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NM_000245.4(MET):c.1484C>G (p.Thr495Arg) AND Renal cell carcinoma

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 23, 2025
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:
RCV001328504.7

Allele description [Variation Report for NM_000245.4(MET):c.1484C>G (p.Thr495Arg)]

NM_000245.4(MET):c.1484C>G (p.Thr495Arg)

Gene:
MET:MET proto-oncogene, receptor tyrosine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q31.2
Genomic location:
Preferred name:
NM_000245.4(MET):c.1484C>G (p.Thr495Arg)
HGVS:
  • NC_000007.14:g.116740041C>G
  • NG_008996.1:g.72637C>G
  • NM_000245.4:c.1484C>GMANE SELECT
  • NM_001127500.3:c.1484C>G
  • NM_001324401.3:c.1484C>G
  • NM_001324402.2:c.194C>G
  • NP_000236.2:p.Thr495Arg
  • NP_001120972.1:p.Thr495Arg
  • NP_001311330.1:p.Thr495Arg
  • NP_001311331.1:p.Thr65Arg
  • LRG_662t1:c.1484C>G
  • LRG_662:g.72637C>G
  • NC_000007.13:g.116380095C>G
  • NM_001127500.1:c.1484C>G
Protein change:
T495R
Links:
dbSNP: rs45585831
NCBI 1000 Genomes Browser:
rs45585831
Molecular consequence:
  • NM_000245.4:c.1484C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127500.3:c.1484C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324401.3:c.1484C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324402.2:c.194C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Renal cell carcinoma (RCCP1)
Identifiers:
MONDO: MONDO:0005086; MeSH: D002292; MedGen: C0007134; Human Phenotype Ontology: HP:0005584

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000294263Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 23, 2025) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Clinical genetic testing outcome with multi-gene panel in Asian patients with multiple primary cancers.

Chan GHJ, Ong PY, Low JJH, Kong HL, Ow SGW, Tan DSP, Lim YW, Lim SE, Lee SC.

Oncotarget. 2018 Jul 17;9(55):30649-30660. doi: 10.18632/oncotarget.25769.

PubMed [citation]
PMID:
30093976
PMCID:
PMC6078133

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. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000294263.9

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

Description

This sequence change replaces threonine, which is neutral and polar, with arginine, which is basic and polar, at codon 495 of the MET protein (p.Thr495Arg). This variant is present in population databases (rs45585831, gnomAD 0.006%). This missense change has been observed in individual(s) with parathyroid cancer (PMID: 30093976). ClinVar contains an entry for this variant (Variation ID: 246625). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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: Feb 25, 2025