Case#: Case 1, male, Brazilian

DiseaseAssertion: APDS1

FamilyInfo: We identified a kinship that included 3 half-siblings with symptoms typical for APDS1. The patient's father (I.4), a truck driver, reported that in addition to the index case, he had 4 additional children with 3 other women living in different Brazilian cities along his truck route and that 2 of these children (II.4 and II.5) had symptoms similar to the index case (Fig 1A). Of his 5 children, 1 had died at 3 years of age (II.1) with clinical symptoms similar to the index case, including hepatosplenomegaly, fever, and recurrent infections; immunologic studies were not performed. The other symptomatic half-brother (II.5) was evaluated at 5 years of age with a history of 5 episodes of pneumonia, recurrent oral candidiasis, several upper respiratory infections, and hepatosplenomegaly. The pedigree suggested that the father (I.4) carried the same autosomal-dominant PIK3CD mutation that affected 3 sons born to different mothers. However, neither he nor the mothers of the affected boys had any symptoms suggestive of APDS. Sanger sequencing demonstrated that neither the father nor the mothers of the affected boys carried the identified PIK3CD mutation in blood. This raised the possibility of germline or gonadal mosaicism in the father. To test this hypothesis, genomic DNA was extracted from his semen. As illustrated in Figure 1F, semen-derived DNA carried the heterozygous p.E1021K mutation identified in the affected sons. Based on relative peak heights, we estimated that 20% to 25% of the semen carried the mutation.

CaseHPOFreeText: The index case (II.4 in Fig 1A) had 10 episodes of pneumonia, 2 episodes of sepsis, several upper respiratory infections, and oral moniliasis within the first year of life. He subsequently developed hepatosplenomegaly, lymphadenopathy, and an axillary abscess owing to Candida albicans. At 3 years of age, laboratory investigation showed increased immunoglobulin (Ig) M (368 mg/dL) and IgG (1,450 mg/dL) levels, normal IgA level (107 mg/dL), low CD4 (330/mm3) and increased CD8 (1,229/mm3) counts, and low CD19 B cells (17/mm3). IgG subclasses showed normal absolute levels of IgG1 (1,020 mg/dL), IgG2 (79.0 mg/dL), IgG3 (78.3 mg/dL), and IgG4 (28.1 mg/dL); however, their ratio showed a proportional decrease of IgG2.

GenotypingMethod: Sanger sequencing. Unclear if entire PIK3CD gene was sequenced across intron/exon boundaries.

Variant: a heterozygous PIK3CD hotspot mutation (c.3061G→A, p.E1021K) was identified by Sanger sequencing.

CAID: CA145460

gnomAD: absent from gnomAD v2.1.1

Case#: Takeda_2017_B.1, male, 0 years (onset)

DiseaseAssertion: APDS

FamilyInfo: unaffected mother was tested and found not to have the variant. Father was unavailable for testing

CasePresentingHPOs: abscess, severe diaper rash, recurrent otitis media, eczema, pneumonia, bloody stool, lymphoma, poor growth, low bone age, hypergammaglobulinema lymphocytopenia, elevated transitional B cells, sinopulmonary bacterial infection, decreased CD4+ T cell, decreased CD8+ T cells, decreased naive CD4+ T cells

(HP:0025615, HP:0011131, HP:0000403, HP:0000964, HP:0002090, HP:0025085, HP:0002665, HP:0002716, HP:0001510, HP:0002750, HP:0010702, HP:0001888, HP:0030381, HP:0005425, HP:0032218, HP:0005415, HP:0410378)

CaseHPOFreeText: marginal zone hyperplasia, EBV lymphadenitis, increased CD19+ B cells

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: NR

GenotypingMethod: WES + Sanger

PreviouslyPublished: NR

Variant: c.241G>A (p.E81K)

ClinVarID: NR

CAID: CA338300169

gnomAD: NR

SupplementalData:

Case#: Case 1, 12 year old, male

DiseaseAssertion: APDS-1 presenting as MAS/HL

FamilyInfo: born to not consanguineous parents of Rumenian origin

CaseHPOFreeText: His clinical history was uneventful until the age of 12, when he presented arthralgias and arthritis of the right ankle. After 4 months, the patient was admitted in a peripheral hospital due to fever, diffuse rash followed by desquama- tion. Initial blood work-up revealed increased ferritin (40.000 μg/L; normal values: 30–400 μg/L) and increased AST (88 U/L; normal va- lues: 18–32 U/L). The index patient was transferred to our clinic where additional blood work-up confirmed increased ferritin and AST. Radiologic evaluation revealed splenomegaly and lymphadenomegaly. Bone marrow aspirate revealed the presence of rare hemophagocytes. Based on available diagnostic criteria, MAS/HLH was suspected (Supplemental Table 1). Natural killer (NK) cell activity was normal, and genetic screening for HLH-related genes did not yield any patho- genic variants. The patient was put on high-dose steroid treatment with good clinical response. Progressive reduction of steroids upon dismission led to a novel flair of the febrile condition, requiring a novel admission. High dose steroid treatment was repeated with good clinical response. Considering the initial articular involvement, anakinra was also added for a period of 8 weeks. Upon progressive treatment sus- pension, another flair of fever associated with malaise, diffuse lym- phadenopathies, pruritus and arthralgias occurred. Screening for in- fectious aetiologies (including Epstein Barr Virus (EBV), Cytomegalovirus (CMV)) yielded negative results. Whole body mag- netic resonance imaging (MRI) revealed diffuse lymphadenopathies (Fig. 1A, upper panels). Positron emission tomography (PET) confirmed increased glucose metabolism in lymph nodes and spleen, suggestive of lymphoma (Fig. 1A, lower panels). In order to exclude lymphoid ma- lignancies, a lymph node excision was performed. The inguinal lymph node (1.2 cm in maximum diameter) that was removed showed a pre- served architecture, with reactive B-cell follicles and expanded para- cortex (Supplemental Text and Supplemental Fig. S1).

CasePreviousTesting: NGS (not specified if any other genes were sequenced).

