NM_032119.4(ADGRV1):c.3974C>T (p.Thr1325Met) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Sep 12, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000659018.6

Allele description [Variation Report for NM_032119.4(ADGRV1):c.3974C>T (p.Thr1325Met)]

NM_032119.4(ADGRV1):c.3974C>T (p.Thr1325Met)

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.3974C>T (p.Thr1325Met)
HGVS:
  • NC_000005.10:g.90653548C>T
  • NG_007083.2:g.129205C>T
  • NM_032119.4:c.3974C>TMANE SELECT
  • NP_115495.3:p.Thr1325Met
  • LRG_1095t1:c.3974C>T
  • LRG_1095:g.129205C>T
  • LRG_1095p1:p.Thr1325Met
  • NC_000005.9:g.89949365C>T
  • NM_032119.3:c.3974C>T
  • NR_003149.2:n.4073C>T
Protein change:
T1325M
Links:
dbSNP: rs756414393
NCBI 1000 Genomes Browser:
rs756414393
Molecular consequence:
  • NM_032119.4:c.3974C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_003149.2:n.4073C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
3

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000780821CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(Jul 1, 2018)
germlineclinical testing

Citation Link,

SCV001202716Invitaecriteria provided, single submitter
Uncertain significance
(Sep 12, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes3not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome.

Krawitz PM, Schiska D, Kr├╝ger U, Appelt S, Heinrich V, Parkhomchuk D, Timmermann B, Millan JM, Robinson PN, Mundlos S, Hecht J, Gross M.

Mol Genet Genomic Med. 2014 Sep;2(5):393-401. doi: 10.1002/mgg3.92. Epub 2014 Jun 15.

PubMed [citation]
PMID:
25333064
PMCID:
PMC4190874

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV000780821.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

From Invitae, SCV001202716.2

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

Description

This sequence change replaces threonine with methionine at codon 1325 of the ADGRV1 protein (p.Thr1325Met). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs756414393, ExAC 0.009%). This variant has been observed in individual(s) with Usher syndrome or clinical features of retinitis pigmentosa (PMID: 25333064, Invitae). ClinVar contains an entry for this variant (Variation ID: 546975). 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: Probably Damaging; Align-GVGD: Class C0). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Nov 27, 2021

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