9-21974733-A-G

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PP3_Strong PP5_Very_Strong

The NM_000077.5(CDKN2A):c.95T>C(p.Leu32Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000411 in 1,460,584 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L32V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 4.47

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 14 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 16 uncertain in NM_000077.5
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.972
• PP5: Variant 9-21974733-A-G is Pathogenic according to our data. Variant chr9-21974733-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 236992.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKN2A	NM_000077.5	c.95T>C	p.Leu32Pro	missense_variant	1/3	ENST00000304494.10
CDKN2A	NM_058195.4	c.194-3525T>C		intron_variant		ENST00000579755.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2A	ENST00000304494.10	c.95T>C	p.Leu32Pro	missense_variant	1/3	1	NM_000077.5	P2
CDKN2A	ENST00000579755.2	c.194-3525T>C		intron_variant		1	NM_058195.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000411 AC: 6 AN: 1460584 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 726616

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: 0.00000540

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial melanoma Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 03, 2018	Variant summary: CDKN2A c.95T>C (p.Leu32Pro) results in a non-conservative amino acid change located in the Ankyrin repeat-containing domain (IPR020683) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 239900 control chromosomes (gnomAD). The variant, c.95T>C, has been reported in the literature in individuals affected with Cutaneous Malignant Melanoma (Jouenne_2016, Jovanovic_2010, Box_2001, McKenzie_2010). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (McKenzie_2010). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Mar 10, 2021	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 Experimental studies have shown that this missense change interferes with the interaction between p16INK4a and its binding partners CDK4 and CDK6 (PMID: 20340136, 19712690). This variant has been reported in patients and families affected with melanoma and pancreatic cancer (PMID: 19759551, 17218939, 16905682, 20340136, 17047042, 28592523).  It has been shown to segregate with disease in one family (PMID: 8595405). ClinVar contains an entry for this variant (Variation ID: 236992). This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with proline at codon 32 of the CDKN2A (p16INK4a) protein (p.Leu32Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 26, 2016

The p.L32P variant (also known as c.95T>C), located in coding exon 1 of the CDKN2A gene, results from a T to C substitution at nucleotide position 95. The leucine at codon 32 is replaced by proline, an amino acid with similar properties. This variant has been reported in numerous individuals with a personal and/or family history of cutaneous melanoma (Aitken J et al, J. Natl. Cancer Inst. 1999 Mar; 91(5):446-52; Begg CB et al, J. Natl. Cancer Inst. 2005 Oct; 97(20):1507-15; Berwick M et al, Cancer Epidemiol. Biomarkers Prev. 2006 Aug; 15(8):1520-5; Bishop DT et al, J. Natl. Cancer Inst. 2002 Jun; 94(12):894-903; Goldstein AM et al, Cancer Res. 2006 Oct; 66(20):9818-28; Goldstein AM et al, J. Med. Genet. 2007 Feb; 44(2):99-10; Jovanovic B et al, J. Invest. Dermatol. 2010 Feb; 130(2):618-20; Orlow I et al, J. Invest. Dermatol. 2007 May; 127(5):1234-43). Further, a functional analysis of the p.L32P variant has demonstrated abolished CDK4 binding capability (McKenzie HA et al, Hum. Mutat. 2010 Jun; 31(6):692-701). 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 majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.94
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.32
Cadd	Pathogenic	27
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.68	D;T;.
Eigen	Pathogenic	0.92
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.84	T;T;T
M_CAP	Pathogenic	0.89	D
MetaRNN	Pathogenic	0.97	D;D;D
MetaSVM	Uncertain	0.70	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.72	T
PROVEAN	Pathogenic	-5.7	D;.;D
REVEL	Pathogenic	0.80
Sift	Uncertain	0.0010	D;.;D
Sift4G	Pathogenic	0.0010	D;D;D
Polyphen		1.0	D;.;.
Vest4		0.81
MutPred		0.74		Gain of disorder (P = 0.0175);Gain of disorder (P = 0.0175);Gain of disorder (P = 0.0175);
MVP		0.97
MPC		1.6
ClinPred		1.0	D
GERP RS		4.9
Varity_R		0.89
gMVP		1.0

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: rs878853650; hg19: chr9-21974732; COSMIC: COSV58685103; COSMIC: COSV58685103;