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

Case#: P1

DiseaseAssertion: APDS1

FamilyInfo: Chinese

CaseHPOFreeText:

CasePreviousTesting: WES

Variant: E1021K

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

ClinVar: 88675

CAID: CA145460

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

Case#: P3

DiseaseAssertion: APDS1

FamilyInfo: Chinese

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

CasePreviousTesting: WES

Variant: E1021K

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

ClinVar: 88675

CAID: CA145460

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

Case#: P10

DiseaseAssertion: APDS1

FamilyInfo: Chinese

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

CasePreviousTesting: WES

Variant: E1025G

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

ClinVar: 422410

CAID: CA16617216

gnomAD: absent from gnomad v4.1.0

Case#: P3, 9-years-old Saudi girl

CasePresentingHPOs: HP:0002028, HP:0005425, HP:0100281

CaseHPOFreeText: P3 is a 9 years old girl with history of chronic diarrhea and recurrent sinopulmonary infections since the age of 4 months. Immunological evaluation at age of 3 years showed normal complete blood counts and differential, lymphocytes subsets, lymphocytes proliferation and oxidative burst assays. Her IgG level was 3.1 gm/L with normal IgA and IgM levels and her antibody response to pneumococcal polysaccharide vaccine could not be well assessed as she received conjugated pneumococcal vaccines (Table 1). Her recurrent chest infections improved after starting intravenous immunoglobulins. Upper and lower endoscopies showed architectural distortion with focal cryptitis from cecum, ascending and transverse colon biopsies and severe active chronic colitis with crypt abscesses and ulcerations from sigmoid and rectal biopsies with no viral cytopathic changes or granuloma. Her diarrhea was treated mainly with sulfasalazine therapy. Her weight and height are normal in spite of her chronic diarrhea.

Variant: NM_005026.4: c.433delinsGA: p.Q145Efs*51

GenotypingMethod: DNA from all individuals we had access to was submitted for whole-genome genotyping, to determine regions of autozygosity that are shared between all affecteds. This was done under the assumption of an autosomal recessive inheritance pattern, given the nature of the pedigree and the presence of parental consanguinity. Three such regions were highlighted by the software, of which the largest was a 12.3 Mb block on Chr 1 (Fig. 1B). Simultaneously we submitted the DNA from patient P1 for WES, and followed the NGS filtering scheme indicated in Fig. 1C. Once we had limited our search area to the regions of shared autozygosity which were exclusive to the three patients, no variants survived our filtering except for one

CAID: CA3252646241

**Case#: ** P1, 19-years-old Saudi male

**DiseaseAssertion: ** P1 is asserted to have "Crohn disease" and "CMV gastritis"

CasePresentingHPOs: HP:0002028, HP:0005425, HP:0000964, HP:0011473, HP:0200120

CaseHPOFreeText: P1 is a 19 year old boy with history of chronic diarrhea, recurrent sinopulmonary infections and dermatitis since the age of 2 months. At age of 1 year full upper and lower endoscopy showed duodenal villous atrophy and mild duodenitis, and antrum biopsy was suggestive of CMV gastritis with no significant colon biopsy findings. At 13 years of age he was evaluated by immunology service to rule out IEI. His complete blood counts and differential, lymphocytes subsets, lymphocytes proliferation and oxidative burst assays were normal. His IgG level was subnormal for age (4.2 gm/L) with undetectable IgM levels (Table 1). He was started on intravenous immunoglobulins with good clinical response in regard to his recurrent sinopulmonary infections. He continued to have chronic diarrhea that on frequent occasions was bloody, but he had normal weight gain and growth. Upper and lower endoscopies were performed on several occasions and showed severe chronic active colitis with ulcerations, epithelial reactive changes with granulomatous tissue formation suggestive of Crohn disease. His diarrhea responded partially to sulfasalazine therapy and short courses of steroids.

