NM_005609.4:c.415C>T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_005609.4(PYGM):c.415C>T(p.Arg139Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,613,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005609.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251172Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135778
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461654Hom.: 0 Cov.: 34 AF XY: 0.00000688 AC XY: 5AN XY: 727144
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74414
ClinVar
Submissions by phenotype
Glycogen storage disease, type V Pathogenic:4Uncertain:3
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The PYGM c.415C>T (p.Arg139Trp) variant is a stop-gained variant predicted to result in premature termination of the protein. The p.Arg139Trp variant has been reported in two studies in which it is found a total of four individuals with glycogen storage disease type V, including three homozygotes (two of whom are siblings), and one compound heterozygote in trans with a known pathogenic variant (Martin et al. 2004; Deschauer et al. 2007). Control data are unavailable for this variant which is reported at a frequency of 0.000046 in the European (non-Finnish) population of the Genome Aggregation Database. Based on the evidence, the p.Arg139Trp variant is classified as likely pathogenic for glycogen storage disease type V. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
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This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 139 of the PYGM protein (p.Arg139Trp). This variant is present in population databases (rs367990192, gnomAD 0.006%). This missense change has been observed in individuals with McArdle disease (PMID: 14748827, 17404776, 34373715, 34534370). ClinVar contains an entry for this variant (Variation ID: 555716). 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 expected to disrupt PYGM protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. -
The c.415C>T;p.(Arg139Trp) missense change has been observed in affected individual(s)(PMID: 17404776; 32075227; 34534370; 34373715) - PS4. The variant is present at low allele frequencies population databases (rs367990192– gnomAD 0.0003287%; ABraOM no frequency - http://abraom.ib.usp.br/) -PM2_supporting. The p.(Arg139Trp) was detected in trans with a Pathogenic variant (PMID: 17404776; 32075227; 34534370; 34373715) - PM3_strong. The variant co-segregated with disease in multiple affected family members (PMID: 34373715) - PP1. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is Pathogenic -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at