rs368371895
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 3P and 9B. PM1PP2BP4_StrongBP6BS2
The NM_152296.5(ATP1A3):c.2489G>A(p.Arg830Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,614,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. R830R) has been classified as Likely benign.
Frequency
Consequence
NM_152296.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.2489G>A | p.Arg830Gln | missense_variant | 18/23 | ENST00000648268.1 | |
ATP1A3 | NM_001256214.2 | c.2528G>A | p.Arg843Gln | missense_variant | 18/23 | ||
ATP1A3 | NM_001256213.2 | c.2522G>A | p.Arg841Gln | missense_variant | 18/23 | ||
ATP1A3 | XM_047438862.1 | c.2399G>A | p.Arg800Gln | missense_variant | 18/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.2489G>A | p.Arg830Gln | missense_variant | 18/23 | NM_152296.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000954 AC: 24AN: 251458Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135910
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461894Hom.: 0 Cov.: 34 AF XY: 0.0000715 AC XY: 52AN XY: 727248
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 18, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | ATP1A3: PP2 - |
Dystonia 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at