ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.1855A>T (p.Asn619Tyr)

gnomAD frequency: 0.00004  dbSNP: rs374401585
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000727414 SCV000621424 uncertain significance not provided 2023-02-23 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; This variant is associated with the following publications: (PMID: 24282183)
Eurofins Ntd Llc (ga) RCV000727414 SCV000708310 uncertain significance not provided 2017-05-03 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001045068 SCV001208898 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2022-03-19 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 619 of the POMGNT1 protein (p.Asn619Tyr). This variant is present in population databases (rs374401585, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with POMGNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 452605). 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 POMGNT1 protein function. 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.
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001199124 SCV001370119 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O 2019-02-21 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PM1,PPM2,PP3.
Revvity Omics, Revvity RCV000727414 SCV003811723 uncertain significance not provided 2020-07-06 criteria provided, single submitter clinical testing
Natera, Inc. RCV001834710 SCV002089580 uncertain significance Muscle eye brain disease 2020-02-29 no assertion criteria provided clinical testing

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