rs137852329
Variant summary
Our verdict is Pathogenic. Variant got 24 ACMG points: 24P and 0B. PS1_Very_StrongPM1PM2PM5PP3_ModeratePP5_Very_Strong
The NM_001360016.2(G6PD):c.1089C>G(p.Asn363Lys) variant causes a missense change involving the alteration of a non-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 nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N363I) 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 24 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PD | NM_001360016.2 | c.1089C>G | p.Asn363Lys | missense_variant | 10/13 | ENST00000393562.10 | |
G6PD | NM_000402.4 | c.1179C>G | p.Asn393Lys | missense_variant | 10/13 | ||
G6PD | NM_001042351.3 | c.1089C>G | p.Asn363Lys | missense_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PD | ENST00000393562.10 | c.1089C>G | p.Asn363Lys | missense_variant | 10/13 | 1 | NM_001360016.2 | P4 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 30, 2018 | - - |
Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | curation | Dunham Lab, University of Washington | Aug 12, 2022 | Variant found in hemizygotes with G6PD deficiency and anemia (PP4). Inherited with deficiency through five generations in one family (PP1). Decreased activity in red blood cells (3-30%) (PS3). Not found in gnomAD (PM2). Leads to same amino acid change as pathogenic variant (ClinVar ID 10390) (PS1). Post_P 0.999 (odds of pathogenicity 6551, Prior_P 0.1). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at