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#: 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#: Case 1, male

DiseaseAssertion: APDS

FamilyInfo: non-related Caucasian parents

CaseHPOFreeText: Suffered from Haemophilus b epiglottitis at the age of 2. He had received only one vaccine dose against diphtheria, tetanus, and poliomyelitis, due to parental choice, and had a history of recurrent respiratory tract infections. Biological features at diagnosis included: reduced serum levels of IgG2 and IgG4, normal IgA, IgG1, and IgG3 levels, and elevated IgM levels. The total lymphocyte count was normal but with quantitatively decreased T cells and CD21+ B cells, and an immune profile in favor of excessive memory CD4+ T cells. Later on, he suffered from frequent respiratory tract infections and a chest computed-tomography showed bronchiectasis at the age of 4. Digestive symptoms also appeared at the age of 4 when he presented with hematochezia related to colic malacoplakia (polypoid mucosal infiltration with histiocytes containing intra-cytoplasmic inclusions stained by Michaelis-Gutmann coloration) and lymphoid hyperplasia, which were both diagnosed on gastro-intestinal biopsies. From the age of 8 onward, he began to experience diarrhea that was linked to infections by Giardia and Cryptosporidium (diagnosed through acid-fast staining performed on stool samples). The cryptosporidiosis evolved toward a chronic infection with multiple episodic recurrences. He then developed celiac-mesenteric and hepatic lymphadenopathy, chronic ileitis with malabsorption syndrome, colitis with exudative diarrhea, and cholestasis with mild hepatic cytolysis due to grade II hepatic fibrosis (chronic hepatitis with inflammation and portal fibrosis, Metavir scoring F2-F3) with no sclerotic cholangitis. A recurrence of cryptosporidiosis accompanied by a C. difficile infection led to another intensive care unit stay, at the age of 9. Lymphadenopathy increased thereafter, with the appearance of hepatosplenomegaly, but lymphoma was not diagnosed on biopsies. He also developed cutaneous candidiasis, asymptomatic EBV reactivation (age 10) and persistent shedding of Adenovirus in the stools without viremia. The biological phenotype also worsened with time, leading to a TlowBlowNK+ CID. The evolution of the main immunologic parameters is shown in Fig. 1. Further analyses identified the following: absence of class-switched B cells, low and temporary immunoglobulin response to tetanus and diphtheria antigens and no response to Pneumococcus or Haemophilus b antigens, no lymphocyte proliferation to antigens after revaccination, and low or nonexistent proliferation with mitogens. Immunological explorations performed up to the age of 9 did not provide us with the precise diagnosis: IL-6 and IL-10 levels, double negative T cells, ADA and PNP levels, class I and II HLA molecules and CD40L, sequencing of CD40L and RAG1/2 genes, and Vβ repertoire of T cells were all normal. Proliferation of B cells with CD40L and IL-4 was present but weak.

CasePreviousTesting: No previous testing

GenotypingMethod: we decided to sequence PIK3CD in our patient. Sanger?

Variant: the E1021K mutation was identified.

CAID: CA145460

gnomAD: Absent from gnonAD v2.1.1

Case#: Case 1

DiseaseAssertion: APDS

FamilyInfo: no familial history of PID

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

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

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

Variant: E1021K

CAID: CA145460

gnomAD: absent in gnomAD v2.1.1

SupplementalData: Clinical features of patients 3-8 in supplementary

Case#: Dulau_Florea_2018_10, M, 7 y.o. (report), origin in ?

DiseaseAssertion: APDS

FamilyInfo:

CasePresentingHPOs: EBV viremia (HP:0020072), Varicella after live vaccine (HP:0032170), sinopulmonary infection (HP:0005425), lymphadenopathy (HP:0002716), nodular lymph hyperplasia in the intestine (HP:0011956), splenomegaly (HP:0001744),<br /> elevated IgM (HP:0003496), decreased IgG (HP:0004315), decreased IgA (HP:0002720), Granulocytic hyperplasia (HP:0012138),

HP:0020072, HP:0032170, HP:0005425, HP:0002716, HP:0011956, HP:0001744, HP:0003496, HP:0004315, HP:0002720, HP:0012138

CaseHPOFreeText: abnormal IgE, decreased T4/T8 ratio, DAT autoantibodis present, 95% cellularity BM morphology, B cell expansion observed

CaseNotHPOs: lymphoma (HP:0002665)

CaseNotHPOFreeText:

CasePreviousTesting:

GenotypingMethod: unknown

PreviouslyPublished:

Variant: heterozygous NM_005026.5:c.3061G>A (p.E1025G)

ClinVarID: 422410

CAID: CA16617216

gnomAD: Not present in gnomAD

SupplementalData: Phenotypic info in supplemental table E2