rs137852536
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_000291.4(PGK1):c.140T>A(p.Ile47Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I47M) has been classified as Uncertain significance.
Frequency
Consequence
NM_000291.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGK1 | NM_000291.4 | c.140T>A | p.Ile47Asn | missense_variant | 3/11 | ENST00000373316.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGK1 | ENST00000373316.5 | c.140T>A | p.Ile47Asn | missense_variant | 3/11 | 1 | NM_000291.4 | P1 | |
PGK1 | ENST00000644362.1 | c.56T>A | p.Ile19Asn | missense_variant | 3/11 | ||||
PGK1 | ENST00000477335.5 | n.276T>A | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
PGK1 | ENST00000491291.1 | n.132T>A | non_coding_transcript_exon_variant | 3/7 | 5 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Glycogen storage disease due to phosphoglycerate kinase 1 deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at