13-24691017-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001676.7(ATP12A):c.835C>T(p.Arg279Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000223 in 1,614,150 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R279H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001676.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP12A | ENST00000381946.5 | c.835C>T | p.Arg279Cys | missense_variant | Exon 8 of 23 | 1 | NM_001676.7 | ENSP00000371372.3 | ||
ATP12A | ENST00000218548.10 | c.853C>T | p.Arg285Cys | missense_variant | Exon 8 of 23 | 1 | ENSP00000218548.6 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251472Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135916
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461878Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727238
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.853C>T (p.R285C) alteration is located in exon 8 (coding exon 8) of the ATP12A gene. This alteration results from a C to T substitution at nucleotide position 853, causing the arginine (R) at amino acid position 285 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at