2-70963244-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001692.4(ATP6V1B1):c.992G>A(p.Arg331Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000781 in 1,613,766 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000081 ( 1 hom. )
Consequence
ATP6V1B1
NM_001692.4 missense
NM_001692.4 missense
Scores
16
2
1
Clinical Significance
Conservation
PhyloP100: 9.95
Genes affected
ATP6V1B1 (HGNC:853): (ATPase H+ transporting V1 subunit B1) This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c'', and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This encoded protein is one of two V1 domain B subunit isoforms and is found in the kidney. Mutations in this gene cause distal renal tubular acidosis associated with sensorineural deafness. [provided by RefSeq, Jul 2008]
VAX2 (HGNC:12661): (ventral anterior homeobox 2) This gene encodes a homeobox protein and is almost exclusively expressed in the ventral portion of the retina during development. In mouse studies, this gene was found to be required for the correct formation of the optic fissure and other aspects of retinal development. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.93
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP6V1B1 | NM_001692.4 | c.992G>A | p.Arg331Gln | missense_variant | 10/14 | ENST00000234396.10 | NP_001683.2 | |
ATP6V1B1 | XM_011532907.3 | c.1112G>A | p.Arg371Gln | missense_variant | 9/13 | XP_011531209.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP6V1B1 | ENST00000234396.10 | c.992G>A | p.Arg331Gln | missense_variant | 10/14 | 1 | NM_001692.4 | ENSP00000234396 | P1 | |
ATP6V1B1 | ENST00000412314.5 | c.992G>A | p.Arg331Gln | missense_variant | 10/14 | 5 | ENSP00000388353 | |||
VAX2 | ENST00000432367.6 | c.*837-328G>A | intron_variant, NMD_transcript_variant | 5 | ENSP00000405114 | |||||
VAX2 | ENST00000646783.1 | c.*880G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/13 | ENSP00000495231 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152084Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251272Hom.: 1 AF XY: 0.0000957 AC XY: 13AN XY: 135838
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GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461682Hom.: 1 Cov.: 33 AF XY: 0.0000935 AC XY: 68AN XY: 727136
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74290
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Renal tubular acidosis with progressive nerve deafness Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 10, 2022 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 21, 2017 | The p.Arg331Gln variant in ATP6V1B1 has not been previously reported in individu als with hearing loss, but has been identified in 11/30780 South Asian chromosom es including 1 homozygote by the Genome Aggregation Database (gnomAD, http://gno mad.broadinstitute.org; dbSNP rs148429410). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathog enic role. Computational prediction tools and conservation analysis suggest that the p.Arg331Gln variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significa nce of the p.Arg331Gln variant is uncertain. ACMG/AMP Criteria applied: PP3. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.992G>A (p.R331Q) alteration is located in exon 10 (coding exon 10) of the ATP6V1B1 gene. This alteration results from a G to A substitution at nucleotide position 992, causing the arginine (R) at amino acid position 331 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 22, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
D;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
H;.
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at