rs80356758
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP3PP5
The NM_012463.4(ATP6V0A2):c.2293C>T(p.Gln765Ter) variant causes a stop gained, splice region change. The variant allele was found at a frequency of 0.00000683 in 1,611,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_012463.4 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V0A2 | NM_012463.4 | c.2293C>T | p.Gln765Ter | stop_gained, splice_region_variant | 18/20 | ENST00000330342.8 | |
ATP6V0A2 | XM_024448910.2 | c.2173C>T | p.Gln725Ter | stop_gained, splice_region_variant | 17/19 | ||
ATP6V0A2 | XM_024448911.2 | c.1780C>T | p.Gln594Ter | stop_gained, splice_region_variant | 14/16 | ||
ATP6V0A2 | XM_024448912.2 | c.1471C>T | p.Gln491Ter | stop_gained, splice_region_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V0A2 | ENST00000330342.8 | c.2293C>T | p.Gln765Ter | stop_gained, splice_region_variant | 18/20 | 1 | NM_012463.4 | P1 | |
ENST00000623681.1 | n.258G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251478Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135916
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1458824Hom.: 0 Cov.: 29 AF XY: 0.00000551 AC XY: 4AN XY: 725940
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
Cutis laxa with osteodystrophy Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at