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NM_000077.5(CDKN2A):c.45G>T (p.Trp15Cys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 9, 2014
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:
RCV000766725.1

Allele description [Variation Report for NM_000077.5(CDKN2A):c.45G>T (p.Trp15Cys)]

NM_000077.5(CDKN2A):c.45G>T (p.Trp15Cys)

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.45G>T (p.Trp15Cys)
Other names:
p.W15C:TGG>TGT
HGVS:
  • NC_000009.12:g.21974783C>A
  • NG_007485.1:g.24709G>T
  • NM_000077.5:c.45G>TMANE SELECT
  • NM_001195132.2:c.45G>T
  • NM_001363763.2:c.-3-3575G>T
  • NM_058195.4:c.194-3575G>T
  • NM_058197.5:c.45G>T
  • NP_000068.1:p.Trp15Cys
  • NP_000068.1:p.Trp15Cys
  • NP_001182061.1:p.Trp15Cys
  • NP_478104.2:p.Trp15Cys
  • LRG_11t1:c.45G>T
  • LRG_11t2:c.194-3575G>T
  • LRG_11:g.24709G>T
  • LRG_11p1:p.Trp15Cys
  • NC_000009.11:g.21974782C>A
  • NM_000077.4:c.45G>T
  • NM_058195.3:c.194-3575G>T
Protein change:
W15C
Links:
dbSNP: rs138677674
NCBI 1000 Genomes Browser:
rs138677674
Molecular consequence:
  • NM_001363763.2:c.-3-3575G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_058195.4:c.194-3575G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000077.5:c.45G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195132.2:c.45G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_058197.5:c.45G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000210953GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Oct 9, 2014) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000210953.10

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

Description

This variant is denoted CDKN2A c.45G>T at the cDNA level, p.Trp15Cys (W15C) at the protein level, and results in the change of a Tryptophan to a Cysteine (TGG>TGT). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. CDKN2A Trp15Cys was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Tryptophan and Cysteine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CDKN2A Trp15Cys occurs at a position that is variable across species and is located in the first Ankyrin repeat domain (UniProt). In silico analyses predict that this variant is unlikely to alter protein structure or function. Based on currently available information, it is unclear whether CDKN2A Trp15Cys is pathogenic or benign. We consider it to be a variant of uncertain significance.

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

Last Updated: Apr 6, 2024