1-63629539-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_002633.3(PGM1):c.361G>C(p.Gly121Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_002633.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM1 | NM_002633.3 | c.361G>C | p.Gly121Arg | missense_variant | 2/11 | ENST00000371084.8 | |
PGM1 | NM_001172818.1 | c.415G>C | p.Gly139Arg | missense_variant | 2/11 | ||
PGM1 | NM_001172819.2 | c.-231G>C | 5_prime_UTR_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM1 | ENST00000371084.8 | c.361G>C | p.Gly121Arg | missense_variant | 2/11 | 1 | NM_002633.3 | P1 | |
PGM1 | ENST00000650546.1 | c.361G>C | p.Gly121Arg | missense_variant | 2/12 | ||||
PGM1 | ENST00000371083.4 | c.415G>C | p.Gly139Arg | missense_variant | 2/11 | 2 | |||
PGM1 | ENST00000540265.5 | c.-231G>C | 5_prime_UTR_variant | 2/11 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248944Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134828
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461372Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727002
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
PGM1-congenital disorder of glycosylation Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at