rs137853589
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_000294.3(PHKG2):c.317T>A(p.Val106Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,104 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 Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V106V) has been classified as Likely benign.
Frequency
Consequence
NM_000294.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHKG2 | NM_000294.3 | c.317T>A | p.Val106Glu | missense_variant | 4/10 | ENST00000563588.6 | NP_000285.1 | |
PHKG2 | NM_001172432.2 | c.317T>A | p.Val106Glu | missense_variant | 4/11 | NP_001165903.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHKG2 | ENST00000563588.6 | c.317T>A | p.Val106Glu | missense_variant | 4/10 | 1 | NM_000294.3 | ENSP00000455607.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461104Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726908
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Glycogen storage disease IXc Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Human Genetics | Aug 27, 2020 | disease causing - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 1996 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at