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    1. ZZ.II.1

      Case#: Schwab_2018_Patient_129, 16 y.o. (onset) and 19 y.o. (death), male, origin in Germany

      DiseaseAssertion: CTLA4 Haploinsufficiency

      FamilyInfo: mother (patient 128) was heterozygous with same variant. This patient was recored as 'affected' but type-1 diabetes was the only phenotype reported.

      CasePresentingHPOs: HP:0001973, HP:0001945, HP:0001744, HP:0001058, HP:0004313, HP:0004315, HP:0002720, HP:0031378, HP:0002240, HP:0002716, HP:0002093, HP:0000964, HP:0001047 (ITP, fever, splenomegaly, wound healing disorder, hypogammaglobulinemia, low IgG, Low IgA, lymphoproliferation, hepatomegaly, lymphadenopathy, respiratory involvement, eczema, atopic dermatitis)

      CaseHPOFreeText: organ infiltration (brain and lung), GLILD, neurological involvement,

      CaseNotHPOs: large phenotype table with unreported symptoms in table S1

      CaseNotHPOFreeText: n/a

      CasePreviousTesting: unknown

      GenotypingMethod: unknown

      PreviouslyPublished: n/a

      Variant: NM_005214.5(CTLA4):c.151C>T (p.Arg51Ter)

      ClinVarID: 161109

      CAID: CA173992

      gnomAD: not found

      SupplementalData: extensive data in S1

      Note: functionally tested using transendocytosis

    1. A 27-month-old girl was referred due to recurrent fever, arthritis, and erythema nodosum to the rheumatology clinic of Mofid Children’s Hospital (Tehran, Iran). She was the second alive child of consanguineous marriage (G2P2L2) with a 3800-gram birth weight and a history of neurodevelopmental delays in walking (at the age of 21 months) and speaking (at the age of 24 months). There is no positive point in the family history, except for the mother, who had hypothyroidism and a history of frequent respiratory infections in childhood.She had a history of several hospital admissions after her birth. First, she was admitted at two months old with a fever and high levels of ESR and CRP. She received antibiotics for five days and was discharged with no signs or symptoms but still had high ESR and CRP.At 8 months old, she was evaluated due to failure to thrive (FTT). During patient examinations, the low heart rate, muffled heart sound, and massive pericardial effusion were found in her echocardiography. The pericardial effusion caused her to be hospitalized for 16 days in the intensive care unit (ICU). Pericardial effusion was tapped without any infectious resources. Pericardial effusion was treated with prednisolone, and she was discharged in good condition. Two months later, she was hospitalized again with recurrent pericardial effusion for 19 days. In evaluations, she had hypothyroidism and a little pericardial effusion. She was treated with dexamethasone, ibuprofen, and levothyroxine.Fourth and fifth hospitalizations occurred due to high-grade fever and elevated ESR and CRP levels at the 13th and 18th months of old, respectively.She got COVID-19 at 24 months old and was admitted to the hospital for the 6th time because of her past medical history. She had only a fever as a COVID-19 manifestation. After 4 months, she got COVID-19 again and had gastrointestinal manifestations without any adverse effects.At the age of 27 months, the patient was referred to the rheumatology clinic due to several episodes of high grade fever, inflammatory pericardial effusion, and active left knee arthritis with an increase in inflammatory marker levels without any localized origin, as well as an erythematous plaque on the leg and a history of multiple hospitalizations. A skin biopsy revealed septal panniculitis compatible with erythema nodosum. The patient was thoroughly evaluated in terms of rheumatology, her height, and weight were 82 cm and 10 kg in physical examination, respectively. We found blonde hair, frontal bossing, and macular rashes on limbs, and eventually, according to the lack of response to treatment and the history of respiratory infections, an immunological examination including CBC, CD markers, and immunoglobulins levels was performed. The clinical manifestations of the patient are shown in Fig. 1.Open in a separate windowFig. 1The clinical manifestation of the patient Low serum IgG levels, decreased CD4/CD8 ratio and CD27 level, and a poor response to candida in the lymphocyte transformation test (LTT) were detected (Table 1). Intravenous immunoglobulin (IVIG) and prophylactic antibiotics were started which led to the control of the patient’s fever and other symptoms.Table 1The results of hematological, biochemical and immunological tests of the patientTestValueNormal RangeTestValueNormal Range WBC(cell/mm 3 ) 89006000–17,000 IgM ( mg/dl) 5940–150 Neutrophil(cell/mm 3 ) 44501500–8500 IgG( mg/dl) 520600–1100 Lymphocyte(cell/mm 3 ) 36043000–9500 IgA ( mg/dl) 2151–297 Hb(g/dl) 7.411.5–13.5 IgE ( IU/ml) 1Up to 144 PLT 566,000150,000–450,000 CD3%(total count) 65.2 (3338)35–78% ANA NegativeNL < 1/160 CD4%(total count) 33 (1690)22–62% RF NegativeNeg < 10 CD8%(total count) 32.3 (1654)12–36% Anti Ds DNA NegativeNeg < 2.6 CD19%(total count) 11 (563)3–14% HLAB51 Negative CD20%(total count) 13.2 (676)3–15% Anti CCP NegativeNeg < 0.3 CD16%(total count) 15.4 (229)3–5% Anti Phospholipid Ab NegativeNegative CD56%(total count) 16.23–5%Anti SSA(RO)NegativeNeg < 15 CD4/CD8 1.021.5-2Anti SSB(La)NegativeNeg < 20 CD27% 3.909–35% ESR (mm/hr) 57 (H)Nl < 20 LTT(PHA) 7.1Nl˃3.5 CRP (mg/L) 43Nl < 6 LTT (Candida) 1.5Nl˃2.5Anti-Tetanus Ab(IU/ml)1.57˃0.1LTT (BCG)6.2Nl˃2.5Anti-Diphtheria Ab(IU/ml)0.29˃0.01Open in a separate windowWBC: White Blood cell, Hb: Hemoglobin, PLT: Platelet, ANA: AntiNuclear Antibody, RF: Rheumatoid Factor, Anti Ds DNA: Anti Double stranded DNA, Anti CCP: Anti Cyclic Citrullinated Peptide, Anti SSA Ab: anti–Sjögren’s-syndrome-related antigen A autoantibody, Anti SSB: anti–Sjögren’s-syndrome-related antigen B autoantibody, ESR: Erythrocyte Sedimentation Rate, CRP: C-reactive Protein, Ig: Immunoglobulin, LTT: lymphocyte transformation test, PHA: Phytohemagglutinin, BCG: Bacillus Calmette-Guerin After about 5 months of the follow-up, the patient was hospitalized due to polyuria, polydipsia, tachypnea, and lethargy with the diagnosis of diabetic ketoacidosis and was discharged with injectable insulin. Whole-exome sequencing was performed on the patient’s whole blood sample. Variant interpretation of interested variants was accomplished through the American College of Medical Genetics and Genomics (ACMG). A novel heterozygous variant (c.1429 G > A; p.Glu477Lys) was found in the PIK3CD gene (Table 2). The variant was validated in the patient, and segregation analysis showed the mother is the carrier for the variant. According to the ACMG guideline, this variant can be classified as a Variant of Unknown Significance (VUS).Table 2The result of genetic sequencing of the patientGene/TranscriptVariant LocationChromosome position(GRCh37)Relationship with the patientZygosityVariant classificationPIK3CDENST00000377346.4NM-005026Exon11c.1429G > Ap.E477KProbandHetVUSMotherHetFatherN

