chrX-154532411-C-T
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_001360016.2(G6PD):c.1339G>A(p.Gly447Arg) 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G447V) has been classified as Likely 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.1339G>A | p.Gly447Arg | missense_variant | 11/13 | ENST00000393562.10 | |
G6PD | NM_000402.4 | c.1429G>A | p.Gly477Arg | missense_variant | 11/13 | ||
G6PD | NM_001042351.3 | c.1339G>A | p.Gly447Arg | missense_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PD | ENST00000393562.10 | c.1339G>A | p.Gly447Arg | 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 unrelated hemizygotes with deficiency and jaundice, acute anemia, and CNSHA (PS4_M, PP4). In one family, variant segregates with deficiency (PP1). In another, hemizygote with CNSHA does not have variant, so assumed de novo (PM6). Decreased activity in red blood cells of hemizygotes (1-5%) (PS3). Not found in gnomAD (PM2). Reported as pathogenic by Eurofins (PP5). Post_P 0.999 (odds of pathogenicity 13661, Prior_P 0.1). - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 25, 1989 | - - |
Malaria, susceptibility to;C2720289:Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 03, 2022 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 18, 2013 | - - |
G6PD SANTIAGO DE CUBA Other:1
other, no assertion criteria provided | literature only | OMIM | May 24, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at