NM_032119.4(ADGRV1):c.14365C>T (p.Arg4789Trp) AND Rare genetic deafness

Clinical significance:Likely pathogenic (Last evaluated: Nov 19, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000609544.1

Allele description [Variation Report for NM_032119.4(ADGRV1):c.14365C>T (p.Arg4789Trp)]

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

Gene:
ADGRV1:adhesion G protein-coupled receptor V1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q14.3
Genomic location:
Preferred name:
NM_032119.4(ADGRV1):c.14365C>T (p.Arg4789Trp)
HGVS:
  • NC_000005.10:g.90791194C>T
  • NG_007083.2:g.266851C>T
  • NM_032119.4:c.14365C>TMANE SELECT
  • NP_115495.3:p.Arg4789Trp
  • LRG_1095t1:c.14365C>T
  • LRG_1095:g.266851C>T
  • LRG_1095p1:p.Arg4789Trp
  • NC_000005.9:g.90087011C>T
  • NM_032119.3:c.14365C>T
  • NR_003149.2:n.14381C>T
Protein change:
R4789W
Links:
dbSNP: rs1131691924
NCBI 1000 Genomes Browser:
rs1131691924
Molecular consequence:
  • NM_032119.4:c.14365C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_003149.2:n.14381C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Rare genetic deafness
Identifiers:
MedGen: CN826980; Orphanet: 96210

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000710878Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Likely pathogenic
(Nov 19, 2016)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

Non-USH2A mutations in USH2 patients.

Besnard T, Vaché C, Baux D, Larrieu L, Abadie C, Blanchet C, Odent S, Blanchet P, Calvas P, Hamel C, Dollfus H, Lina-Granade G, Lespinasse J, David A, Isidor B, Morin G, Malcolm S, Tuffery-Giraud S, Claustres M, Roux AF.

Hum Mutat. 2012 Mar;33(3):504-10. doi: 10.1002/humu.22004. Epub 2012 Jan 6.

PubMed [citation]
PMID:
22147658

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000710878.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

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 GPR98 ( Besnard 2012). This variant was absent from large population studies. Computati onal prediction tools and conservation analyses suggest that this variant may im pact the protein, though this information is not predictive enough to determine pathogenicity. In summary, although additional studies are required to fully est ablish its clinical significance, this variant is likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Jul 7, 2021

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