozygous G > A mutation at the position c.3061 resulting in E1021K substitution

CAID: CA145460

gnomAD: variant is absent in gnomAD v2.1.1

Case#: case_Kiyota_2018, female,1 yo (onset), Japanese ancestry reported

DiseaseAssertion: APDS + 22q13 deletion syndrome

FamilyInfo: de novo

CasePresentingHPOs: (HP:0001973, HP:0000969, HP:0011134, HP:0000123, HP:0000093, HP:0003073, HP:0004431, HP:0003493, HP:0020151, HP:0033604, HP:0001263, HP:0001290, HP:0000729, HP:0002463, HP:0001249, HP:0007021, HP:0012433

ITP systemic edema mild fever lupus nephritis proteinuria hypoalbuminemia decreased complement levels antinuclear antibody double strand DNA antibody wire-loop lesions in glomeruli delayed psychmotor development hypotonia autistic features language delay intellectual disability reduced sensitivity to pain poor social functioning

CaseHPOFreeText: positive staining for IgG, IgA, IgM, C3 and C1q and electron-dense deposits observed through renal biopsy, along with wire-loop lesions

CaseNotHPOs: (HP:0030882, 0010783, HP:0030880) coronary aneurysm butterfly erythema Raynaud's phenomenon

CaseNotHPOFreeText: dysmorphic features

CasePreviousTesting: G-band karyotyping + whole genome SNP microarray revealed 22q13 deletion syndrome

GenotypingMethod: WES

PreviouslyPublished:

Variant: NM_005026.3:c.1534C > T; p.(Arg512Trp)

ClinVarID: 1347382

CAID: CA577258

gnomAD: v2.1.1 Grpmax 0.00007392 (4/18252 alleles) East Asian population

SupplementalData:

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

PMID: 34692603 Case: Italian, Female child, 7-8yo DiseaseAssertion: NLH FamilyInfo: non-consanguineous parents, Italian, family and personal history were unremarkable, without any opportunistic or severe infection. CasePresentingHPOs: HP:0032203; HP:0011956, hematochezia, which progressively evolved into chronic bloody mucous diarrhea lasting for over 4 weeks, activated PI3 kinase δ syndrome (APDS) CaseHPOFreeText: Sugar intestinal permeability was markedly altered (lactulose/mannitol ratio 0.09, normal value < 0.03). Upper and lower gastrointestinal digestive endoscopy showed numerous small nodules throughout the entire gastrointestinal tract from the stomach to the rectum (Figures 1A–F), whose histopathologic features were consistent with the diagnosis of NLH (Figures 1G–I). No signs of chronic intestinal inflammation or autoimmune enteropathy, such as enterocyte apoptosis, were observed in the multiple biopsies taken at endoscopy. CaseNotHPOs: HP:0005202, HP:0034890, HP:0032247, HP:0033624, HP:0033431, HP:0033185, HP:0031693, HP:0020072, HP:0033508, HP:0033509, HP:0005215, HP:0002720, HP:0004433, HP:0011837 CaseNotHPOFreeText: HIV, bacterial Yersinia enterocolitica, cow's milk protein allergy, familial Mediterranean fever (FMF) (ORPHA:342), and other inborn errors of immunity (IEI) CasePreviousTesting: Stool culture, Fecal Calprotein, CRP, Erythrocyte sedimentation, ANCA, ASCA, GI endoscopy GenotypingMethod: Whole exome sequencing, Cell Culture, Western Blot. PreviouslyPublished: NR Variant: 582515, p.Glu525Gly (c.1574A>G) ClinVarID: 557431 CAID: CA338303813 gnomAD: n/a SupplementalData: The patient received a short course of steroids (oral prednisone at an initial dose of 1.5 mg/kg/day) with complete resolution of symptoms and normalization of calprotectin during treatment but rapid clinical and biochemical (i.e., calprotectin elevation) relapse upon discontinuation.