GenotypingMethod: NGS

Variant: Next generation sequencing revealed the novel c.323G > T: p.R108L mutation in the linker region of the adaptor binding domain (ABD) of p110δ. monoallelic

CAID: CA576828

gnomAD: Largest allele frequency in gnomAD v2.1.1 is 0.00002823 (1/35426 alleles) in the Latino/Admixed population

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

DiseaseAssertion: APDS1

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

CasePreviousTesting: exome sequencing

GenotypingMethod: Diagnostic exome sequencing confirmed by Sanger

Variant: E1021K, heterozygous

CAID: CA145460

gnomAD: variant is absent in gnomAD v2.1.1

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

DiseaseAssertion: APDS1

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

CasePreviousTesting: exome sequencing

GenotypingMethod: Diagnostic exome sequencing confirmed by Sanger

Variant: E1021K, heterozygous

CAID: CA145460

gnomAD: variant is absent in gnomAD v2.1.1

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

DiseaseAssertion: APDS1

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

CasePreviousTesting: exome sequencing

GenotypingMethod: Diagnostic exome sequencing confirmed by Sanger

Variant: E1021K, heterozygous

CAID: CA145460

gnomAD: variant is absent in gnomAD v2.1.1

Case#: 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#: 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#: Wang_2018_P1, M, 2 y.o. (onset), origin in China

DiseaseAssertion: APDS

FamilyInfo: None reported

CasePresentingHPOs: RRTI (HP:0002205) Tonsillitis (HP:0011110) Diarrhea (HP:0002014) Lymphadenopathy (HP:0002716) Hepatomegaly (HP:0002240) Splenomegaly (HP:0001744) ASD (HP:0001631) Dacrocystitis (HP:0000620) Inguinal hernia (HP:0000023) autoimmune cytopenia (HP:0001973) increased transitional B cells (HP:0030381) increased plasmablasts (HP:0032128) decreased CD3 (HP:0045080) increased CD4 (HP:0032219) decreased CD4 naive (HP:0410378) increased CD4 EM (HP:0025625) decreased CD8 naive (HP:0410377) decreased T cells (HP:0005403) decreased b cells (HP:0010976) decreased CD4/CD8 (HP:0033222) decreased IgG (HP:0004315) increased IgM (HP:0003496)

HP:0002205, HP:0011110, HP:0002014, HP:0002716, HP:0002240, HP:0001744, HP:0001631, HP:0000620, HP:0000023, HP:0001973, HP:0030381, HP:0032128, HP:0045080, HP:0032219, HP:0410378, HP:0025625, HP:0410377, HP:0010976, HP:0004315, HP:0003496

CaseHPOFreeText: EBV DNA, decreased antibodies to Hepatitis-B, presence of autoantibodies, decreased CD19, increased CD8, increased CD8 CM, increased NK cells, increased CD8 EM

CaseNotHPOs: abnormal naive B cells (HP:0030370) abnormal memory B cells (HP:0030373) abnormal CD8 TEMRA (HP:0020177) abnormal wbc counts (HP:0011893) abnormal IgA (HP:0410240)

HP:0030370, HP:0020177, HP:0410240, HP:0011893, HP:0020177

CaseNotHPOFreeText: CMV-IgM negative, Fungus negative, abnormal CD4 CM, abnormal DNT

CasePreviousTesting: None reported

GenotypingMethod: WES + Sanger

PreviouslyPublished: Additional info published in 2022 (PMID:35799777)

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

ClinVarID: 88675

CAID: CA145460

gnomAD: Not present in gnomAD

SupplementalData: Phenotypic info in table S4

Case#: 20-year-old Spanish man

DiseaseAssertion: Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation

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

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

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

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

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

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

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

PreviouslyPublished: No

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

ClinVar: 161114

CAID: CA173999

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

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

ClinVar: 717363

CAID: CA6443934

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

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

Case#: Hui_2016, female, 2 yo (presentation), origin NR

DiseaseAssertion: APDS

FamilyInfo: variants verified in patient's parents, found to be de novo. It is unclear if case 2 and case 4 are related or unrelated.

CasePresentingHPOs: recurrent respiratory infections, enlargement of lymph node, hepatosplenomegaly, decreased number of native CD4 + T cells, inverted CD4 + /CD8 + T cell ratio and increased IgM, decreased IgA, decreased IgG,

HP:0002205, HP:0002716, HP:0001433, HP:0002720, HP:0032218, HP:0033222, HP:0002720, HP:0003496

CaseHPOFreeText: cytomegalovirus (CMV) or Epstein-Barr virus (EBV) viremia

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

CasePreviousTesting: NR

GenotypingMethod: WGS

PreviouslyPublished: NR

Variant: HOMOZYGOUS 3061G>A (E1021K)

ClinVarID: 88675

CAID: N/A

gnomAD: not found in v2.1.1

SupplementalData: unknown

Note: Full access to article denied. Info in annotation gathered from abstract. Also, please be advised the curator translated the article from Chinese to English, and mistranslations are possible.

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#: 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#: P1, M, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0000490 (Deeply set eye/Ocular depression), HP:0000680 (Delayed eruption of primary teeth/Teeth delay), HP:0000540 (Hypermetropia/Hyperopia), HP:0000483 (Astigmatism), HP:0007485 (Absence of subcutaneous fat/Lack of subcutaneous fat), HP:0000831 (Insulin-resistant diabetes mellitus), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0012371 (Hyperplasia of midface/Mild midface hypoplasia), HP:0000347 (Micrognathia), HP:0100678 (Premature skin wrinkling/Thin, wrinkled skin), HP:0001256 (Intellectual disability, mild/Mild impairment),

CaseHPOFreeText: Proband was noted to have readily visible veins and delayed bone age.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: N/A.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1615_1617del (p.Ile539del).

ClinVar: 60761.

CAID: CA344796.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: P2, M, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0000490 (Deeply set eye/Ocular depression), HP:0000680 (Delayed eruption of primary teeth/Teeth delay), HP:0007485 (Absence of subcutaneous fat/Lack of subcutaneous fat), HP:0000831 (Insulin-resistant diabetes mellitus), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0012371 (Hyperplasia of midface/Mild midface hypoplasia), HP:0000347 (Micrognathia), HP:0100678 (Premature skin wrinkling/Thin, wrinkled skin), HP:0001256 (Intellectual disability, mild/Mild impairment),

CaseHPOFreeText: Proband was noted to have readily visible veins and delayed bone age.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: N/A..

