ClinVar Miner

Submissions for variant NM_013382.7(POMT2):c.551C>T (p.Thr184Met)

gnomAD frequency: 0.00003  dbSNP: rs267606971
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000723643 SCV000700592 pathogenic not provided 2017-05-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001203060 SCV001374206 likely pathogenic 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 2023-11-10 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 184 of the POMT2 protein (p.Thr184Met). This variant is present in population databases (rs267606971, gnomAD 0.003%). This missense change has been observed in individuals with muscular dystrophy-dystroglycanopathy (PMID: 17878207, 17923109, 25214167, 27447704, 30060766, 32528171, 33176815, 34413876). ClinVar contains an entry for this variant (Variation ID: 3229). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt POMT2 protein function with a negative predictive value of 95%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Revvity Omics, Revvity RCV000723643 SCV002024728 likely pathogenic not provided 2020-02-21 criteria provided, single submitter clinical testing
MGZ Medical Genetics Center RCV000003385 SCV002579158 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2N 2022-05-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV003472965 SCV004204089 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 2024-01-25 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004700184 SCV005204269 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy 2024-06-13 criteria provided, single submitter clinical testing Variant summary: POMT2 c.551C>T (p.Thr184Met) results in a non-conservative amino acid change located in the Glycosyl transferase family 39/83 domain (IPR003342) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 248200 control chromosomes. c.551C>T has been reported in the literature in homozygous and compound heterozygous individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive (Biancheri_2007, Chen_2021, Godfrey_2007, Lin_2020, Panicucci_2023, Savarese_2014). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 17923109, 34413876, 17878207, 33176815, 36797079, 25214167). ClinVar contains an entry for this variant (Variation ID: 3229). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Fulgent Genetics, Fulgent Genetics RCV001203060 SCV005635525 likely pathogenic 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 2024-06-15 criteria provided, single submitter clinical testing
OMIM RCV000003385 SCV000023543 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2N 2007-11-30 no assertion criteria provided literature only
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille RCV001252357 SCV001428109 uncertain significance Intellectual disability 2019-01-01 no assertion criteria provided clinical testing

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