rs387906594
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP2PP3_ModeratePP5
The NM_170665.4(ATP2A2):c.2093C>T(p.Ala698Val) 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. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A698P) has been classified as Pathogenic.
Frequency
Consequence
NM_170665.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A2 | NM_170665.4 | c.2093C>T | p.Ala698Val | missense_variant | 14/20 | ENST00000539276.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A2 | ENST00000539276.7 | c.2093C>T | p.Ala698Val | missense_variant | 14/20 | 1 | NM_170665.4 | P3 | |
ATP2A2 | ENST00000308664.10 | c.2093C>T | p.Ala698Val | missense_variant | 14/21 | 1 | A1 | ||
ATP2A2 | ENST00000548169.2 | c.1766C>T | p.Ala589Val | missense_variant | 10/16 | 2 | |||
ATP2A2 | ENST00000377685.9 | c.*1933C>T | 3_prime_UTR_variant, NMD_transcript_variant | 13/20 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Acrokeratosis verruciformis of Hopf Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2010 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at