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1465G>A (p.Glu489Lys).

ClinVar: 60762.

CAID: CA344798.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: P3, F, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0001382 (Joint hypermobility/Hyperextensibility of joints), HP:0000490 (Deeply set eye/Ocular depression), HP:0000558 (Rieger anomaly), HP:0000680 (Delayed eruption of primary teeth/Teeth delay), HP:0000540 (Hypermetropia/Hyperopia), HP:0000483 (Astigmatism), HP:0000565 (Esotropia), HP:0007485 (Absence of subcutaneous fat/Lack of subcutaneous fat), HP:0000831 (Insulin-resistant diabetes mellitus), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0011220 (Prominent forehead), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0012371 (Hyperplasia of midface/Mild midface hypoplasia), HP:0000347 (Micrognathia), HP:0000138 (Ovarian cyst), HP:0001256 (Intellectual disability, mild/Mild impairment), HP:0003100 (Slender long bone/Gracile long bones)

CaseHPOFreeText: Proband was noted to have delayed bone age and mild impairment and/or speech delay

CaseNotHPOs: N/A.

CaseNotHPOFreeText: N/A..

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1945C>T (p.Arg649Trp).

ClinVar: 60763.

CAID: CA344799.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: P4, M, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0004322 (Short stature), HP:0004325 (Decreased body weight), HP:0040195 (Decreased head circumference), HP:0000490 (Deeply set eye/Ocular depression), HP:0000680 (Delayed eruption of primary teeth/Teeth delay), HP:0000540 (Hypermetropia/Hyperopia), HP:0007485 (Absence of subcutaneous fat/Lack of subcutaneous fat), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0011220 (Prominent forehead), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0012371 (Hyperplasia of midface/Mild midface hypoplasia), HP:0000347 (Micrognathia), HP:0100678 (Premature skin wrinkling/Thin, wrinkled skin),

CaseHPOFreeText: Proband was noted to readily visible veins, normal mental development.

Proband was not evaluated for insulin resistance, ovarian cysts, delayed bone age or gracile long bones.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Proband was noted to not have hyperextensibility of joints, inguinal hernia, Rieger anomaly, astigmatism, myopia, esotropia, diabetes, frequent illnesses, mild impairment and/or speech delay.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1945C>T (p.Arg649Trp).

ClinVar: 60763.

CAID: CA344799.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: P5, F, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0001382 (Joint hypermobility/Hyperextensibility of joints), HP:0000490 (Deeply set eye/Ocular depression), HP:0000558 (Rieger anomaly), HP:0000680 (Delayed eruption of primary teeth/Teeth delay), HP:0000545 (Myopia), HP:0007485 (Absence of subcutaneous fat/Lack of subcutaneous fat), HP:0000831 (Insulin-resistant diabetes mellitus), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0011220 (Prominent forehead), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0012371 (Hyperplasia of midface/Mild midface hypoplasia), HP:0000347 (Micrognathia),

CaseHPOFreeText: Proband was noted to have insulin resistance, frequent illnesses, ovarian cysts, normal mental development,

Proband was not evaluated for delayed bone age or gracile long bones.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Proband was noted to not have inguinal hernia, hyperopia, astigmatism, esotropia, thin, wrinkled skin, readily visible veins, mild impairment and/or speech delay.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1945C>T (p.Arg649Trp).

ClinVar: 60763.

CAID: CA344799.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: P6, M, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0000490 (Deeply set eye/Ocular depression), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0011220 (Prominent forehead), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0012371 (Hyperplasia of midface/Mild midface hypoplasia), (Micrognathia),

CaseHPOFreeText: Proband was not evaluated for inguinal hernia, Rieger anomaly, teeth delay, hyperopia, astigmatism, myopia, esotropia, lack of subcutaneous fat, insulin resistance, diabetes, thin, wrinkled skin, readily visible veins, frequent illnesses, ovarian cysts, normal mental development, mild impairment and/or speech delay, delayed bone age or gracile long bones.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Proband was noted to not have hyperextensibility of joints,

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1945C>T (p.Arg649Trp).

ClinVar: 60763.

CAID: CA344799.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: P7, F, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0000680 (Delayed eruption of primary teeth/Teeth delay), HP:0000483 (Astigmatism), HP:0007485 (Absence of subcutaneous fat/Lack of subcutaneous fat), HP:0000831 (Insulin-resistant diabetes mellitus), HP:0011220 (Prominent forehead), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0000347 (Micrognathia),

CaseHPOFreeText: : Proband was noted to have insulin resistance, ovarian cysts, normal mental development,

Proband was not evaluated for hyperextensibility of joints, ocular depression, hyperopia, myopia, esotropia, Triangular face, Mild midface hypoplasia, frequent illnesses, delayed bone age or gracile long bones.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Proband was noted to not have inguinal hernia, Rieger anomaly, thin, wrinkled skin, readily visible veins, mild impairment and/or speech delay,

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1945C>T (p.Arg649Trp).

ClinVar: 60763.

CAID: CA344799.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: P8, F, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0007485 (Absence of subcutaneous fat/Lack of subcutaneous fat), HP:0000831 (Insulin-resistant diabetes mellitus), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0011220 (Prominent forehead), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0012371 (Hyperplasia of midface/Mild midface hypoplasia), HP:0000347 (Micrognathia),

CaseHPOFreeText: Proband was noted to have insulin resistance, thin, wrinkled skin, readily visible veins, frequent illnesses, normal mental development,

Proband was not evaluated for hyperextensibility of joints, teeth delay, hyperopia, astigmatism, myopia, esotropia, ovarian cysts, delayed bone age or gracile long bones.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Proband was noted to not have inguinal hernia, Rieger anomaly, mild impairment and/or speech delay.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1943dup (p.Arg649ProfsTer5).

ClinVar: 60764.

CAID: CA344800.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: P9, M, Age of Report: N/A, Ethnicity: N/A.

