ClinVar Miner

Submissions for variant NM_020458.4(TTC7A):c.1616C>T (p.Ser539Leu)

gnomAD frequency: 0.00001  dbSNP: rs776906926
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000754082 SCV001516075 uncertain significance Multiple gastrointestinal atresias 2022-08-25 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 440890). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This missense change has been observed in individual(s) with multiple intestinal atresia, inflammatory bowel disease, and primary immune defects (PMID: 24292712, 29174094). This variant is present in population databases (rs776906926, gnomAD 0.005%). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 539 of the TTC7A protein (p.Ser539Leu).
Mayo Clinic Laboratories, Mayo Clinic RCV001509150 SCV001715707 uncertain significance not provided 2020-07-09 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002476020 SCV002784870 uncertain significance Gastrointestinal defects and immunodeficiency syndrome 1 2022-04-07 criteria provided, single submitter clinical testing
OMIM RCV002476020 SCV000882418 pathogenic Gastrointestinal defects and immunodeficiency syndrome 1 2022-01-24 no assertion criteria provided literature only

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