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NM_032119.4(ADGRV1):c.9877C>T (p.Arg3293Ter) AND Usher syndrome type 2C

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 10, 2022
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:
RCV002221563.2

Allele description [Variation Report for NM_032119.4(ADGRV1):c.9877C>T (p.Arg3293Ter)]

NM_032119.4(ADGRV1):c.9877C>T (p.Arg3293Ter)

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.9877C>T (p.Arg3293Ter)
HGVS:
  • NC_000005.10:g.90724960C>T
  • NG_007083.2:g.200617C>T
  • NM_032119.4:c.9877C>TMANE SELECT
  • NP_115495.3:p.Arg3293Ter
  • LRG_1095t1:c.9877C>T
  • LRG_1095:g.200617C>T
  • LRG_1095p1:p.Arg3293Ter
  • NC_000005.9:g.90020777C>T
  • NM_032119.3:c.9877C>T
  • NR_003149.2:n.9893C>T
  • p.Arg3293X
Protein change:
R3293*
Links:
dbSNP: rs769215629
NCBI 1000 Genomes Browser:
rs769215629
Molecular consequence:
  • NR_003149.2:n.9893C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_032119.4:c.9877C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Usher syndrome type 2C
Synonyms:
USHER SYNDROME, TYPE IIC; Usher syndrome, type 2B
Identifiers:
MONDO: MONDO:0011558; MedGen: C2931213; Orphanet: 231178; Orphanet: 886; OMIM: 605472

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002499406DASA
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Apr 10, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

An innovative strategy for the molecular diagnosis of Usher syndrome identifies causal biallelic mutations in 93% of European patients.

Bonnet C, Riahi Z, Chantot-Bastaraud S, Smagghe L, Letexier M, Marcaillou C, Lefèvre GM, Hardelin JP, El-Amraoui A, Singh-Estivalet A, Mohand-Saïd S, Kohl S, Kurtenbach A, Sliesoraityte I, Zobor D, Gherbi S, Testa F, Simonelli F, Banfi S, Fakin A, Glavač D, Jarc-Vidmar M, et al.

Eur J Hum Genet. 2016 Dec;24(12):1730-1738. doi: 10.1038/ejhg.2016.99. Epub 2016 Jul 27.

PubMed [citation]
PMID:
27460420
PMCID:
PMC5117943

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From DASA, SCV002499406.1

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

Description

The c.9877C>T;p.(Arg3293*) variant creates a premature translational stop signal in the ADGRV1 gene. It is expected to result in an absent or disrupted protein product -PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 517415; PMID: 27460420) - PS4. The variant is present at low allele frequencies population databases (rs769215629 – gnomAD 0.00008302%; ABraOM no frequency - https://abraom.ib.usp.br/) - PM2_supporting. The p.(Arg3293*) was detected in trans with a pathogenic variant (PMID: 27460420) - PM3_supporting. In summary, the currently available evidence indicates that the variant is pathogenic.

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

Last Updated: May 7, 2024