9-21971108-T-G

Position:

• chr9-21971108-T-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1 PP3_Moderate PP5_Very_Strong

The NM_000077.5(CDKN2A):​c.251A>C​(p.Asp84Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000482 in 1,452,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 7.41

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]

CDKN2A (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PM1: In a chain Cyclin-dependent kinase inhibitor 2A (size 155) in uniprot entity CDN2A_HUMAN there are 42 pathogenic changes around while only 12 benign (78%) in NM_000077.5
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.915
• PP5: Variant 9-21971108-T-G is Pathogenic according to our data. Variant chr9-21971108-T-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 142882.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2A	NM_000077.5	c.251A>C	p.Asp84Ala	missense_variant	2/3	ENST00000304494.10	NP_000068.1
CDKN2A	NM_058195.4	c.294A>C	p.Arg98Arg	synonymous_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.251A>C	p.Asp84Ala	missense_variant	2/3	1	NM_000077.5	ENSP00000307101.5
CDKN2A	ENST00000579755.2	c.294A>C	p.Arg98Arg	synonymous_variant	2/3	1	NM_058195.4	ENSP00000462950.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000482 AC: 7 AN: 1452176 Hom.: 0 Cov.: 31 AF XY: 0.00000830 AC XY: 6 AN XY: 722834

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000630

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	May 15, 2024	This variant has been reported in multiple individuals with cutaneous melanoma (see for example, Table 2, Orlow et al. 2001. PubMed ID: 11687599; Figure 2, Niendorf et al. 2005. PubMed ID: 16169933; Table 1, Miller et al. 2011. PubMed ID: 21462282). This variant has not been reported in a large population database, indicating it is rare. An in vitro experimental study using multiple cell lines suggests this variant increases cell proliferation (Table S2, Kimura et al. 2022. PubMed ID: 35001868). This variant has been classified as pathogenic/likely pathogenic by other institutions in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/142882/). Alternate nucleotide substitutions affecting the same amino acid (p.Asp84Tyr, p.Asp84Asn, and p.Asp84Val) have been reported in multiple individuals with cutaneous melanoma (see for example, Table 2, Ruiz et al. 1999. PubMed ID: 10874641; Table 2, Maubec et al. 2012. PubMed ID: 22841127; Table 3, Borroni et al. 2017. PubMed ID: 28060055). In summary, the c.251A>C (p.Asp84Ala) variant is interpreted as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 26, 2024	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: 20876876, 16169933, 25780468, 11687599, 21325014, 15761864, 10498896, 21462282, 28615371, 35001868) -

Melanoma and neural system tumor syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Jun 21, 2023

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 15, 2023

The p.D84A variant (also known as c.251A>C), located in coding exon 2 of the CDKN2A gene, results from an A to C substitution at nucleotide position 251. The aspartic acid at codon 84 is replaced by alanine, an amino acid with dissimilar properties. This variant has been identified in numerous families with clinical histories that are consistent with a familial melanoma syndrome (Orlow I et al. J Mol Diagn, 2001 Nov;3:158-63; Harland M et al. Hered Cancer Clin Pract, 2014 Nov;12:20; Harland M et al. Genes Chromosomes Cancer, 2005 Jun;43:128-36; Cust AE et al. J. Med. Genet., 2011 Apr;48:266-72; Demenais F et al. J. Natl. Cancer Inst., 2010 Oct;102:1568-83; Miller PJ et al. Hum. Mutat., 2011 Aug;32:900-11; Niendorf KB et al. J. Med. Genet., 2006 Jun;43:501-6; Ambry internal data). In addition, this amino acid sits at the interface with CDK6 and is anticipated to result in decreased binding affinity (Yuan C et al. Protein Sci., 2000 Jun;9:1120-8; Ambry internal data). A functional study reported this variant as deleterious based on in-vitro assessment of impact on proliferation in human pancreatic cancer cell lines (Kimura H et al. Elife, 2022 01;11). Another alteration at the same codon, p.D84N (c.250G>A), has been detected in a Slovenian patient with multiple primary cutaneous melanomas (CM) who has no family history and in a French patient with a CM who has a first-degree relative with a CM (Peric B, BMC Med. Genet. 2008 ; 9():86; Maubec E, J. Am. Acad. Dermatol. 2012 Dec; 67(6):1257-64). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is also considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Familial melanoma Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 28, 2024

This sequence change replaces aspartic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 84 of the CDKN2A (p16INK4a) protein (p.Asp84Ala). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with familial cutaneous melanoma (PMID: 11687599, 15761864, 16169933, 20876876, 21462282; Invitae). ClinVar contains an entry for this variant (Variation ID: 142882). 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). This variant disrupts the p.Asp84 amino acid residue in CDKN2A (p16INK4a). Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10491434, 21462282, 28060055). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.51
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.53	D;T;.;.;.;.;T;.
Eigen	Uncertain	0.63
Eigen_PC	Uncertain	0.66
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.95	D;D;.;D;.;D;T;T
M_CAP	Pathogenic	0.71	D
MetaRNN	Pathogenic	0.91	D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.70	D
PrimateAI	Uncertain	0.67	T
PROVEAN	Pathogenic	-7.4	D;.;.;D;.;.;.;.
REVEL	Pathogenic	0.79
Sift	Uncertain	0.0030	D;.;.;D;.;.;.;.
Sift4G	Uncertain	0.044	D;T;D;D;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.;.;.
Vest4		0.83
MutPred		0.53		Gain of methylation at R87 (P = 0.0585);Gain of methylation at R87 (P = 0.0585);.;Gain of methylation at R87 (P = 0.0585);.;.;.;.;
MVP		1.0
MPC		1.4
ClinPred		0.99	D
GERP RS		5.9
Varity_R		0.82
gMVP		0.87

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: rs587782792; hg19: chr9-21971107; COSMIC: COSV58702489; COSMIC: COSV58702489;