PIK3CD (p.Glu525Gly)

Case#: 1_Edwards_2019, F, 40 yo (report), white ethnicity reported

DiseaseAssertion: APDS

FamilyInfo: NR

CasePresentingHPOs: EBV + (HP:0430064)

CaseHPOFreeText: NR

CaseNotHPOs: CMV, Lymphoma

CaseNotHPOFreeText: NR

CasePreviousTesting: NR

GenotypingMethod: NR

PreviouslyPublished: Yes PMID: 28414062

Variant: PIK3CD c.371G>A, p.G124D

ClinVarID: 2733822

CAID: CA338300460

gnomAD: not found

SupplementalData:

Case#: 3_Edwards_2019, F, 60 yo (report), white ethnicity reported

DiseaseAssertion: APDS

FamilyInfo: NR

CasePresentingHPOs: EBV +, diffuse large B-cell lymphoma (HP:0430064, HP:0002665)

CaseHPOFreeText: NR

CaseNotHPOs: CMV, Lymphoma (HP:0430087)

CaseNotHPOFreeText: NR

CasePreviousTesting: NR

GenotypingMethod: NR

PreviouslyPublished: No

Variant: PIK3CD c.1573G>A p.E525K

ClinVarID: 132807

CAID: n/a

gnomAD: not found

SupplementalData:

Case#: 2_Edwards_2019, F, 12 yo (report), African American ethnicity reported

DiseaseAssertion: APDS

FamilyInfo: NR

CasePresentingHPOs: EBV + (HP:0430064)

CaseHPOFreeText: NR

CaseNotHPOs: CMV, Lymphoma (HP:0430087, HP:0002665)

CaseNotHPOFreeText: NR

CasePreviousTesting: NR

GenotypingMethod: NR

PreviouslyPublished: Yes PMID: 24165795

Variant: PIK3CD c.1002C>A, p.N334K

ClinVarID: 132806

CAID: CA156204

gnomAD: not found

SupplementalData:

Case#: 12, M, 5 y.o., Ethnicity: Indian.

CasePresentingHPOs: HP:0001945 (Fever), HP:0001824 (Weight loss), HP:0002716 (Lymphadenopathy/FHL), HP:0003212 (Increased circulating IgE level), HP:0002716 (Lymphadenopathy), HP:0009098 (Chronic oral candidiasis), HP:0002841 (Recurrent fungal infections), HP:0032326 (Methicillin-resistant Staphylococcus aureus infection), HP:0020271 (Increased lymph-node eosinophils), HP:0100827 (Lymphocytosis), HP:0003237 (Increased circulating IgG level), HP:0002090 (Pneumonia)

CaseHPOFreeText: Eosinophils 17%, fungal scrapes—positive. Methicillin-resistant Staphylococcus aureus pneumonia, oral candidiasis/Hyper IgE.

Suspected recurring pneumonia.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: N/A.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: Sanger sequencing and NGS targeting a customized panel of genes.

Variant: NM_005026.5:c.2296G>A.

ClinVar: 846790.

CAID: CA577485.

gnomAD: 0.00001611. https://gnomad.broadinstitute.org/variant/1-9722305-G-A?dataset=gnomad_r4.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: 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#: Female, age of onset: 56, age at testing: 69, age of last documented clinical stability: 74

DiseaseAssertion: suspected hyperactivation of the PI3K pathway; implied earlier in the paper as "activated PI3Kδ syndrome (APDS)"

FamilyInfo: no relevant family history

CasePresentingHPOs: HP:0001878, HP:0012735, HP:0000975, HP:0002716, HP:0012387, HP:0001744, HP:6000143, HP:0004313, HP:0002721, HP:0006530, HP:0002788 (hemolytic anemia, cough, diaphoresis, lymphadenopathy, bronchitis, splenomegaly, perforated appendicitis, hypogammaglobulinemia, immunodeficiency, interstitial lung disease, recurrent upper respiratory tract infections)

