rs137852324
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_001360016.2(G6PD):c.1361G>C(p.Arg454Pro) variant causes a missense change. 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R454C) has been classified as Pathogenic.
Frequency
Consequence
NM_001360016.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PD | NM_001360016.2 | c.1361G>C | p.Arg454Pro | missense_variant | 11/13 | ENST00000393562.10 | |
G6PD | NM_000402.4 | c.1451G>C | p.Arg484Pro | missense_variant | 11/13 | ||
G6PD | NM_001042351.3 | c.1361G>C | p.Arg454Pro | missense_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PD | ENST00000393562.10 | c.1361G>C | p.Arg454Pro | missense_variant | 11/13 | 1 | NM_001360016.2 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD4 exome Cov.: 40
GnomAD4 genome ? Cov.: 25
ClinVar
Submissions by phenotype
Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:2
Pathogenic, criteria provided, single submitter | curation | Dunham Lab, University of Washington | Aug 12, 2022 | Variant found in hemizygote with deficiency (PP4). Decreased activity in red blood cells (5%) (PS3). Affects same amino acid as pathogenic 454R>C (ClinVar ID 93493) (PM5). In silico analyses support deleterious effect (PP3). Not found in gnomAD (PM2). Post_P 0.994 (odds of pathogenicity 1517, Prior_P 0.1). - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 10, 2023 | - - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 08, 2019 | Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.