ClinVar Miner

Submissions for variant NM_013382.7(POMT2):c.1121C>G (p.Thr374Ser)

gnomAD frequency: 0.00003  dbSNP: rs973161535
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001055921 SCV001220336 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2; Autosomal recessive limb-girdle muscular dystrophy type 2N 2022-08-16 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 374 of the POMT2 protein (p.Thr374Ser). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with POMT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 851511). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Revvity Omics, Revvity RCV003132185 SCV003809732 uncertain significance not provided 2019-12-26 criteria provided, single submitter clinical testing
GeneDx RCV003132185 SCV005391986 uncertain significance not provided 2024-11-01 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004960381 SCV005481254 uncertain significance Inborn genetic diseases 2024-11-24 criteria provided, single submitter clinical testing The c.1121C>G (p.T374S) alteration is located in exon 10 (coding exon 10) of the POMT2 gene. This alteration results from a C to G substitution at nucleotide position 1121, causing the threonine (T) at amino acid position 374 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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