ClinVar Miner

Submissions for variant NM_020458.4(TTC7A):c.1433T>C (p.Leu478Pro)

gnomAD frequency: 0.00002  dbSNP: rs201100272
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000795715 SCV000935185 uncertain significance Multiple gastrointestinal atresias 2022-08-23 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 478 of the TTC7A protein (p.Leu478Pro). This variant is present in population databases (rs201100272, gnomAD 0.003%). This missense change has been observed in individual(s) with inflammatory bowel disease and primary immune defects (PMID: 25174867). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 642279). 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"). 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.
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV000795715 SCV001190495 likely pathogenic Multiple gastrointestinal atresias 2019-12-18 criteria provided, single submitter research ACMG codes: PM2, PM3, PP3, PP4
Baylor Genetics RCV000795715 SCV001520481 likely pathogenic Multiple gastrointestinal atresias 2019-12-16 criteria provided, single submitter clinical testing This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
GeneDx RCV002245672 SCV002513646 likely pathogenic not provided 2022-05-11 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 25174867, 31787977)

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