ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.1195G>A (p.Ala399Thr)

gnomAD frequency: 0.00004  dbSNP: rs1276215978
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000596846 SCV000709351 uncertain significance not provided 2017-06-14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001860220 SCV002215350 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2024-01-02 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 399 of the POMGNT1 protein (p.Ala399Thr). This variant is present in population databases (no rsID available, 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: 502560). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on 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.
Ambry Genetics RCV004955707 SCV005481215 uncertain significance Inborn genetic diseases 2024-10-20 criteria provided, single submitter clinical testing The c.1195G>A (p.A399T) alteration is located in exon 14 (coding exon 13) of the POMGNT1 gene. This alteration results from a G to A substitution at nucleotide position 1195, causing the alanine (A) at amino acid position 399 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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