CasePresentingHPOs: HP:0004325 (Decreased body weight), HP:0007485 (Absence of subcutaneous fat/Lack of subcutaneous fat), HP:0000831 (Insulin-resistant diabetes mellitus), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0000331 (Short chin/Small chin), HP:0000369 (Low-set ears), HP:0000347 (Micrognathia),

CaseHPOFreeText: Proband was noted to have insulin resistance, normal mental development, mild impairment and/or speech delay,

Proband was not evaluated for height/length, occipitofrontal circumference, hyperextensibility of joints, teeth delay, hyperopia, astigmatism, myopia, esotropia, thin, wrinkled skin, readily visible veins, frequent illnesses, ovarian cysts, delayed bone age or gracile long bones.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Proband was noted to not have inguinal hernia, ocular depression, Rieger anomaly, Prominent forehead, Mild midface hypoplasia,

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: NM_181523.3:c.1892G>A (p.Arg631Gln).

ClinVar: 126459.

CAID: CA347796.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: 14-year old female index patient, F, Age of Report:, Ethnicity: Austrian.

CasePresentingHPOs: HP:0001252 (Hypotonia), HP:0001945 (Fever), HP:0025297 (Prolonged), HP:0001873 (Thrombocytopenia), HP:0002155 (Hypertriglyceridemia), HP:0025435 (Increased circulating lactate dehydrogenase concentration/increased lactate dehydrogenase), HP:0003281 (Increased circulating ferritin concentration/markedly elevated ferritin), HP:0012156 (Hemophagocytosis),

CaseHPOFreeText: Here we investigated a 14-year old female index patient, born to non-consanguineous healthy Austrian parents, who was hospitalized with severe hypotonia and prolonged fever. She had neither lymphadenopathy nor hepatosplenomegaly, and no infectious agent was found. Initial laboratory findings showed a mild thrombocytopenia, hypertriglyceridemia, increased lactate dehydrogenase (LDH) and markedly elevated ferritin (Table 1 and Figure 1A), prompting work up for hemophagocytic lymphohistiocytosis (HLH). Hemophagocytosis was indeed visible in the bone marrow aspirate (Figure 1B). Soluble CD25 was mildly elevated at 2204 U mL-1 (Table 1) but below the levels typically seen in HLH.6 NK-cell activity as measured by CD107a expression upon stimulation was in the low normal range in the initial diagnostic (Table 1). The presence of fever, hypertriglyceridemia, hyperferritinemia and hemophagocytosis, did not allow the diagnosis of HLH, but gave evidence of macrophage activation in the context of a hyperferritinemic inflammatory syndrome (Table 1).6We initiated treatment with dexamethasone, leading to clinical improvement and normalization of LDH and ferritin levels. Tapering of dexamethasone resulted in clinical deterioration and rise in ferritin (Figure 1A), and was accompanied by the development of autoimmune neutropenia as documented by HNA-1b antibodies. As the disease was distinct from classical HLH,6 we decided to treat the patient with recombinant human anti-IL-1β (Anakinra, 100 mg twice daily) in combination with dexamethasone, rather than using the etoposide-based HLH-94 protocol. We discontinued dexamethasone treatment after eight weeks and, one month later, reduced the Anakinra dose to a maintenance dose of 100 mg daily. The patient has remained clinically stable and is currently receiving Anakinra (decreased to 60 mg once daily) without any inflammatory manifestations. Immunological characterization of patient peripheral blood in the asymptomatic phase after ceasing dexamethasone revealed reduced absolute natural killer (NK)-cell counts and low frequency of monocytes, and slightly low absolute lymphocyte counts (Table 1)..

CaseNotHPOs: N/A.

CaseNotHPOFreeText: She had neither lymphadenopathy nor hepatosplenomegaly, and no infectious agent was found.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES.

Variant: Variant 1: NM_001282426.2:c.145C>A (p.Arg49Ser) . Variant 2: NM_001282426.2:c.3254A>G (p.Asn1085Ser).

ClinVar: Variant 1: 1675220. Variant 2: 1675219.

CAID: Variant 1: CA4429087. Variant 2: CA368817268.

gnomAD: Variant 1: Frequency: 0.001519. Link: https://gnomad.broadinstitute.org/variant/chr7-106867706-C-A?dataset=gnomad_r4. Variant 2: N/A.

VariantEvidence: N/A.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: A.1, F, Age of Report: 9 y.o., Ethnicity: European-American.

CasePresentingHPOs: HP:0012378 (Fatigue), HP:0001878 (Hemolytic anemia), HP:0006510 (Chronic pulmonary obstruction/early obstructive pulmonary impairment), HP:0003651 (Foam cells), HP:0004313 (Decreased circulating antibody concentration/Hypogammaglobulinemia), HP:0001873 (Thrombocytopenia), HP:0001888 (Lymphopenia), HP:0001880 (Eosinophilia), HP:0100721 (Mediastinal lymphadenopathy), HP:0034388 (Hilar lymph node enlargement), HP:0001744 (Splenomegaly), HP:0004387 (Enterocolitis), HP:0002014 (Diarrhea), HP:0002027 (Abdominal pain), HP:0002583 (Colitis), HP:0005425 (Recurrent sinopulmonary infections), HP:0410018 (Recurrent ear infections), HP:0001581 (Recurrent skin infections), HP:0000010 (Recurrent urinary tract infections), HP:0001742 (Nasal congestion), HP:0011010 (Chronic), HP:0000964 (Eczematoid dermatitis/Eczema),

CaseHPOFreeText: A female patient (hereafter called A.1) from a European-American family presented at nine years of age with fatigue and hemolytic anemia followed by early obstructive pulmonary impairment. A subsequent chest CT scan revealed bilateral nodular infiltrates and areas of patchy, peripheral-basal consolidation in lungs, and histological examination revealed a pattern of interstitial CD3+ lymphocytic infiltration, foamy histiocytes, scattered noncaseating granulomas, and luminal obstruction initially characterized as cryptogenic organizing pneumonia (Fig. 1a–b). Further follow up and analysis revealed clinical progression to hypogammaglobulinemia, thrombocytopenia, various lymphopenias, eosinophilia, mediastinal and hilar lymphadenopathy, and splenomegaly (Table 1). More recently, at sixteen years of age, patient A.1 developed enterocolitis with diarrhea and abdominal pain. Histological assessment of gut tissue revealed interstitial infiltrate of more than 25 CD3+ lymphocytes per 100 epithelial cells (Fig. 1b, bottom). Episodes of pneumonitis and colitis continue to recur intermittently, have an apparent noninfectious etiology (with separate incidences of infectious colitis), and respond to pulse doses of corticosteroids and steroid-sparing measures including mycophenolate mofetil.

