rs587777403
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The ENST00000371084.8(PGM1):c.184G>A(p.Asp62Asn) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D62H) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000371084.8 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGM1 | NM_002633.3 | c.184G>A | p.Asp62Asn | missense_variant | 1/11 | ENST00000371084.8 | NP_002624.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGM1 | ENST00000371084.8 | c.184G>A | p.Asp62Asn | missense_variant | 1/11 | 1 | NM_002633.3 | ENSP00000360125 | P1 | |
PGM1 | ENST00000650546.1 | c.184G>A | p.Asp62Asn | missense_variant | 1/12 | ENSP00000497812 | ||||
ITGB3BP | ENST00000478138.1 | n.50C>T | non_coding_transcript_exon_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at