rs143509747
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000330342.8(ATP6V0A2):c.422G>A(p.Arg141His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. R141L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000330342.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP6V0A2 | NM_012463.4 | c.422G>A | p.Arg141His | missense_variant | 4/20 | ENST00000330342.8 | NP_036595.2 | |
ATP6V0A2 | XM_024448910.2 | c.422G>A | p.Arg141His | missense_variant | 4/19 | XP_024304678.1 | ||
ATP6V0A2 | XM_024448911.2 | c.-3G>A | 5_prime_UTR_variant | 1/16 | XP_024304679.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP6V0A2 | ENST00000330342.8 | c.422G>A | p.Arg141His | missense_variant | 4/20 | 1 | NM_012463.4 | ENSP00000332247 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152040Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251460Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135896
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461296Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 726984
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152040Hom.: 0 Cov.: 30 AF XY: 0.0000673 AC XY: 5AN XY: 74260
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2024 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
ALG9 congenital disorder of glycosylation Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 23, 2022 | This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 141 of the ATP6V0A2 protein (p.Arg141His). This variant is present in population databases (rs143509747, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with ATP6V0A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1303408). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ATP6V0A2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Cutis laxa with osteodystrophy;C0406587:Wrinkly skin syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 27, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at