The childhood of patient A.1 was remarkable for recurrent sinopulmonary, ear, skin, and urinary tract infections (commonly with S. aureus), chronic nasal congestion, and eczema. Additional episodes of colitis were sometimes associated with stool cultures positive for C. difficile and Salmonella. Vaccination responses were protective for tetanus, borderline protective for diphtheria, and protective for 4 of 23 pneumococcal strains. Warm autoimmune hemolytic anemia at nine years of age (preceding the initial pneumonitis by several months) was treated with steroids and blood transfusions; a recurrence of autoimmune cytopenias at seventeen years prompted CD20+ B cell depletion with rituximab. Patient A.1 is currently treated with immunoglobulin replacement therapy to restore humoral protection and mycophenolate mofetil to suppress inflammation.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: N/A.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: WES and Sanger.

Variant: NM_001282426.2:c.3062G>C (p.Arg1021Pro).

ClinVar: 1675218.

CAID: CA164129242.

gnomAD: Frequency: 0.00002988. Link: https://gnomad.broadinstitute.org/variant/chr7-106905140-G-C?dataset=gnomad_r4.

VariantEvidence: N/A.

CaseAddInfo: Patient A.1 inherited an allele from her healthy mother in whom a single base-pair deletion causes a frameshift beginning at R982 of p110γ, and an allele from her healthy father in whom a missense mutation results in an R1021P amino acid substitution in the kinase domain.

CasePMIDs: N/A.

Case#: 15-year-old female, F, Age of Report: 15 y.o., Ethnicity: From China.

CasePresentingHPOs: HP:0001511 (Intrauterine growth retardation/Intrauterine growth restriction), HP:0004322 (Short stature), HP:0000684 (Delayed eruption of teeth/teething delay), HP:0000858 (Irregular menstruation/irregular menstrual cycle), HP:0001007 (Hirsutism), HP:0000820 (Abnormality of the thyroid gland/thyroid disease), HP:0005328 (Progeroid facial appearance/Progeroid facial appearance), HP:0000545 (Myopia), HP:0000678 (Dental crowding/overcrowded teeth), HP:0000855 (Insulin resistance)

CaseHPOFreeText: Proband was noted to have "characteristic facial gestalts/"characteristic facial dysmorphim", low weight at birth,

The proband was admitted to our department due to irregular menstrual cycle and hirsutism with short stature, who had a history of intrauterine growth restriction and presented with short stature, teething delay, characteristic facial gestalts, hirsutism, and thyroid disease. Whole-exome sequencing and Sanger sequencing revealed c.1960C > T, a novel de novo nonsense mutation, leading to the termination of protein translation (p. Gln654*).

This is the first case report of SHORT syndrome complicated with thyroid disease in China, identifying a novel de novo heterozygous nonsense mutation in PIK3R1 gene (p. Gln654*).

The phenotypes are mildly different from other cases previously described in the literature, in which our patient presents with lipoatrophy, facial feature, and first reported thyroid disease. Thyroid disease may be a new clinical symptom of patients with SHORT syndrome.

The patient was a girl born to a physically healthy and non-consanguineous couple by spontaneous delivery at the 37th week. Birth weight was 2150 g (− 3.39SD) and birth length was 44 cm (− 3.41SD), indicating that the patient had intrauterine growth restriction (IUGR). The proband also had teething delay, getting the first tooth at 1 year old. During childhood, the patient was bothered by short stature. Psychomotor and speech development was normal. The height of proband’s father and mother was 168 cm and 155 cm respectively. The patient also had a healthy 20-month-old brother.

At the age of 15 years and 4 months, the proband was referred to our department due to irregular menstrual cycle and hirsutism with a height of 149 cm (− 2.04SD), weight of 43 kg (− 1.22SD) and body mass index (BMI) of 19.4 kg/m2. The height of the proband had remained 149 cm, ever since 13 years old. Physical examination showed a triangular-shaped face, small chin, large low-set ears, thin lip, downturned mouth, obvious beard and bushy eyebrows (Fig. 1a,b,c,d). Oral examination showed overcrowded and irregular teeth, hypodontia, and severe dental caries (Fig. 1g). Pubertal development was assessed according to the Tanner stage, with pubic hair at PH5 stage and breast at B2 stage. The second phalanx of little finger in the left hand was short and thicken, which was confirmed with X-ray (Fig. 1e,f). Ultrasound of neck showed diffuse thyroid disease. Ultrasound biomicroscopy of the eyes, examination of ocular fundus, abdominal ultrasound, reproductive system ultrasound, and chest X-ray were normal. The cranial magnetic resonance imaging (MRI) indicated a small posterior pituitary.

Not evaluated on the proband: OFC at birth, thin, wrinkled skin with readily visible veins, inguinal hernia,

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Proband was noted to not have: Hyperextensibility of joints, ocular depression, Riegar anomaly, lipoatrophy, glaucoma, hyperopia, astigmatism, delayed bone age, intellectual deficiency, speech delay, diabetes, hearing loss, frequent infections, congenital heart diseases, pulmonary stenosis and ovarian cysts.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: Whole-exome sequencing and Sanger sequencing.

Variant: NM_181523.3:c.1960C>T (p.Gln654Ter).

ClinVar: N/A.

CAID: CA359884699.

gnomAD: N/A.

VariantEvidence: A novel de novo heterozygous nonsense mutation in the PIK3R1 gene (p. Gln654*) was found in the proband.

WES was performed to make a clear clinical diagnose. The candidate variants were first screened by a minor allele frequency < 3% against the 1000 Genomes Project, the NHLBI exome variant server or in 50 HapMap control exomes. Then, short stature, facial abnormalities were selected as the filtering clinical symptoms to analyze the screened candidate variants. According to the guidelines recommended by the American College of Medical Genetics and Genomics, a pathogenic variant of PIK3R1 gene was identified to contribute to the patient’s conditions. Sequencing result indicated c.1960C > T of PIK3R1 gene a novel nonsense mutation, leading to the termination of protein translation (p. Gln654*), which was confirmed by sanger sequencing (Fig. 2). In addition, direct sequencing results showed the genotypes of proband’s parents were wild-type, suggesting it was a de novo mutation.

