NM_032119.4(ADGRV1):c.7129C>T (p.Arg2377Ter) AND Rare genetic deafness

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 23, 2015
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000214702.1

Allele description

NM_032119.4(ADGRV1):c.7129C>T (p.Arg2377Ter)

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.7129C>T (p.Arg2377Ter)

HGVS:

NC_000005.10:g.90692782C>T
NG_007083.2:g.168439C>T
NM_032119.4:c.7129C>TMANE SELECT
NP_115495.3:p.Arg2377Ter
LRG_1095t1:c.7129C>T
LRG_1095:g.168439C>T
LRG_1095p1:p.Arg2377Ter
NC_000005.9:g.89988599C>T
NM_032119.3:c.7129C>T
NR_003149.2:n.7145C>T
p.Arg2377X

Protein change:

R2377*

Links:

dbSNP: rs758718347

NCBI 1000 Genomes Browser:

rs758718347

Molecular consequence:

NR_003149.2:n.7145C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_032119.4:c.7129C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000271377	Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Pathogenic (Jun 23, 2015)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24498627, 24033266

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000271377

Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Pathogenic
(Jun 23, 2015)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	2	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

Experience of targeted Usher exome sequencing as a clinical test.

Besnard T, García-García G, Baux D, Vaché C, Faugère V, Larrieu L, Léonard S, Millan JM, Malcolm S, Claustres M, Roux AF.

Mol Genet Genomic Med. 2014 Jan;2(1):30-43. doi: 10.1002/mgg3.25. Epub 2013 Jul 10.

PubMed [citation]

PMID:: 24498627
PMCID:: PMC3907913

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, SCV000271377.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (2)

Description

The p.Arg2377X variant in GPR98 has been reported in one individual with Usher s yndrome type 2 (Besnard 2014). It has also been identified in 1/10908 South Asia n chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstit ute.org). Although this variant has been seen in the general population, its fr equency is low enough to be consistent with a recessive carrier frequency. This nonsense variant leads to a premature termination codon at position 2377, which is predicted to lead to a truncated or absent protein. In summary, this variant meets our criteria to be classified as pathogenic for hearing loss in an autosom al recessive manner (http://www.partners.org/personalizedmedicine/LMM) based upo n predicted impact to protein.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		2	not provided	1	not provided

Last Updated: Apr 8, 2022

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