rs573535377
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP2PP3_StrongPP5
The NM_152296.5(ATP1A3):c.1109C>A(p.Thr370Asn) variant causes a missense change involving the alteration of a conserved nucleotide. 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 Lovd as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T370A) has been classified as Likely pathogenic.
Frequency
Consequence
NM_152296.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.1109C>A | p.Thr370Asn | missense_variant | 9/23 | ENST00000648268.1 | |
ATP1A3 | NM_001256214.2 | c.1148C>A | p.Thr383Asn | missense_variant | 9/23 | ||
ATP1A3 | NM_001256213.2 | c.1142C>A | p.Thr381Asn | missense_variant | 9/23 | ||
ATP1A3 | XM_047438862.1 | c.1019C>A | p.Thr340Asn | missense_variant | 9/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.1109C>A | p.Thr370Asn | missense_variant | 9/23 | NM_152296.5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at