CaseAddInfo: The height of proband’s father and mother was 168 cm and 155 cm respectively. The patient also had a healthy 20-month-old brother.

CasePMIDs: N/A.

Case#: patient, M, Age of Report: newborn, Ethnicity: Korean.

CasePresentingHPOs: HP:0004322 (Short stature), HP:0004325 (Decreased body weight), HP:0040195 (Decreased head circumference), HP:0003074 (Hyperglycemia), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0011220 (Prominent forehead), HP:0000490 (Deeply set eye/Ocular depression), HP:0009125 (Lipodystrophy), HP:0000023 (Inguinal hernia), HP:0001642 (Pulmonic stenosis), HP:0001684 (Secundum atrial septal defect/ASD secundum), HP:0000684 (Delayed eruption of teeth)

CaseHPOFreeText: To the best of our knowledge, this is the first case report of SHORT syndrome with TNDM.

The patient was a newborn male and the only child of a healthy non-consanguineous Korean couple with a non-contributory family history. The height of his father and mother was 170 cm (−0.70 SD score) and 160 cm (−0.04 SD score), respectively. They had no dysmorphic features. The mother had regular antenatal check-up and did not have any history of medical and obstetric problems during pregnancy. He was born at 38 weeks of gestation but displayed features of IUGR during pregnancy. His birth weight was 1.8 kg (<3rd percentile), length 44 cm (<3rd percentile), and head circumference 31 cm (<3rd percentile) according to the Korean reference for birth weight based on gestational age and sex. The initial blood glucose level was 70 mg/dl. The baby was exclusively breastfed starting on day 3 and was in generally good condition. However, blood glucose level was between 218 and 263 mg/dl at 5 day of age. At the age of 20 day, his blood glucose level was still high (205–260 mg/dl), and the infant was referred to the endocrine clinic for persistent hyperglycemia assessment. On physical examination, several dysmorphic features (triangular-shaped face, prominent forehead, ocular depression, lipodystrophy at the lumbar region) and inguinal hernia were present. The systolic and diastolic blood pressure measurements were 74 and 42 mmHg, respectively. The serum c-peptide and insulin levels were 2.83 ng/ml (normal: 1.0–3.5) and 120 μU/ml (normal: 2.8–13.5), respectively. Baseline chemistry including serum blood urea nitrogen was 15.3 mg/dl (normal: 7.0–20.0), creatinine 0.9 mg/dl (normal: 0.6–1.2), aspartate aminotransferase 38 U/L (normal: 14–40), and alanine aminotransferase 16 U/L (normal: 9–45), as well as complete blood count profile were within normal range. Urinalysis showed no glucose or ketones. There was no sign of ketoacidosis and the patient had no type 1 diabetes autoantibodies (antibodies against glutamic acid decarboxylase, islet cell, islet antigen-2, and insulin). The liver and pancreas ultrasonography revealed no structural abnormality. Echocardiography at the age of 1 month confirmed mild pulmonary stenosis and ASD secundum (2 mm) which did not require surgical intervention. Neonatal diabetes mellitus (NDM) was suspected on the basis of hyperglycemia occurring within the first month of life that lasted for >2 weeks and required insulin therapy. At age of 25 day, clinical exome sequencing was performed to identify the genetic cause of NDM.

To monitor the glycemic level, his blood glucose was measured at the beginning of each feeding session. The patient was treated with subcutaneous insulin, and blood glucose level gradually stabilized. The blood glucose levels ranged from 110–250 mg/dl during the next 10 days. An adequate glucose level was achieved at 6 weeks of age without insulin treatment. His body weight was 4.4 kg (<3rd percentile) and his length was 61.6 cm (<3rd percentile) at 10 months of age. The patient experienced no hyperglycemic episode and the glycated hemoglobin was 5.0% and insulin level 2.8 μU/ml. At 10 months of age, the patient had no teeth erupted in the oral cavity.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Urinalysis showed no glucose or ketones. There was no sign of ketoacidosis and the patient had no type 1 diabetes autoantibodies (antibodies against glutamic acid decarboxylase, islet cell, islet antigen-2, and insulin). The liver and pancreas ultrasonography revealed no structural abnormality.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: TruSight One sequencing panel and Sanger sequencing.

Variant: NM_181523.3:c.1945C>T (p.Arg649Trp).

ClinVar: 60763.

CAID: CA344799.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo: Segregation analysis could not be performed due to the unavailability of parental samples.

CasePMIDs: N/A.

Case#: proband, M, Age of Report: 8 y.o., Ethnicity: British.

CasePresentingHPOs: HP:0008846 (Severe intrauterine growth retardation), HP:0004322 (Short stature), HP:0004325 (Decreased body weight), HP:0040195 (Decreased head circumference), HP:0001510 (Growth delay), HP:0011968 (Feeding difficulties/behavioral feeding difficulties), HP:0001263 (Global developmental delay/psychomotor development delay), HP:0000252 (Microcephaly), HP:0000684 (Delayed eruption of teeth/Dentition), HP:0100543 (Cognitive impairment/delayed intellectual development), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0011220 (Prominent forehead), HP:0000582 (Upslanted palpebral fissure/upward-slanting palpebral fissures), HP:0000430 (Underdeveloped nasal alae/thin alae nasi), HP:0100678 (Premature skin wrinkling/Thin, wrinkled skin), HP:0001187 (Hyperextensibility of the finger joints), HP:0010485 (Hyperextensibility at elbow), HP:0009125 (Lipodystrophy)

CaseHPOFreeText:The proband, 8 years of age, is the first child of non-consanguineous Caucasian parents. There are no manifestations of SHORT syndrome in the family. There is no family history of microcephaly or intellectual disability. Following an otherwise uneventful pregnancy, delivery was induced at 38 weeks of gestation on discovery of severe intrauterine growth restriction. His birth weight was 1.97 kg (<0.4th centile, −3.7 SD).

