rs200425518
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP2PP3_Strong
The NM_000702.4(ATP1A2):āc.2062G>Cā(p.Ala688Pro) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A688S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000702.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A2 | NM_000702.4 | c.2062G>C | p.Ala688Pro | missense_variant | 15/23 | ENST00000361216.8 | |
ATP1A2 | XM_047421286.1 | c.1171G>C | p.Ala391Pro | missense_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A2 | ENST00000361216.8 | c.2062G>C | p.Ala688Pro | missense_variant | 15/23 | 1 | NM_000702.4 | P1 | |
ATP1A2 | ENST00000392233.7 | c.2062G>C | p.Ala688Pro | missense_variant | 15/23 | 5 | |||
ATP1A2 | ENST00000447527.1 | c.1195G>C | p.Ala399Pro | missense_variant | 8/16 | 2 | |||
ATP1A2 | ENST00000472488.5 | n.2165G>C | non_coding_transcript_exon_variant | 15/20 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152178Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome Cov.: 33
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74456
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at