CTLA4 p.Pro136Leu

NM_005214.5(CTLA4):c.407C>T is a missense variant encoding a substitution of proline with leucine at amino acid 136. This variant is located within the MYPPPY functional domain (residues 134-139), which is required for interaction with CD80 and CD86 (PM1, PMID: 31396201). Another missense variants in the same codon, NM_005214.5(CTLA4):c.406C>G (p.Pro136Ala), has a lower Grantham score (27) than the variant under investigation (98) and has been classified as likely pathogenic for autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency by the ClinGen Antibody Deficiencies VCEP (PM5, PMID: 27379089, PMID: 29729943). Splicing prediction using SpliceAI did not strongly predict an effect on splicing due to either of these variants. This variant is absent from gnomAD v4.1.1 (PM2_Supporting). The computational predictors REVEL (0.453) and CADD (25.4) give scores below and above their respective ClinGen Antibody Deficiencies VCEP thresholds (>0.75 and >20 respectively), with no consistent predicted effect on CTLA4 function. This variant has been reported in 3 apparently unrelated probands meeting the VCEP standard for phenotypic criteria, exceeding 10 phenotype points without genotyping that excluded causes in other loci (PS4_Moderate, PMID: 29729943). At least one patient harboring this variant had a phenotype that included decreased circulating antibody level (2 pts), non-malignant lymphoproliferation (1 pt), viral infections with herpes and EBV (1 pt), EBV-associated lymphoma (1 pt), mycoplasma or tuberculosis infection (1 pt), diarrhea and enteropathy (4 pts), autoimmune thrombocytopenia and hemolytic anemia, neutropenia in presence of anti-neutrophil antibodies (1 pt), neurological involvement (1 pt), and eczema and alopecia (1pt), (PMID: 29729943). Additionally, patient Treg cells endogenously expressing the p.Pro136Leu variant showed reduced CTLA-4 expression at the cell surface and reduced transendocytosis-mediated uptake of exogenously expressed CD80-GFP from co-cultured Chinese hamster ovary cells, relative to Treg cells from unaffected patients (PMID: 34111452). However, genotyping to rule out an alternative basis for disease in LRBA had not been performed, so the phenotype was not sufficiently specific for autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency to meet PP4 ( PMID: 29729943). The variant has been reported to segregate with CTLA4 insufficiency through at least 2 affected meioses from 1 family (PP1; PMID: 29729943, PMID: 30250467). The second affected family member had phenotypes that included gastrointestinal involvement / enteropathy (4 pts,) dermatological involvement (1 pt), and neurological involvement (1 pt), while the third affected family member had a phenotype that included diarrhea and enteropathy (4 pts), neurological involvement (1 pt), vitiligo (1 pt), and autoimmune thyroiditis and type 1 diabetes (1 pt). Together, these features were sufficient to confirm affected status. In summary, this variant meets the criteria to be classified as Likely Pathogenic for autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Antibody Deficiencies VCEP: PS4_Moderate, PM2_Supporting, PP1_Moderate, PM1, and PM5. (VCEP specifications version 2.0.0).