Despite adequate nutritional intake, the patient's growth was significantly delayed. At 12 months of age, his weight was 6.88 kg (<0.4th centile, −3.2 SD), length was 69.5 cm (1st centile, −2.98 SD) and head circumference was 39.5 cm (<0.4th centile, −5.26 SD). Enteral tube feeding was initiated at 9 months of age, which the patient continues to remain dependent on today. Despite extensive investigation of the proband's feeding disorder, no organic cause was identified, and he was diagnosed with behavioral feeding difficulties. Follow-up consultations revealed a persistent development delay and sustained striking microcephaly. Dentition did not start until the age of 2.5 years. At 6 years of age, his weight was 16.2 kg (1st centile, −2.39SD), length was 105.4 cm (1st centile, −2.47 SD) and head circumference was 43.8 cm (<0.4th centile, −6.16 SD). Skeletal survey and extensive endocrine investigation did not find any abnormalities. The patient has not been formally diagnosed with diabetes and is awaiting an oral glucose tolerance test.

Intellectual and psychomotor development is moderate to severely delayed. The patient first walked at 20 months, first smiled at 3 months and spoke his first words aged 3 years. At his current age of 8 years, he attends a special needs school and requires substantial multidisciplinary support. Magnetic resonance imaging of the brain and electroencephalogram performed at 12 months of age was normal. Neurometabolic investigation was also normal. Recurrent ophthalmology investigations revealed a myopic left eye and hypermetropic right eye at 4 years of age. No anterior chamber defects were noted and his ocular pressure was reported as normal. His hearing was formally assessed and reported as normal.

Facial dysmorphic features are subtle but present (see Figure 2): triangular face, prominent forehead, broad eyebrows, slight upward-slanting palpebral fissures, and hypoplastic alae nasi leading to an impression of low columnella nasi. The patient has thin, wrinkled skin with visible veins, most prominently seen on his chest wall. He has hyperextensibility in his finger and elbow joints. Of note, local lipodystrophy of his proximal finger phalanges is also observed.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: Skeletal survey and extensive endocrine investigation did not find any abnormalities. The patient has not been formally diagnosed with diabetes and is awaiting an oral glucose tolerance test.

No anterior chamber defects were noted and his ocular pressure was reported as normal.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: Chromosome breakage studies, Angelman methylation studies and a 60 gene developmental delay and epilepsy panel were normal. Comparative genomic hybridization microarray identified a likely benign maternally inherited Xp11.4 duplication (GRch X:38646145-38687854). Trio-exome sequencing revealed a de novo heterozygous missense variant, c.1456G>A (p.Ala486Thr) in PIK3R1 (NM_181523.3).

Variant: NM_181523.3:c.1456G>A (p.Ala486Thr).

ClinVar: N/A.

CAID: CA359881414.

gnomAD: N/A.

VariantEvidence: N/A.

CaseAddInfo:N/A.

CasePMIDs: N/A.

Case#: 17-year-old female, F, Age of Report:17 y.o., Ethnicity: Cuban descent.

CasePresentingHPOs: HP:0001510 (Growth delay), HP:0004322 (Short stature), HP:0000696 (Delayed eruption of permanent teeth/secondary tooth eruption delay), HP:0000858 (Irregular menstruation/irregular menses), HP:0100607 (Dysmenorrhea), HP:0012384 (Rhinitis), HP:0002099 (Asthma), HP:0001025 (Urticaria), HP:0031796 (Recurrent), HP:0000403 (Recurrent otitis media), HP:0010606 (Hordeolum/hordeolums), HP:0031796 (Recurrent), HP:0012204 (Recurrent vulvovaginal candidiasis/vaginal candidiasis), HP:0032168 (Clostridium difficile colitis), HP:0004315 (Decreased circulating IgG concentration/low IgG levels), HP:0045082 (Decreased body mass index/low BMI), HP:0001382 (Joint hypermobility/hyperextensible joints), HP:0011220 (Prominent forehead), HP:0000325 (Triangular face/Facial dysmorphim Triangular shape), HP:0009765 (Low hanging columella), HP:0000219 (Thin upper lip vermilion/thin upper lip), HP:0007495 (Prematurely aged appearance/aged appearance), HP:0010976 (B lymphocytopenia/low absolute B cells), HP:0410376 (Increased proportion of naive CD8 T cells/elevated CD8 T cell),

CaseHPOFreeText: This is a 17-year-old female of Cuban descent, born to nonconsanguineous parents at 36 weeks gestational age to an uncomplicated pregnancy. Her birth weight and length were average for gestational age (7 pounds, 18 in.). She presented with a history of growth delay, short stature, and secondary tooth eruption delay. She measured below her growth curve at 1 year of age. She had growth hormone testing which resulted normal; however, she received growth hormone therapy from 3 to 10 years of age with a good response. At that time, she underwent genetic testing for short stature; however, no genetic causes of short stature were found. She has a history of irregular menses and dysmenorrhea with work-up for possible etiologies, including polycystic ovarian syndrome (PCOS), resulting negative. She has met all developmental milestones appropriately and has normal cognition.

She has nonallergic rhinitis, mild intermittent asthma, and acute recurrent urticaria. Her history of infections includes recurrent episodes of otitis media since she was toddler requiring placement of 3 sets of ear tubes and tonsillectomy and adenoidectomy. She has a history of recurrent hordeolums and frequent episodes of vaginal candidiasis attributed to the many courses of antibiotics she has received for her various infections. She had one episode of Clostridium difficile colitis 6 months prior to presentation to our clinic. Prior immunologic evaluation at a different institution at 9 years of age was remarkable for low IgG levels, which ranged from 435 to 511 mg/dL [ref 759–1549 mg/dL]. A skin prick test to aeroallergens resulted negative. She did not receive intravenous immunoglobulin (IVIG) or subcutaneous immunoglobulin therapy at that time.

