NM_000077.5(CDKN2A):c.59C>G (p.Ala20Gly) AND Familial melanoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 24, 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:: RCV000204448.9

Allele description [Variation Report for NM_000077.5(CDKN2A):c.59C>G (p.Ala20Gly)]

NM_000077.5(CDKN2A):c.59C>G (p.Ala20Gly)

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.59C>G (p.Ala20Gly)

HGVS:

NC_000009.12:g.21974769G>C
NG_007485.1:g.24723C>G
NM_000077.5:c.59C>GMANE SELECT
NM_001195132.2:c.59C>G
NM_001363763.2:c.-3-3561C>G
NM_058195.4:c.194-3561C>G
NM_058197.5:c.59C>G
NP_000068.1:p.Ala20Gly
NP_000068.1:p.Ala20Gly
NP_001182061.1:p.Ala20Gly
NP_478104.2:p.Ala20Gly
LRG_11t1:c.59C>G
LRG_11:g.24723C>G
LRG_11p1:p.Ala20Gly
NC_000009.11:g.21974768G>C
NM_000077.4:c.59C>G

Protein change:

A20G

Links:

dbSNP: rs864622484

NCBI 1000 Genomes Browser:

rs864622484

Molecular consequence:

NM_001363763.2:c.-3-3561C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_058195.4:c.194-3561C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000077.5:c.59C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001195132.2:c.59C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_058197.5:c.59C>G - 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
SCV000260815	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 24, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 35001868, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000260815

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 24, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Functional CDKN2A assay identifies frequent deleterious alleles misclassified as variants of uncertain significance.

Kimura H, Paranal RM, Nanda N, Wood LD, Eshleman JR, Hruban RH, Goggins MG, Klein AP; Familial Pancreatic Cancer Genome Sequencing Project., Roberts NJ.

Elife. 2022 Jan 10;11. doi:pii: e71137. 10.7554/eLife.71137.

PubMed [citation]

PMID:: 35001868
PMCID:: PMC8824478

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, SCV000260815.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces alanine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 20 of the CDKN2A (p16INK4a) protein (p.Ala20Gly). This variant is present in population databases (no rsID available, gnomAD 0.001%). This variant has not been reported in the literature in individuals affected with CDKN2A (p16INK4a)-related conditions. ClinVar contains an entry for this variant (Variation ID: 220344). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects CDKN2A (p16INK4a) function (PMID: 35001868). 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.

#	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: Sep 29, 2024

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