9-21971109-C-A

Position:

• chr9-21971109-C-A

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1 PM2 PP3_Moderate PP5

The NM_000077.5(CDKN2A):​c.250G>T​(p.Asp84Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,452,146 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 Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:2
• Conservation: PhyloP100: 7.31

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 Likely_pathogenic. Variant got 7 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
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.924
• PP5: Variant 9-21971109-C-A is Pathogenic according to our data. Variant chr9-21971109-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 376306.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Pathogenic=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2A	NM_000077.5	c.250G>T	p.Asp84Tyr	missense_variant	2/3	ENST00000304494.10	NP_000068.1
CDKN2A	NM_058195.4	c.293G>T	p.Arg98Leu	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.250G>T	p.Asp84Tyr	missense_variant	2/3	1	NM_000077.5	ENSP00000307101	P2
CDKN2A	ENST00000579755.2	c.293G>T	p.Arg98Leu	missense_variant	2/3	1	NM_058195.4	ENSP00000462950

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000432 AC: 1 AN: 231524 Hom.: 0 AF XY: 0.00000783 AC XY: 1 AN XY: 127750

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000293

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.89e-7 AC: 1 AN: 1452146 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 722814

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 25, 2020	This missense variant replaces aspartic acid with tyrosine at codon 84 of the CDKN2A (p16INK4A) protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. A functional study has reported this variant to have no detectable binding to CDK4 and CDK6 in vitro (PMID: 10498896). This variant has been reported in an affected member of a Spanish cutaneous malignant melanoma family, however, segregation with two other affected members could not be examined (PMID: 10874641). The variant also has been detected in two affected members of a melanoma-prone family and at least two additional carriers whose cancer spectrum are not consistent with CDKN2A-associated cancers (Color internal data and communication with external laboratories). This variant has been identified in 1/231524 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Two different missense variants, p.Asp84Ala and p.Asp84Asn, have conflicting reports between likely pathogenic and uncertain significance in ClinVar (variation ID: 142882, 229806). Although there is a suspicion that this variant may be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 20, 2022	The p.D84Y pathogenic mutation (also known as c.250G>T), located in coding exon 2 of the CDKN2A gene, results from a G to T substitution at nucleotide position 250. The aspartic acid at codon 84 is replaced by tyrosine, an amino acid with highly dissimilar properties. Functional studies demonstrate that this alteration results in impaired binding with CDK4 and CDK6 (Miller PJ et al. Hum. Mutat. 2011 Aug;32(8):900-11; Ruas M et al. Oncogene 1999 Sep;18(39):5423-34). Further, this alteration occurs at a mutational hotspot, with p.D84N and p.D84H also demonstrating impaired binding (Ruas M et al. Oncogene 1999 Sep;18(39):5423-34). Structural analysis indicates that this alteration dramatically alters the electrostatic character of the CDK-binding surface of p16, resulting in a severe pertubation of the protein structure which likely leads to misfolding and loss of binding (Ruas M et al. Oncogene 1999 Sep;18(39):5423-34; Rajasekaran R et al. Biochimie 2008 Oct;90(10):1523-9; Ambry internal data). In addition, this alteration has been reported in multiple families with familial melanoma, including one family with three individuals with cutaneous malignant melanoma and two individuals with dysplastic nevi (Ambry internal data; Miller PJ et al. Hum. Mutat. 2011 Aug; 32(8):900-11; Ruiz A et al. J. Med. Genet. 1999 Jun;36(6):490-3). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Neoplasm Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Database of Curated Mutations (DoCM)

Jul 14, 2015

- -

Familial melanoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 22, 2023

The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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. Experimental studies have shown that this missense change affects CDKN2A (p16INK4a) function (PMID: 10360174, 10498896). 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. ClinVar contains an entry for this variant (Variation ID: 376306). This variant is also known as c.293G>T (p.Arg98Leu) in the CDKN2A (p14AFR) transcript. This missense change has been observed in individual(s) with melanoma (PMID: 10874641, 21462282, 26650189, 26681309). This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 84 of the CDKN2A (p16INK4a) protein (p.Asp84Tyr). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.75
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Uncertain	0.13
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.53	D;T;.;.;.;.;T;.
Eigen	Pathogenic	0.74
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.97	D;D;.;D;.;D;D;D
M_CAP	Pathogenic	0.67	D
MetaRNN	Pathogenic	0.92	D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.30	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.73	T
PROVEAN	Pathogenic	-8.4	D;.;.;D;.;.;.;.
REVEL	Pathogenic	0.75
Sift	Uncertain	0.0010	D;.;.;D;.;.;.;.
Sift4G	Uncertain	0.0090	D;T;D;D;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.;.;.
Vest4		0.86
MutPred		0.58		Loss of disorder (P = 0.0438);Loss of disorder (P = 0.0438);.;Loss of disorder (P = 0.0438);.;.;.;.;
MVP		0.99
MPC		1.4
ClinPred		0.99	D
GERP RS		5.9
Varity_R		0.93
gMVP		0.91

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: rs11552822; hg19: chr9-21971108; COSMIC: COSV58683210; COSMIC: COSV58683210;