2-70963289-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_001692.4(ATP6V1B1):c.1037C>T(p.Pro346Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,306 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P346R) has been classified as Pathogenic.
Frequency
Consequence
NM_001692.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V1B1 | NM_001692.4 | c.1037C>T | p.Pro346Leu | missense_variant | 10/14 | ENST00000234396.10 | |
ATP6V1B1 | XM_011532907.3 | c.1157C>T | p.Pro386Leu | missense_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V1B1 | ENST00000234396.10 | c.1037C>T | p.Pro346Leu | missense_variant | 10/14 | 1 | NM_001692.4 | P1 | |
ATP6V1B1 | ENST00000412314.5 | c.1009+28C>T | intron_variant | 5 | |||||
VAX2 | ENST00000432367.6 | c.*837-283C>T | intron_variant, NMD_transcript_variant | 5 | |||||
VAX2 | ENST00000646783.1 | c.*925C>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/13 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250624Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135596
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461132Hom.: 0 Cov.: 36 AF XY: 0.00000275 AC XY: 2AN XY: 726910
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at