rs80356750
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_012463.4(ATP6V0A2):c.187C>T(p.Arg63Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,608,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_012463.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V0A2 | NM_012463.4 | c.187C>T | p.Arg63Ter | stop_gained | 2/20 | ENST00000330342.8 | |
LOC105370042 | XR_945477.4 | n.82-3129G>A | intron_variant, non_coding_transcript_variant | ||||
ATP6V0A2 | XM_024448910.2 | c.187C>T | p.Arg63Ter | stop_gained | 2/19 | ||
LOC105370042 | XR_945478.4 | n.82-3129G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V0A2 | ENST00000330342.8 | c.187C>T | p.Arg63Ter | stop_gained | 2/20 | 1 | NM_012463.4 | P1 | |
ENST00000652313.1 | n.161-3129G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151950Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250700Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135516
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1456714Hom.: 0 Cov.: 28 AF XY: 0.0000110 AC XY: 8AN XY: 724724
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151950Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74204
ClinVar
Submissions by phenotype
Cutis laxa with osteodystrophy Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2008 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Alpha-1-antitrypsin deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 18, 2024 | Variant summary: SERPINA1 c.187C>T (p.Arg63Cys) results in a non-conservative amino acid change located in the Serpin domain (IPR023796) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0011 in 251314 control chromosomes in the gnomAD database, including 1 homozygotes. c.187C>T has been reported in the literature in multiple individuals affected with Alpha-1-Antitrypsin Deficiency. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 10%-<30% of normal activity. Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 30, 2013 | - - |
Cutis laxa Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 18, 2024 | Variant summary: ATP6V0A2 c.187C>T (p.Arg63X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 1.6e-05 in 250700 control chromosomes (gnomAD). c.187C>T has been reported in the literature in individuals affected with Cutis Laxa - ATP6V0A2 Related (example: Fischer_2012). These data indicate that the variant is likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 22773132). ClinVar contains an entry for this variant (Variation ID: 845). Based on the evidence outlined above, the variant was classified as pathogenic. - |
ALG9 congenital disorder of glycosylation Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 01, 2023 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 845). This premature translational stop signal has been observed in individual(s) with cutis laxa (PMID: 18157129, 27896089, 31980526). This variant is present in population databases (rs80356750, gnomAD 0.009%). This sequence change creates a premature translational stop signal (p.Arg63*) in the ATP6V0A2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATP6V0A2 are known to be pathogenic (PMID: 18157129, 19321599). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at