rs1555136375
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_005609.4(PYGM):c.521G>A(p.Gly174Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,200 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G174S) has been classified as Pathogenic.
Frequency
Consequence
NM_005609.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYGM | NM_005609.4 | c.521G>A | p.Gly174Asp | missense_variant | 4/20 | ENST00000164139.4 | |
PYGM | NM_001164716.1 | c.257G>A | p.Gly86Asp | missense_variant | 2/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYGM | ENST00000164139.4 | c.521G>A | p.Gly174Asp | missense_variant | 4/20 | 1 | NM_005609.4 | P1 | |
PYGM | ENST00000377432.7 | c.257G>A | p.Gly86Asp | missense_variant | 2/18 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460200Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 726544
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Glycogen storage disease, type V Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at