22-19176221-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_005984.5(SLC25A1):c.845G>A(p.Arg282His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000262 in 1,605,714 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. R282C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_005984.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A1 | NM_005984.5 | c.845G>A | p.Arg282His | missense_variant | 9/9 | ENST00000215882.10 | |
SLC25A1 | NM_001256534.2 | c.866G>A | p.Arg289His | missense_variant | 8/8 | ||
SLC25A1 | NM_001287387.2 | c.536G>A | p.Arg179His | missense_variant | 9/9 | ||
SLC25A1 | NR_046298.3 | n.769G>A | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A1 | ENST00000215882.10 | c.845G>A | p.Arg282His | missense_variant | 9/9 | 1 | NM_005984.5 | P1 | |
SLC25A1 | ENST00000451283.5 | c.536G>A | p.Arg179His | missense_variant | 9/9 | 2 | |||
SLC25A1 | ENST00000470922.5 | n.987G>A | non_coding_transcript_exon_variant | 8/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151518Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250730Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135618
GnomAD4 exome AF: 0.0000268 AC: 39AN: 1454196Hom.: 0 Cov.: 33 AF XY: 0.0000290 AC XY: 21AN XY: 723614
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151518Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 73996
ClinVar
Submissions by phenotype
D,L-2-hydroxyglutaric aciduria Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at