NM_032119.4(ADGRV1):c.17933A>G (p.His5978Arg) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Pathogenic(1);Uncertain significance(1) (Last evaluated: May 21, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000309426.3

Allele description [Variation Report for NM_032119.4(ADGRV1):c.17933A>G (p.His5978Arg)]

NM_032119.4(ADGRV1):c.17933A>G (p.His5978Arg)

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.17933A>G (p.His5978Arg)
HGVS:
  • NC_000005.10:g.90965491A>G
  • NG_007083.2:g.441148A>G
  • NM_032119.4:c.17933A>GMANE SELECT
  • NP_115495.3:p.His5978Arg
  • LRG_1095t1:c.17933A>G
  • LRG_1095:g.441148A>G
  • LRG_1095p1:p.His5978Arg
  • NC_000005.9:g.90261308A>G
  • NM_032119.3:c.17933A>G
  • NR_003149.2:n.17949A>G
  • Q8WXG9:p.His5978Arg
Protein change:
H5978R
Links:
UniProtKB: Q8WXG9#VAR_068033; dbSNP: rs756460900
NCBI 1000 Genomes Browser:
rs756460900
Molecular consequence:
  • NM_032119.4:c.17933A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_003149.2:n.17949A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000343852EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Jul 25, 2016)
germlineclinical testing

Citation Link,

SCV001385198Invitaecriteria provided, single submitter
Pathogenic
(May 21, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot 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

High-throughput sequencing for the molecular diagnosis of Usher syndrome reveals 42 novel mutations and consolidates CEP250 as Usher-like disease causative.

Fuster-García C, García-García G, Jaijo T, Fornés N, Ayuso C, Fernández-Burriel M, Sánchez-De la Morena A, Aller E, Millán JM.

Sci Rep. 2018 Nov 20;8(1):17113. doi: 10.1038/s41598-018-35085-0.

PubMed [citation]
PMID:
30459346
PMCID:
PMC6244211
See all PubMed Citations (3)

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000343852.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV001385198.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces histidine with arginine at codon 5978 of the ADGRV1 protein (p.His5978Arg). The histidine residue is moderately conserved and there is a small physicochemical difference between histidine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with Usher syndrome type 2 (PMID: 22147658, 30459346). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 289480). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Possibly Damaging; Align-GVGD: Class C0). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 10, 2021

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