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NM_000077.5(CDKN2A):c.35C>A (p.Ser12Ter) AND CDKN2A-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 3, 2023
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:
RCV003396344.6

Allele description [Variation Report for NM_000077.5(CDKN2A):c.35C>A (p.Ser12Ter)]

NM_000077.5(CDKN2A):c.35C>A (p.Ser12Ter)

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.35C>A (p.Ser12Ter)
HGVS:
  • NC_000009.12:g.21974793G>T
  • NG_007485.1:g.24699C>A
  • NM_000077.5:c.35C>AMANE SELECT
  • NM_001195132.2:c.35C>A
  • NM_001363763.2:c.-3-3585C>A
  • NM_058195.4:c.194-3585C>A
  • NM_058197.5:c.35C>A
  • NP_000068.1:p.Ser12Ter
  • NP_000068.1:p.Ser12Ter
  • NP_001182061.1:p.Ser12Ter
  • NP_478104.2:p.Ser12Ter
  • LRG_11t1:c.35C>A
  • LRG_11:g.24699C>A
  • LRG_11p1:p.Ser12Ter
  • NC_000009.11:g.21974792G>T
  • NM_000077.4:c.35C>A
Protein change:
S12*
Links:
dbSNP: rs141798398
NCBI 1000 Genomes Browser:
rs141798398
Molecular consequence:
  • NM_001363763.2:c.-3-3585C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_058195.4:c.194-3585C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000077.5:c.35C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001195132.2:c.35C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_058197.5:c.35C>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004103601PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Nov 3, 2023) 		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, SCV004103601.3

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

Description

The CDKN2A c.35C>A variant is predicted to result in premature protein termination (p.Ser12*). This variant corresponds to c.35C>A (p.Ser*) in both p16INK4A (NM_000077.4) and p14ARF (NM_058195.3). This variant has been reported in individuals with cutaneous malignant melanoma (Table 1, Casula et al. 2007. PubMed ID: 17055252; Table 1, Casula et al. 2009. PubMed ID: 19799798; Table S3, Taylor et al. 2017. PubMed ID: 28830827). It has also been reported in an individual with a personal history of breast cancer and multiple melanomas (Table 2, Seifert et al. 2016. PubMed ID: 27083775). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. It is interpreted as pathogenic in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/630390/). Nonsense variants in CDKN2A are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Oct 13, 2024