CaseHPOFreeText: asthenia, sarcoidosis due to chronic granulomatous sarcoid-type inflammation without necrosis, bronchiectasis with bronchiolitis, wound infection, abdominal wall dehiscence, common variable immunodeficiency (CVID) with immune dysregulation, CVID-associated interstitial lung disease, granulomatous-lymphocytic interstitial lung disease

CaseNotHPOs: HP:0012759 (neurodevelopmental abnormalities)

CaseNotHPOFreeText: dysmorphic features, learning difficulties

CasePreviousTesting: clinical exome sequencing targeting genes associated with primary immunodeficiencies

GenotypingMethod: sequencing

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

Variant: NM_181504.3(PIK3R1):c.5A > T (p.Tyr2Phe)

ClinVar: not found

CAID:CA3290217

gnomAD: 0.3004% https://gnomad.broadinstitute.org/variant/5-67586561-A-T?dataset=gnomad_r2_1

SupplementalData: There is no supplemental data, clinical timeline and schematic with noted variants are in Figure 2 and Figure 3

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

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#: 20‐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: No relevant family history

CasePresentingHPOs: HP:0001511, HP:0000819, HP:0000855, HP:0040063, HP:0000484, HP:0000540, HP:0000483, HP:0000646, HP:0000684, HP:0000325, HP:0011220, HP:0000430, HP:0000331, HP:0000233, HP:0002714, HP:0100578

CaseHPOFreeText: Born at 39 weeks of gestation with a birth length of 45 cm and a birth weight of 1,990 g (−3.0 SD relative to the average for this gestational age). Weight at time of diagnosis was 38.5 kg (−1.2 SD), height 163.4 cm (−2.7 SD), body mass index 14.4 kg/m2 (−2.1 SD). He was found to have glycosuria during a school urine test at the age of 12 years and started treatment with metformin for diabetes at 15 years. Fasting plasma glucose, serum immunoreactive insulin (IRI) concentrations, and serum C‐peptide at evaluation were 161 mg/dL, 35.8 μIU/mL, and 5.20 ng/mL, respectively. HOMA‐IR was 14.2, and his HOMA‐β was 131.5%. Patient has facial characteristics of SHORT syndrome and adipose tissue atrophy in the upper body.

CaseNotHPOs: HP:0004322, HP:0001382, HP:0000023, HP:0000490, HP:0000558, HP:0000369, HP:0005328, HP:0000545, HP:0000593, HP:0000501, HP:0000963, HP:0007392, HP:0001249, HP:0000750, HP:0000365, HP:0000400

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.1945C>T

ClinVar: 60763

gnomAD: NR

SupplementalData: Table 1

Case#: 6‐year‐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: No relevant family history

CasePresentingHPOs: HP:0001511, HP:0000855, HP:0004322, HP:0000490, HP:0000684, HP:0000325, HP:0000430, HP:0000400, HP:0000369, HP:0005328, HP:0000545, HP:0000963, HP:0007392, HP:0000365

CaseHPOFreeText: Born with a birth length of 43.1 cm (−1.3 SD relative to the average for this gestational age) and birth weight of 1,544 g (−2.7 SD relative to the average for this gestational age). Her height was 104.0 cm and weight 12.6 kg at the time of evaluation for this study, indicating no apparent short stature (−1.0 SD relative to the average for this age). Her fasting plasma glucose, serum IRI concentrations, and serum C‐peptide were 108 mg/dL, 56.4 μIU/mL, and 6.95 ng/mL, respectively, with an HbA1c level of 5.2%. Her HOMA‐IR was 15.0, and her HOMA‐β was 451.2%. She had a hearing threshold of 30 and 50 dB in the right and left ears, respectively. Otitis media was apparent in the right ear, but not in the left. Patient had readily visible veins.

CaseNotHPOs: HP:0000819, HP:0001382, HP:0000023, HP:0011220, HP:0000331, HP:0000233, HP:0002714, HP:0000540, HP:0000483, HP:0000593, HP:0000501, HP:0100578, HP:0001249, HP:0000750

CaseNotHPOFreeText: N/A

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.1945C>T

ClinVar: 60763

gnomAD: NR

SupplementalData: Table 1, Figure 1a,b

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#: 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#: 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 7 (P7) is a 50-year-old Chinese male.

