rs267606650
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_005989.4(AKR1D1):c.781C>T(p.Arg261Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000372 in 1,613,972 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R261H) has been classified as Uncertain significance.
Frequency
Consequence
NM_005989.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKR1D1 | NM_005989.4 | c.781C>T | p.Arg261Cys | missense_variant | 7/9 | ENST00000242375.8 | |
AKR1D1 | NM_001190907.2 | c.781C>T | p.Arg261Cys | missense_variant | 7/8 | ||
AKR1D1 | NM_001190906.2 | c.658C>T | p.Arg220Cys | missense_variant | 6/8 | ||
AKR1D1 | XM_047420763.1 | c.613C>T | p.Arg205Cys | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKR1D1 | ENST00000242375.8 | c.781C>T | p.Arg261Cys | missense_variant | 7/9 | 1 | NM_005989.4 | P1 | |
AKR1D1 | ENST00000432161.5 | c.781C>T | p.Arg261Cys | missense_variant | 7/8 | 2 | |||
AKR1D1 | ENST00000411726.6 | c.658C>T | p.Arg220Cys | missense_variant | 6/8 | 2 | |||
AKR1D1 | ENST00000468877.2 | n.804C>T | non_coding_transcript_exon_variant | 8/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251400Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135864
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461844Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727222
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
Congenital bile acid synthesis defect 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2004 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at