      Case#: 27-month-old girl Iranian girl

      DiseaseAssertion: Combined immunodeficiency.

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

      DiseaseAssertion: Combined immunodeficiency

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

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

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

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

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

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

      PreviouslyPublished: No

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

      ClinVar: Was not found on ClinVar

      CAID: CA577192

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

    1. A 54-year-old woman

      Case#: Ayrignac_2020_Patient_3, female, 42 y.o. (onset), origin unknown

      DiseaseAssertion: CTLA4-related haploinsufficiency

      FamilyInfo: unremarkable family history

      CasePresentingHPOs: HP:0001138, HP:0000009, HP:0000572, HP:0020036, HP:0002015, HP:0002167, HP:0001285, HP:0002346, HP:0001272, HP:0002719, HP:0002720, HP:0004315, HP:0002923, HP:0002110 (bilateral axonal optic neuropathy, bladder urgency, vision loss, upper limb dysmetria, speech/swallowing disorder, spastic tetra paresis, head tremor, cerebellar atrophy, recurrent infections, IgA and IgG deficiency, autoantibodies [rheumatoid factor], bronchiectasis)

      CaseHPOFreeText: white matter and deep basal ganglia FLAIR hyperintensities

      CaseNotHPOs: lymphoproliferation

      CaseNotHPOFreeText: abnormal CSF analysis

      CasePreviousTesting: CSF analysis, "multiple panel gene excluded the main known causes of inherited leukoencephalopathy, cerebellar ataxia, and mitochondrial diseases."

      GenotypingMethod: mini-exome analysis

      PreviouslyPublished: n/a

      Variant: NM_005214.5(CTLA4):c.151C>T (p.Arg51Ter)

      ClinVarID: 161109

      CAID: CA173992

      gnomAD: not reported

      SupplementalData: n/a

    1. This patient was the second daughter of the index case.

      Case#: Grammatikos_2021_Case2, female, 10 months (onset) 25 y.o. (report), origin not reported

      DiseaseAssertion: CTLA4 haploinsufficiency

      FamilyInfo: Mother and brother are also affected. Extensive family history of autoimmune phenotypes in Figure S1.

      CasePresentingHPOs: HP:0002315, HP:000340, HP:0003394, HP:0004313, HP:0012115, HP:0001878, HP:0007565, HP:0001744, HP:0004315, HP:0006577, HP:0002090, HP:0002829, HP:0005263, HP:0006532, HP:0033542, HP:0032174, HP:0002110, HP:0011473 (headache, peripheral paresthesia, muscle cramps, hypogammaglobulinemia, autoimmune hepatitis, hemolytic anaemia, cafe au lait spots, splenomegaly, low IgG, macronodular cirrhosis, fungal pneumonia, arthralgia, antral gastritis, recurrent bacterial pneumonias, bronchial wall thickening, diffuse tree-in-bud infiltrates, bronchiectasis, focal total villous atrophy)

      CaseHPOFreeText: Severe lesion in right cerebellar hemisphere and left superior frontal gyrus. Evan's syndrome, bronchial associated lymphoid hyperplasia, intestinal metaplasia, intraepithelial lymphocytes

      CaseNotHPOs: HP:0001369, HP:0012538 (artritis, response to gluten)

      CaseNotHPOFreeText: n/a

      CasePreviousTesting: 2 benign polymorphisms found in perforin gene. Other genes tested: Fas, Fas ligand, Caspase 10, Caspase 8, NRAS. Heterozygous VUS found in LRBA gene.

      GenotypingMethod: not specified. It says, "Following her mother’s diagnosis of CTLA4 haploinsufficiency, she was confirmed to have the same genetic mutation." Mother was tested using NGS + Sanger

      PreviouslyPublished: not reported

      Variant: NM_005214.4(CTLA4):c.81_82insT (p.Leu28fs) heterozygous

      ClinVarID: 644629

      CAID: CA645516071

      gnomAD: not found

      SupplementalData: Figure S1 shows extensive family history