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

FamilyInfo:

CasePresentingHPOs: HP:0012735 (Cough), HP:0002014 (Diarrhea), HP:0000988 (Skin rash), HP:0001596 (Alopecia), HP:0004313 (Decreased circulating immunoglobulin concentration), HP:0004386 (Gastrointestinal inflammation)

CaseHPOFreeText: Patient's symptoms onset in his late 30s with respiratory and gastrointestinal symptoms. He developed pruritic rashes on the abdomen and bottom of the feet, as well as alopecia. Gastrointestinal histopathology finding included intestinal metaplasia in the gastric angle and pyloric mucosa, as well as lymphoid follicle formation in the descending duodenum.

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

CaseNotHPOFreeText: Patient was negative for inflammatory bowel disease antibodies.

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.151C>T(p.Arg51Ter) variant.

ClinVar1: 161109

gnomAD1: The variant was not found in gnomAD v4.1.1.

Variant2: The patient is heterozygous for the NM_012452.3(TNFRSF13B):c.788C>T (p.Thr263Ile) variant.

ClinVar2: 1696714

gnomAD2: This variant has an allele frequency of 0.00009138 in gnomAD v4.1.1. (https://gnomad.broadinstitute.org/variant/chr17-16939641-G-A?dataset=gnomad_r4)

Variant3: The patient is heterozygous for the NM_012452.3(TNFRSF13B):c.178C>T (p.Arg60Cys) variant.

CAID3: CA8414096

gnomAD3: This variant has an allele frequency of 0.00006666 in gnomAD v4.1.1. (https://gnomad.broadinstitute.org/variant/chr17-16952467-G-A?dataset=gnomad_r4)

SupplementalData: There is no supplemental data.

Case#: The patient is a 39-year-old female with symptom onset at 14.

DiseaseAssertion: The patient is asserted to have "CTLA-4 happloinsufficiency." "Affected patients develop cytopenia, lymphoproliferative disorders, and hypogammaglobulinemia and are prone to a variety of autoimmune phenomena."

FamilyInfo: None provided

CasePresentingHPOs: HP:0001873 (Thrombocytopenia), HP:0001888 (Lymphopenia), HP:0001903 (Anemia), HP:0004313 (Decreased circulating immunoglobulin concentration), HP:0002028 (Chronic diarrhea), HP:0002024 (Malabsorption), HP:0001596 (Alopecia), HP:4000055 (Intestinal inflammation), HP:0006824 (Cranial nerve paralysis), HP:0002090 (Pneumonia), HP:0001269 (Hemiparesis)

CaseHPOFreeText: CSF analysis showed intrathecal synthesis of immunoglobulins G and M. MRI showed disseminated T2-hyperintense lesions, some lesions indicated long-lasting gadolinium enhancement (Figure 1A). PET scan-guided brain biopsy showed sustained myeline integrity, massive infiltration of T cells, and presence of few perivascular B cells. Infectious or neoplastic conditions were ruled out.

CaseNotHPOs: N/A

CaseNotHPOFreeText: Laboratory testing was negative for infectious or rheumatologic conditions. Brain vessel angiography was normal.

CasePreviousTesting: None reported.

GenotypingMethod: Sequencing of the LRBA and CTLA4 genes was performed. Authors did not elaborate on methodology or assay.

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

Variant: The patient is heterozygous for the NM_005214.5(CTLA4):c.322_323insT (p.Ser108MetfsTer46) variant.

CAID: CA3270658428

gnomAD: This variant is not found in gnomAD v4.1.1.

SupplementalData: Figure 1A shows MRI scans from 2014-2021. Figure 1B shows immunomodulatory treatment of the patient. Figure 1C shows blood lymphocyte count and lymphocyte subsets over time. Figure 1D shows Crohn disease activity index, blood platelet count, and serum immunoglobulins. Figure 2 shows single-cell RNA sequencing of peripheral blood monocular cells.

