rs1555859299
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 6P and 2B. PM1PM2PP2PP3BP6_Moderate
The NM_152296.5(ATP1A3):c.2647C>T(p.Arg883Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,892 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R883H) has been classified as Uncertain significance.
Frequency
Consequence
NM_152296.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.2647C>T | p.Arg883Cys | missense_variant | 19/23 | ENST00000648268.1 | |
ATP1A3 | NM_001256214.2 | c.2686C>T | p.Arg896Cys | missense_variant | 19/23 | ||
ATP1A3 | NM_001256213.2 | c.2680C>T | p.Arg894Cys | missense_variant | 19/23 | ||
ATP1A3 | XM_047438862.1 | c.2557C>T | p.Arg853Cys | missense_variant | 19/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.2647C>T | p.Arg883Cys | missense_variant | 19/23 | NM_152296.5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251480Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135916
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727248
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Dystonia 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at