3-113784310-G-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PM5PP2PP3_StrongPP5
The NM_001690.4(ATP6V1A):c.298G>T(p.Asp100Tyr) 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. 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. D100V) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001690.4 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 |
---|---|---|---|---|---|---|---|
ATP6V1A | NM_001690.4 | c.298G>T | p.Asp100Tyr | missense_variant | 4/15 | ENST00000273398.8 | |
ATP6V1A | XM_047448305.1 | c.298G>T | p.Asp100Tyr | missense_variant | 4/15 | ||
ATP6V1A | XM_047448306.1 | c.298G>T | p.Asp100Tyr | missense_variant | 5/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V1A | ENST00000273398.8 | c.298G>T | p.Asp100Tyr | missense_variant | 4/15 | 1 | NM_001690.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Epileptic encephalopathy, infantile or early childhood, 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at