NM_005609.4:c.2262delA
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_005609.4(PYGM):c.2262delA(p.Lys754AsnfsTer49) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000818 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005609.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PYGM | ENST00000164139.4 | c.2262delA | p.Lys754AsnfsTer49 | frameshift_variant | Exon 18 of 20 | 1 | NM_005609.4 | ENSP00000164139.3 | ||
PYGM | ENST00000377432.7 | c.1998delA | p.Lys666AsnfsTer49 | frameshift_variant | Exon 16 of 18 | 2 | ENSP00000366650.3 | |||
PYGM | ENST00000483742.1 | n.1615delA | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251484Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135922
GnomAD4 exome AF: 0.0000841 AC: 123AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 727228
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74382
ClinVar
Submissions by phenotype
Glycogen storage disease, type V Pathogenic:9
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This frameshifting variant that is predicted to result in premature truncation of the protein. This variant has been listed as pathogenic by two separate clinical laboratories in the ClinVar database. Additionally, this variant has been reported in multiple affected patients in the compound heterozygous state (reviewed in PMID: 17915571). The highest reported allele frequency in the ExAC database is 0.00036 in the South Asian population. Thus, it is presumed to be rare. Based on the combined evidence, this variant is classified as pathogenic. -
The PYGM c.2262delA (p.Lys754AsnfsTer49) variant results in a frameshift, and is predicted to result in premature termination of the protein. The p.Lys754AsnfsTer49 variant has been reported in at least eleven studies in which it is found in a total of 35 individuals including in 22 in a compound heterozygous state, eight in a heterozygous state and five in a homozygous state (Kubisch et al. 1998; Bruno et al. 2006; Aquaron et al. 2007; Rubio et al. 2007; Rubio et al. 2007; Deschauer et al. 2007; Nogales-Gadea et al. 2008; GarcÃa-BenÃtez et al. 2013; de Luna et al. 2014; Hogrel et al. 2015; Inal-Gültekin et al. 2017). At least 12 of the compound heterozygotes carried the same stop-gained variant on the second allele (p.Arg50Ter). This genotype was shown to result in null myophosphorylase activity (GarcÃa-BenÃtez et al. 2013; de Luna et al. 2014). Control data are unavailable for this variant, which is reported at a frequency of 0.00691 in the European American population of the Exome Sequencing Project. Although this allele frequency appears high based on disease prevalence, the symptoms of glycogen storage disease type V are typically mild, and some probands may be asymptomatic, suggesting that the disorder may be underdiagnosed. Based on the evidence from the literature, the p.Lys754AsnfsTer49 variant is classified as pathogenic for glycogen storage disease type V. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
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This sequence change creates a premature translational stop signal (p.Lys754Asnfs*49) in the PYGM gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 89 amino acid(s) of the PYGM protein. This variant is present in population databases (rs398124210, gnomAD 0.03%). This premature translational stop signal has been observed in individuals with McArdle disease (PMID: 9633816, 17324573, 22250184). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 95296). For these reasons, this variant has been classified as Pathogenic. -
Variant summary: PYGM c.2262delA (p.Lys754AsnfsX49) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 0.00012 in 251484 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in PYGM causing Glycogen Storage Disease, Type V (0.00012 vs 0.0035), allowing no conclusion about variant significance. c.2262delA has been reported in the literature in individuals affected with Glycogen Storage Disease, Type V (e.g. Aquaron_2007). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 17324573). 11 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided Pathogenic:6
Frameshift variant predicted to result in protein truncation, as the last 89 amino acids are replaced with 48 different amino acids, and other loss-of-function variants have been reported downstream in HGMD; This variant is associated with the following publications: (PMID: 14748827, 21802952, 11168025, 17994553, 17915571, 17324573, 22832773, 25740218, 16786513, 17221871, 9633816, 25240406, 17404776, 28967462, 29143597, 9506549, 29926259, 29749052, 29350794, 30011114, 22250184, 31517061, 31019026, 31589614, 31319225, 34426522, 34534370, 33072517, 35465342) -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at