Variant: NM_005026.4: c.433delinsGA: p.Q145Efs*51

GenotypingMethod: DNA from all individuals we had access to was submitted for whole-genome genotyping, to determine regions of autozygosity that are shared between all affecteds. This was done under the assumption of an autosomal recessive inheritance pattern, given the nature of the pedigree and the presence of parental consanguinity. Three such regions were highlighted by the software, of which the largest was a 12.3 Mb block on Chr 1 (Fig. 1B). Simultaneously we submitted the DNA from patient P1 for WES, and followed the NGS filtering scheme indicated in Fig. 1C. Once we had limited our search area to the regions of shared autozygosity which were exclusive to the three patients, no variants survived our filtering except for one

CAID: CA3252646241

Case#: P2, 18-years-old Saudi girl

DiseaseAssertion: P1 is asserted to have "eosinophilic colitis"

CasePresentingHPOs: HP:0002028, HP:0005425, HP:0000964

CaseHPOFreeText: P2 is an 18 years old girl with history of chronic diarrhea, recurrent sinopulmonary infections and dermatitis since the age of 5 months. Immunological evaluation at age of 12 years showed normal complete blood counts and differential, lymphocytes subsets, lymphocytes proliferation and oxidative burst assays. Her IgG level was subnormal for age (3.6 gm/L) with undetectable IgM levels and poor antibody response to pneumococcal polysaccharide vaccine (Table 1). Her recurrent chest infections improved after starting intravenous immunoglobulins. She continued to have chronic diarrhea that was frequently bloody, but she also maintained normal weight gain and growth. Upper and lower endoscopies showed colonic heavy infiltration by eosinophils and focal eosinophilic abscesses consistent with eosinophilic colitis. Similar to her brother, the diarrhea responded partially to sulfasalazine therapy and short courses of steroids.

Variant: NM_005026.4: c.433delinsGA: p.Q145Efs*51

GenotypingMethod: DNA from all individuals we had access to was submitted for whole-genome genotyping, to determine regions of autozygosity that are shared between all affecteds. This was done under the assumption of an autosomal recessive inheritance pattern, given the nature of the pedigree and the presence of parental consanguinity. Three such regions were highlighted by the software, of which the largest was a 12.3 Mb block on Chr 1 (Fig. 1B). Simultaneously we submitted the DNA from patient P1 for WES, and followed the NGS filtering scheme indicated in Fig. 1C. Once we had limited our search area to the regions of shared autozygosity which were exclusive to the three patients, no variants survived our filtering except for one

CAID: CA3252646241

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#: A 51-year-old woman

FamilyInfo: the patient (and her affected family members) were heterozygous for a novel, likely pathogenic frameshift deletion variant in CLTA-4 exon

CasePresentingHPOs: HP:0002018, HP:0002141, HP:0003474, HP:0002110, HP:0001891, HP:0000964, HP:0001973, HP:0011108, HP:0100512

CaseHPOFreeText: necrotising granulomatous lymphadenitis, osteonecrosis of the jaw induced by bisphosphonates, diverticulitis, and bowel salt malabsorption. The patient’s daughter had recurrent episodes of CNS inflammation as a child and in adulthood she developed autoimmune hepatitis, autoimmune haemolytic anaemia and bronchiectasis.

FamilyInfo: The patient’s daughter had recurrent episodes of CNS inflammation as a child and in adulthood she developed autoimmune hepatitis, autoimmune haemolytic anaemia and bronchiectasis. The patient’s son was known to have type I diabetes, thyroid disease, pernicious anaemia and autoimmune encephalitis. FAS sequencing for autoimmune lymphoproliferative syndrome (ALPS) was normal and, at the time of presentation, extended panel screening for primary immunodeficiency was ongoing. There was prior exposure to corticosteroids but no other immunomodulatory treatment.

Variant: c.81dup p.(leu28Serfs*32)

ClinVar: 644629

GenotypingMethod: a virtual sub-panel of 194 genes associated with primary immunodeficiencies screened using Agilent ‘Focused Exome’ custom target enrichment system (SureSelectXT) and Next Generation Sequencing demonstrated that the patient (and her affected family members) were heterozygous for a novel, likely pathogenic frameshift deletion variant

Case#: 36 y.o male European

DiseaseAssertion: Limb Girdle

FamilyInfo: None

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

CaseHPOFreeText: Experienced two episodes of atrial fibrillation. High CADD scores. Exercise-induced myalgia and/or rhabdomyolysis

CaseNotHPOs:

CaseNotHPOFreeText:

MotorAchievement: Age 20 he developed exercise intolerance and sporadic myoglobinuria after intense exercise. Able to walk and cycle for long distances with little muscle pain.

CreatineKinase: Ranging from 1700 to 8000 UI/L), at the age of 10 years

CasePreviousTesting: Last neurological examination there was moderate calf hypertrophy.

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

PreviouslyPublished:

Variant: NM_000023.4(SGCA):c.850C>T (p.Arg284Cys)

ClinVar: 9439

CAID:

gnomAD: 0.0007716