9-21971200-C-T

Position:

• chr9-21971200-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PS1 PM1 PM2 PM5 PP5_Very_Strong

The NM_000077.5(CDKN2A):​c.159G>A​(p.Met53Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin Lovd. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M53T) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 5.60

Genes affected

CDKN2A (HGNC:1787): (cyclin dependent kinase inhibitor 2A) This gene generates several transcript variants which differ in their first exons. At least three alternatively spliced variants encoding distinct proteins have been reported, two of which encode structurally related isoforms known to function as inhibitors of CDK4 kinase. The remaining transcript includes an alternate first exon located 20 Kb upstream of the remainder of the gene; this transcript contains an alternate open reading frame (ARF) that specifies a protein which is structurally unrelated to the products of the other variants. This ARF product functions as a stabilizer of the tumor suppressor protein p53 as it can interact with, and sequester, the E3 ubiquitin-protein ligase MDM2, a protein responsible for the degradation of p53. In spite of the structural and functional differences, the CDK inhibitor isoforms and the ARF product encoded by this gene, through the regulatory roles of CDK4 and p53 in cell cycle G1 progression, share a common functionality in cell cycle G1 control. This gene is frequently mutated or deleted in a wide variety of tumors, and is known to be an important tumor suppressor gene. [provided by RefSeq, Sep 2012]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PS1: Transcript NM_000077.5 (CDKN2A) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in Lovd
• PM1: In a repeat ANK 2 (size 28) in uniprot entity CDN2A_HUMAN there are 15 pathogenic changes around while only 3 benign (83%) in NM_000077.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr9-21971201-A-G is described in Lovd as [Pathogenic].
• PP5: Variant 9-21971200-C-T is Pathogenic according to our data. Variant chr9-21971200-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 532294.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-21971200-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2A	NM_000077.5	c.159G>A	p.Met53Ile	missense_variant	2/3	ENST00000304494.10	NP_000068.1
CDKN2A	NM_058195.4	c.202G>A	p.Asp68Asn	missense_variant	2/3	ENST00000579755.2	NP_478102.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2A	ENST00000304494.10	c.159G>A	p.Met53Ile	missense_variant	2/3	1	NM_000077.5	ENSP00000307101	P2
CDKN2A	ENST00000579755.2	c.202G>A	p.Asp68Asn	missense_variant	2/3	1	NM_058195.4	ENSP00000462950

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 25, 2023	This missense variant replaces methionine with isoleucine at codon 53 outside of a highly conserved region of the ankyrin repeats of the CDKN2A (p16INK4A) protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have shown this variant to interfere with CDKN2A (p16INK4a) protein binding to CDK4 (PMID: 9328469, 9389568, 11595726) and result in the loss of cell cycle-inhibitory activity (PMID: 11595726). This variant has been reported in multiple individuals affected with melanoma (PMID: 16234564, 17171691, 31567591) and pancreatic cancer (PMID: 25356972, 32482799). A different nucleotide substitution resulting in the same protein consequence (c.159G>C, p.Met53Ile) is a common cause of melanoma in the Scottish (PMID: 17171691) and Norwegian populations (PMID 27804060). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 16, 2024	The p.M53I pathogenic mutation (also known as c.159G>A), located in coding exon 2 of the CDKN2A gene, results from a G to A substitution at nucleotide position 159. The methionine at codon 53 is replaced by isoleucine, an amino acid with highly similar properties. This alteration has been reported in multiple individuals with either multiple primary melanoma (MPM) or a single primary melanoma (SPM) (Begg CB et al. J. Natl. Cancer Inst., 2005 Oct;97:1507-15; Berwick M et al. Cancer Epidemiol. Biomarkers Prev., 2006 Aug;15:1520-5; Orlow I et al. J. Invest. Dermatol., 2007 May;127:1234-43; Ambry internal data). An alteration resulting in the same amino acid substitution, c.159G>C, is believed to be Scottish founder mutation and has been shown occur in and segregate with disease in multiple large melanoma kindreds (Lang J et al. Br. J. Dermatol., 2005 Dec;153:1121-5; Lang J et al. Genes Chromosomes Cancer, 2007 Mar;46:277-87; FitzGerald MG et al. Proc. Natl. Acad. Sci. U.S.A., 1996 Aug;93:8541-5; Goldstein AM et al. J. Med. Genet., 2007 Feb;44:99-106; MacKie RM et al. J. Invest. Dermatol., 1998 Aug;111:269-72; Monzon et al. N Eng J Med 1998; 338(13): 879-87; Soufir N, et al. Hum. Mol. Genet. 1998 Feb;7(2):209-16; Walker GJ, Hum. Mol. Genet. 1995 Oct; 4(10):1845-52). Functional analyses of proteins harboring p.M53I substitution have demonstrated severely impaired CDK4 binding, reduced CDK6 binding, and reduced colony forming ability (Becker TM, et al. Clin. Cancer Res. 2001 Oct;7(10):3282-8; Harland M et al. Hum. Mol. Genet., 1997 Nov;6:2061-7; McKenzie et al. Hum Mutat 2010; 31(6): 692-701; Sun et al. Int J Cancer 1997; 73(4): 531-6). Based on internal structural analysis, p.M53I sits at the interface between alpha-helices and is anticipated to result in a significant decrease in structural stability and/or protein folding (Ambry internal data). Of note, this alteration is also designated as p.M45I in published literature. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Melanoma and neural system tumor syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 22, 2022

- -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Apr 20, 2022

Observed in multiple individuals with melanoma or pancreatic cancer (Begg 2005, Berwick 2006, Orlow 2007, Zhen 2015, Overbeek 2021); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 11595726, 21462282, 32482799, 9328469, 16234564, 16896043, 17218939, 25356972) -

Familial melanoma Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 27, 2023

The CDKN2A gene encodes two different proteins, p16INK4a and p14ARF, which are translated from alternative transcripts with different open reading frames. Both transcripts have been analyzed. We report either the variant with the higher classification or default to the CDKN2A (p16INK4a) variant. This report therefore includes the details for the CDKN2A (p16INK4a) variant. This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 53 of the CDKN2A (p16INK4a) protein (p.Met53Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with melanoma and/or pancreatic cancer (PMID: 8595405, 9328469, 9389568, 9699728, 11595726, 16234564, 16307646, 16905682, 17171691, 25356972). This variant is also known as c.202G>A (p.Asp68Asn) in the CDKN2A (p14ARF) transcript. ClinVar contains an entry for this variant (Variation ID: 532294). 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: 9328469, 9389568, 11595726). For these reasons, this variant has been classified as Pathogenic. While the evidence indicates that this variant confers risk of developing CDKN2A (p16INK4a)-associated conditions, its association with risk for developing CDKN2A (p14ARF)-associated conditions is still unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Uncertain	0.050
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.12	T;T
Eigen	Uncertain	0.42
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.65	.;T
M_CAP	Pathogenic	0.49	D
MetaRNN	Uncertain	0.48	T;T
MetaSVM	Benign	-0.43	T
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D
PROVEAN	Uncertain	-3.8	.;D
REVEL	Pathogenic	0.72
Sift	Benign	0.033	.;D
Sift4G	Benign	0.069	T;T
Vest4		0.45
MVP		0.95
ClinPred		0.99	D
GERP RS		5.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs104894095; hg19: chr9-21971199; COSMIC: COSV58683319; COSMIC: COSV58683319;