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NM_032119.4(ADGRV1):c.14365C>T (p.Arg4789Trp)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(3);Pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Mar 20, 2020
Accession:
VCV000430362.5
Variation ID:
430362
Description:
single nucleotide variant
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NM_032119.4(ADGRV1):c.14365C>T (p.Arg4789Trp)

Allele ID
421558
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q14.3
Genomic location
5: 90791194 (GRCh38) GRCh38 UCSC
5: 90087011 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.90791194C>T
NC_000005.9:g.90087011C>T
NG_007083.2:g.266851C>T
... more HGVS
Protein change
R4789W
Other names
-
Canonical SPDI
NC_000005.10:90791193:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
Links
ClinGen: CA360401651
dbSNP: rs1131691924
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Nov 19, 2016 RCV000609544.1
Likely pathogenic 1 criteria provided, single submitter Nov 20, 2018 RCV001073322.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Mar 20, 2020 RCV000493267.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ADGRV1 - - GRCh38
GRCh37
2423 2454

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Aug 18, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000583154.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R4789W variant has been reported previously as a likely pathogenic variant in a cohort of patients diagnosed with Usher syndrome type 2 (Besnard et … (more)
Likely pathogenic
(Nov 19, 2016)
criteria provided, single submitter
Method: clinical testing
Rare genetic deafness
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000710878.1
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The p.Arg4789Trp variant in GPR98 has been reported in 1 individual with Usher s yndrome who was compound heterozygous for a second pathogenic variant in … (more)
Uncertain significance
(Jul 02, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001142922.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (2)
Likely pathogenic
(Nov 20, 2018)
criteria provided, single submitter
Method: clinical testing
Retinal dystrophy
Allele origin: germline
Blueprint Genetics
Accession: SCV001238861.1
Submitted: (Oct 15, 2019)
Comment:
My Retina Tracker patient
Evidence details
Pathogenic
(Mar 20, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001580151.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces arginine with tryptophan at codon 4789 of the ADGRV1 protein (p.Arg4789Trp). The arginine residue is highly conserved and there is a … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Sloan-Heggen CM Human genetics 2016 PMID: 26969326
Targeted sequencing of 179 genes associated with hereditary retinal dystrophies and 10 candidate genes identifies novel and known mutations in patients with various retinal diseases. Chen X Investigative ophthalmology & visual science 2013 PMID: 23462753
Non-USH2A mutations in USH2 patients. Besnard T Human mutation 2012 PMID: 22147658

Text-mined citations for rs1131691924...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021