chr19-41970391-G-C
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PS1PM1PM2PM5PP2PP3_StrongPP5_Moderate
The NM_152296.5(ATP1A3):c.2415C>G(p.Asp805Glu) variant causes a missense change. 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 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. D805H) has been classified as Pathogenic.
Frequency
Consequence
NM_152296.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.2415C>G | p.Asp805Glu | missense_variant | 17/23 | ENST00000648268.1 | |
ATP1A3 | NM_001256214.2 | c.2454C>G | p.Asp818Glu | missense_variant | 17/23 | ||
ATP1A3 | NM_001256213.2 | c.2448C>G | p.Asp816Glu | missense_variant | 17/23 | ||
ATP1A3 | XM_047438862.1 | c.2325C>G | p.Asp775Glu | missense_variant | 17/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.2415C>G | p.Asp805Glu | missense_variant | 17/23 | NM_152296.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Dystonia 12 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 12, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at