ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.2097C>A (p.Tyr699Ter)

dbSNP: rs138902646
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000176088 SCV000227686 pathogenic not provided 2016-09-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000535678 SCV000649892 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2023-12-22 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr721*) in the POMT1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 27 amino acid(s) of the POMT1 protein. This variant is present in population databases (rs138902646, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with POMT1-related conditions (PMID: 17559086, 18752264). ClinVar contains an entry for this variant (Variation ID: 195505). This variant disrupts a region of the POMT1 protein in which other variant(s) (p.Asp723Glyfs*8) have been determined to be pathogenic (PMID: 12369018, 16575835, 17559086, 22323514, 24304607, 24491487). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000176088 SCV000890216 likely pathogenic not provided 2022-06-09 criteria provided, single submitter clinical testing Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 27 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 22323514, 28973083, 17559086, 33146414, 18752264, 31127727)
Baylor Genetics RCV003462281 SCV004206052 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 2023-09-10 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000176088 SCV003811827 uncertain significance not provided 2020-12-21 flagged submission clinical testing

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