ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.174CTT[2] (p.Phe60del)

dbSNP: rs750195040
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000498358 SCV000589544 pathogenic not provided 2022-01-19 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect (Yang et al., 2016); Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 17559086, 22323514, 31589614, 33200426, 27193224)
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV000850367 SCV000992550 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2K 2024-09-24 criteria provided, single submitter research ACMG codes: PS3, PS4_Moderate, PM2, PM3, PM4
Labcorp Genetics (formerly Invitae), Labcorp RCV001205238 SCV001376479 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2024-01-30 criteria provided, single submitter clinical testing This variant, c.180_182del, results in the deletion of 1 amino acid(s) of the POMT1 protein (p.Phe60del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs750195040, gnomAD 0.006%). This variant has been observed in individual(s) with cobblestone lissencephaly and/or severe congenital muscular dystrophy (PMID: 17559086, 22323514, 27193224; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.178-180delTTC. ClinVar contains an entry for this variant (Variation ID: 431953). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003476193 SCV004204056 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 2023-04-21 criteria provided, single submitter clinical testing

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