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#: 17-year-old African American male

DiseaseAssertion: Symptomatic paroxysmal atrial fibrillation (AF)

FamilyInfo: Proband's mother experienced symptomatic early-onset paroxysmal AF at 47 years of age. Proband's maternal grandmother presented with minimally symptomatic AF at 52 years of age.

ParentalTesting: Proband, mother, and maternal grandmother tested positive for SCN5A variant.

CasePresentingHPOs: HP:0005110, HP:0004757

CaseHPOFreeText: Symptomatic paroxysmal atrial fibrillation. The initial presenting ECG revealed AF with controlled ventricular rates in the absence of atrioventricular (AV) nodal blockers.

CaseNotHPOs: HP:0001678

CaseNotHPOFreeText: absence of atrioventricular (AV) nodal blockers, LA and LV size normal.

CasePreviousTesting: NR

FunctionalAnalysis: The biophysical properties of the SCN5A-N470K mutant channel were investigated using voltage-clamp recordings following the transient transfection of HEK cells with either wild-type (WT) or N470K channels. The impact of the N470K mutation on the gating properties of the Nav1.5 sodium channel was also investigated. Findings indicate that a gain-of-function mutation.

Variant: 1410C>G (p.Asp470Lys)

ClinVar: 30047

CAID: CA014836

gnomAD: https://gnomad.broadinstitute.org/variant/3-38646328-G-C?dataset=gnomad_r2_1 (FAF: 0.0001656, African/African American)

AdditionalInfo: Clinical characteristics of proband and family members found in Table 1.

Case#: 55-year-old man

DiseaseAssertion: single coronary artery (SCA) and presented with dilated cardiomyopathy (DCM)

FamilyInfo: Unremarkable

ParentalTesting: NR

CasePresentingHPOs: HP:0002094, HP:0031352, HP:0001638, HP:0001644, HP:0010741

CaseHPOFreeText: chest tightness and dyspnoea after activity lasting for 2 months. CTCA showed congenital absence of the right coronary artery. TTE revealed enlargement of the left heart and cardiomyopathy. CMR revealed DCM. oedema of both lower limbs. Laboratory data in Table 1.

CaseNotHPOs: NR

CaseNotHPOFreeText: Stenosis

CasePreviousTesting: See NGS results in Supplementary Table 1

Genotyping Method: Genetic screening (NGS results in Supplementary Table 1) with confirmation by Sanger

FunctionalAnalysis: NR

Variant: c.1858C>T (p.Arg620Cys)

ClinVar: 67694

CAID: CA015449

gnomAD: v4.1.0 GrpMax FAF: 0.00002033 (European non-Finnish)

AdditionalInfo: The patient also has APOA5:c.990_993delAACA (p. Asp332Valfs*5) (P/LP in ClinVar with 2 stars)

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

Case#: 31 y.o Female European

DiseaseAssertion: Limb Girdle

FamilyInfo: Asymptomatic uncle who had persistent high serum CK levels

CasePresentingHPOs: HP:0003701,HP:0003560, HP:0006785, HP:0003236,HP:0003325, HP:0008981,

CaseHPOFreeText: Has seen a specialist for the last 25 years. High CADD scores. Exercise-induced myalgia and/or rhabdomyolysis

CaseNotHPOs:

CaseNotHPOFreeText:

MotorAchievement:

CreatineKinase: Ranging from 500 UI/L to 4500 UI/L

CasePreviousTesting: Latest neurological, cardiac and respiratory examinations were normal

GenotypingMethod: Muscle Biopsy using next generation sequencing and multiple gene panel. Minimal myopathic changes on histological assessment and normal immunofluorescence staining for muscle proteins including α-sarcoglycan.

PreviouslyPublished:

Variant: NM_000023.4(SGCA):c.850C>T (p.Arg284Cys) and NM_000023.4(SGCA):c.739G>A (p.Val247Met)

ClinVar: 9439 and 167677

CAID:

gnomAD: 0.0007716 and 0.0002411