rs138929990
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_032119.4(ADGRV1):c.4149C>G(p.Tyr1383*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
ADGRV1
NM_032119.4 stop_gained
NM_032119.4 stop_gained
Scores
2
2
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0410
Genes affected
ADGRV1 (HGNC:17416): (adhesion G protein-coupled receptor V1) This gene encodes a member of the G-protein coupled receptor superfamily. The encoded protein contains a 7-transmembrane receptor domain, binds calcium and is expressed in the central nervous system. Mutations in this gene are associated with Usher syndrome 2 and familial febrile seizures. Several alternatively spliced transcripts have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.4149C>G | p.Tyr1383* | stop_gained | 20/90 | ENST00000405460.9 | NP_115495.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.4149C>G | p.Tyr1383* | stop_gained | 20/90 | 1 | NM_032119.4 | ENSP00000384582.2 | ||
ADGRV1 | ENST00000640403.1 | c.1440C>G | p.Tyr480* | stop_gained | 10/29 | 5 | ENSP00000492531.1 | |||
ADGRV1 | ENST00000504142.2 | n.2915C>G | non_coding_transcript_exon_variant | 14/14 | 5 | |||||
ADGRV1 | ENST00000639676.1 | n.1747C>G | non_coding_transcript_exon_variant | 8/11 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246212Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133468
GnomAD3 exomes
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AC:
1
AN:
246212
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AC XY:
1
AN XY:
133468
Gnomad AFR exome
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GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
Vest4
0.39
ClinPred
D
GERP RS
Splicing
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Calibrated prediction
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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