NM_000077.5(CDKN2A):c.73G>A (p.Val25Ile) AND Familial melanoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 28, 2021
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:: RCV001885809.5

Allele description [Variation Report for NM_000077.5(CDKN2A):c.73G>A (p.Val25Ile)]

NM_000077.5(CDKN2A):c.73G>A (p.Val25Ile)

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.73G>A (p.Val25Ile)

HGVS:

NC_000009.12:g.21974755C>T
NG_007485.1:g.24737G>A
NM_000077.5:c.73G>AMANE SELECT
NM_001195132.2:c.73G>A
NM_001363763.2:c.-3-3547G>A
NM_058195.4:c.194-3547G>A
NM_058197.5:c.73G>A
NP_000068.1:p.Val25Ile
NP_001182061.1:p.Val25Ile
NP_478104.2:p.Val25Ile
LRG_11:g.24737G>A
NC_000009.11:g.21974754C>T

Protein change:

V25I

Links:

dbSNP: rs2131113089

NCBI 1000 Genomes Browser:

rs2131113089

Molecular consequence:

NM_001363763.2:c.-3-3547G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_058195.4:c.194-3547G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000077.5:c.73G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195132.2:c.73G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_058197.5:c.73G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial melanoma
Synonyms:: Hereditary melanoma; Hereditary cutaneous melanoma
Identifiers:: MONDO: MONDO:0018961; MedGen: C1512419

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002138084	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 28, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002138084

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 28, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Invitae, SCV002138084.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant has not been reported in the literature in individuals with CDKN2A (p16INK4a)-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant is not present in population databases (ExAC no frequency). This sequence change replaces valine with isoleucine at codon 25 of the CDKN2A (p16INK4a) protein (p.Val25Ile). The valine residue is weakly conserved and there is a small physicochemical difference between valine and isoleucine.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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