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NM_000077.5(CDKN2A):c.159G>C (p.Met53Ile) AND CDKN2A-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 14, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004754253.1

Allele description [Variation Report for NM_000077.5(CDKN2A):c.159G>C (p.Met53Ile)]

NM_000077.5(CDKN2A):c.159G>C (p.Met53Ile)

Gene:
CDKN2A:cyclin dependent kinase inhibitor 2A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p21.3
Genomic location:
Preferred name:
NM_000077.5(CDKN2A):c.159G>C (p.Met53Ile)
Other names:
p.M53I:ATG>ATC
HGVS:
  • NC_000009.12:g.21971200C>G
  • NG_007485.1:g.28292G>C
  • NM_000077.5:c.159G>CMANE SELECT
  • NM_001195132.2:c.159G>C
  • NM_001363763.2:c.6G>C
  • NM_058195.4:c.202G>C
  • NM_058197.5:c.*82G>C
  • NP_000068.1:p.Met53Ile
  • NP_000068.1:p.Met53Ile
  • NP_001182061.1:p.Met53Ile
  • NP_001350692.1:p.Met2Ile
  • NP_478102.2:p.Asp68His
  • LRG_11t1:c.159G>C
  • LRG_11:g.28292G>C
  • LRG_11p1:p.Met53Ile
  • NC_000009.11:g.21971199C>G
  • NM_000077.4:c.159G>C
  • NM_058197.4:c.*82G>C
  • P42771:p.Met53Ile
  • p.M53I
Protein change:
D68H; MET53ILE
Links:
UniProtKB: P42771#VAR_001424; OMIM: 600160.0007; dbSNP: rs104894095
NCBI 1000 Genomes Browser:
rs104894095
Molecular consequence:
  • NM_058197.5:c.*82G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000077.5:c.159G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195132.2:c.159G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363763.2:c.6G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_058195.4:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
CDKN2A-related disorder
Synonyms:
CDKN2A-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005361911PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Aug 14, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005361911.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The CDKN2A c.159G>C variant is predicted to result in the amino acid substitution p.Met53Ile. This variant was reported in several individuals with melanoma and in one individual with pancreatic cancer (Table 2. Li et al. 2020. PubMed ID: 31567591; Table 2. Hubert et al. 2021. PubMed ID: 34067022; Table 1, Figure 1b. Flores et al. 1997. PubMed ID: 9416844; Lang et al. 2005. PubMed ID: 16307646; Table 2. FitzGerald et al. 1996. PubMed ID: 8710906; Figure 1. Begg et al. 2005. PubMed ID: 16234564; Table 2. Zhen et al. 2014. PubMed ID: 25356972). In vitro experimental studies show this amino acid change impacts protein function (McKenzie et al. 2010. PubMed ID: 20340136; Figure 3. Monzon et al. 1998. PubMed ID: 9516223). This variant is reported in 0.0075% of alleles in individuals of African descent in gnomAD and is classified as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/9414/). This variant is interpreted as pathogenic.

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

Last Updated: Oct 13, 2024