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NM_002386.4(MC1R):c.530C>T (p.Thr177Met) AND Melanoma, cutaneous malignant, susceptibility to, 5

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 26, 2023
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:
RCV002894899.3

Allele description [Variation Report for NM_002386.4(MC1R):c.530C>T (p.Thr177Met)]

NM_002386.4(MC1R):c.530C>T (p.Thr177Met)

Gene:
MC1R:melanocortin 1 receptor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_002386.4(MC1R):c.530C>T (p.Thr177Met)
HGVS:
  • NC_000016.10:g.89919788C>T
  • NG_012026.1:g.6910C>T
  • NG_027810.1:g.2780C>T
  • NG_134987.1:g.488C>T
  • NM_002386.4:c.530C>TMANE SELECT
  • NP_002377.4:p.Thr177Met
  • NC_000016.9:g.89986196C>T
Protein change:
T177M
Molecular consequence:
  • NM_002386.4:c.530C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Melanoma, cutaneous malignant, susceptibility to, 5
Synonyms:
Cutaneous malignant melanoma 5
Identifiers:
MONDO: MONDO:0013133; MedGen: C2751295; Orphanet: 618; OMIM: 613099

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003244974Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 26, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

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, SCV003244974.2

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

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MC1R protein function. 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. ClinVar contains an entry for this variant (Variation ID: 2038369). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 177 of the MC1R protein (p.Thr177Met). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with MC1R-related conditions.

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

Last Updated: Sep 29, 2024