Her physical exam was relevant for short stature (1 percentile, z = − 2.33), low weight for age (< 1 percentile, z = − 2.69), low BMI (15 percentile), and hyperextensible joints. Her facial features were significant for a prominent forehead, triangular face, low-hanging columella, thin upper lip, and aged appearance. Given concern for immune deficiency, a complete immune evaluation was obtained. Her results revealed hypogammaglobulinemia (IgG of 610 mg/dL [ref 694–1618 mg/dL]), with IgM and IgA within the reference range. The lymphocyte subset panel revealed remarkably low absolute B cells (34 cells/μL [ref 130–800 cells/μL]) and percentage (1% [ref 9–30%]). CD4 T cells were within the reference range, and CD8 T cell counts (1091 cells/μL [ref 240–890 cells/μL]) and percentage (40% [ref 17–36%]) were elevated. She had low CD4:CD8 ratio (0.84 [ref 1.00–2.90]). Follow-up B cell panel corroborated the finding of low absolute B cells (70 cells/μL [ref 100–500 cells/μL]) and revealed increased transitional B cells (6.6% CD19 + CD27-CD21-IgM+ [ref 0.5–2.8%]) and naïve B cells (5.9% CD19 + CD27-CD21-CD38- [ref 0.3–2.3%]). ImmunoCAP IgE to aeroallergens was negative, and total IgE was 2 kU/L [ref < 114 kU/L]. Vaccine boosters to S. pneumoniae, H. influenzae, diphtheria, and tetanus were given. Subsequent titers revealed protective antibodies to S. pneumoniae, H. influenzae, and diphtheria and absent response to tetanus. Her lymphocyte mitogen proliferation showed normal lymphocyte responses to phytohaemagglutinin, concanavalin A, and pokeweed mitogen. Viral testing was not performed. At this time, the decision was made to start amoxicillin prophylaxis and monthly IVIG replacement therapy.

After initiating treatment with IVIG, our patient did not have new episodes of ear or sinus infections. IgG levels have remained within normal limits with monthly IVIG therapy. Given the finding of a PIK3R1 pathogenic variant and its known associations with SHORT syndrome, she was referred to ophthalmology and endocrinology. Of note, she started complaining of frequent headaches, not associated with administration of IVIG. Brain and cervical spine MRI revealed a Chiari I malformation for which she is being evaluated by neurosurgery.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: She did not have protective titers to tetanus, diphtheria, pneumococcus, or influenzae.

CasePreviousTesting: N/A.

CaseMethod1: N/A.

CaseMethod2: N/A.

CaseGenotypingMethod: Invitae primary immunodeficiency 207-gene panel was obtained.

Variant: NM_181523.3:c.1425+1G>C (n.336+1G>C).

ClinVar: 156009.

CAID: CA170736.

gnomAD: N/A.

VariantEvidence: Results revealed a heterozygous “pathogenic variant” in PIK3R1 (c.1425 + 1G > C) with an autosomal dominant mode of inheritance in association with APDS2. This variant is a missense point mutation affecting a donor splice site in intron 11, resulting in exclusion of exon 11 (Fig. 1). Her parents are not carriers of this pathogenic variant, indicating this is a de novo mutation.

CaseAddInfo: N/A.

CasePMIDs: N/A.

Case#: 33-year-old Chinese adult female

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

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

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

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

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

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

CasePreviousTesting: NR

GenotypingMethod: Whole-exome sequencing

PreviouslyPublished: No

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

ClinVar: 60763

gnomAD: NR

SupplementalData: Table 1, 2, 3, 4

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

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

FamilyInfo: Table 1

CasePresentingHPOs: HP:0001433, HP:0002716

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

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

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

DiseaseAssertion: Hashimoto disease

Variant: c.379T >G variant in CTLA4

CasePresentingHPOs: HP:0034954

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

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

DiseaseAssertion: Spondylarthritis

Variant: c.379T >G variant in CTLA4

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

DiseaseAssertion: Evans syndrome (ITP and AIHA)

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

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

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

DiseaseAssertion: Hashimoto disease

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

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

CaseHPOFreeText: Ear, nose and throat infections; Dermatitis

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

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

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

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

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

DiseaseAssertion: Inflammatory polyarthritis

FamilyInfo: Table 1

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

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

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

Case#: 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

Gene Name: DICER1 PMCID: PMC5443331 PMID: 28323992 HGNCID: not found Inheritance Pattern: autosomal dominant Disease Entity: thyroid cancer and familial multinodular doiter Mutation: germline loss-of-function mutation Zygosity: not provided Variant: c.1870C>T; p.Arg624a, c.1870C>T; p.Arg624a, c.1870C>T; p.Arg624a, c.1870C>T; p.Arg624a, c.3726C>A; p.Tyr1242a, c.3675C>G; p.Tyr1225a, c.3675C>G; p.Tyr1225a Family Information: 145 individuals with a DICER1 germline mutation and 135 controls from 48 families Case: family members used; both males and females used and no significant differences seen among sex; ages range from 20-40 with carriers being significantly younger than controls; no significant differences seen among ethnicity but participants located from the US, UK, and Great Britain CasePresentingHPOs: thyroid cancer or MNG diagnosis common to those with a DICER! mutation but with no chemotherapy or radiation treatment yet CasePreviousTesting: tested levels of thyroid-stimulating hormone, thyroxine, thyroxine-binding globulin, and serum albumin; thyroid palpation; thyroid ultrasound; Sanger or next-generation sequencing assays gnomAD: n/a Mutation Type: missense

PatientID: None

KindredID: 1

Case: Sex Unknown, Age Unknown, Ethnicity Unknown

DiseaseAssertion: Adrenal pheochromocytoma

FamilyInfo: The proband was part of a cohort of apparently sporadic cases of pheochromocytoma/ paraganglioma, implying this individual had no family history of VHL disease or pheochromocytoma.

CasePresentingHPOs: HP:0006748 (Adrenal Pheochromocytoma)

CaseHPOFreeText: N/A

CaseNotHPOs: HP:0002668 (Paraganglioma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: RET, SDHB, SDHC, and SDHD

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: ex. p.R161Q (c.482G>A)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: ex. 182983, https://www.ncbi.nlm.nih.gov/clinvar/variation/182983/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: R161Q(c.482G>A)

MultipleGeneVariants: N/A

CaseAJV: 17 years diagnosis, Australia

DiseaseAssertion: Hypertrophic Cardiomyopathy

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

CasePresentingHPOs: HP:0001639, HP:0006536

(Hypertrophic cardiomyopathy, Obstructive lung disease)

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

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CasePreviousTesting: See Table 1

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

Variant:NM_000257.3:c.1954A>G (p.Arg652Gly)

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

gnomAD: Not in gnomAD

Multiple Gene Variants:

MYBPC3 Variant

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

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

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