rs104894099

chr9-21971183-A-Cchr9-21971183-A-Gchr9-21971183-A-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 12P and 1B. PM1 PM2 PP5_Very_Strong BP4

The NM_000077.5(CDKN2A):c.176T>G(p.Val59Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000208 in 1,444,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign 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. V59A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:11 O:1
• Conservation: PhyloP100: 6.84

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 11 ACMG points.

• PM1: In a hotspot region, there are 11 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 16 uncertain in NM_000077.5
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 9-21971183-A-C is Pathogenic according to our data. Variant chr9-21971183-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 9423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.2724597).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKN2A	NM_000077.5	c.176T>G	p.Val59Gly	missense_variant	2/3	ENST00000304494.10
CDKN2A	NM_058195.4	c.219T>G	p.Ser73Arg	missense_variant	2/3	ENST00000579755.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2A	ENST00000304494.10	c.176T>G	p.Val59Gly	missense_variant	2/3	1	NM_000077.5	P2
CDKN2A	ENST00000579755.2	c.219T>G	p.Ser73Arg	missense_variant	2/3	1	NM_058195.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000456 AC: 1 AN: 219096 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 122126

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000296

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: 0.00000208 AC: 3 AN: 1444950 Hom.: 0 Cov.: 31 AF XY: 0.00000278 AC XY: 2 AN XY: 719186

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000225

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: 0.0000166

GnomAD4 genome Cov.: 32

Bravo AF: 0.0000113

ExAC AF: 0.00000838 AC: 1

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:11 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2024	CDKN2A: PP1:Strong, PM2, PS4:Moderate, PS3:Supporting, BP4 -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 29, 2022	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; Published functional studies demonstrate a damaging effect: reduced binding with CDK4 and CDK6 and a moderate impact on cell proliferation (Yacobson et al., 2003; Kannengiesser et al., 2009); This variant is associated with the following publications: (PMID: 15150307, 29506128, 9425228, 25780468, 19571771, 26681309, 21893440, 19260062, 22841127, 19799798, 10874641, 15860862, 16905682, 12700603, 9823374, 28873162, 28717660, 15146471, 16470311, 17492760, 17055252, 29543703, 31589614, 33237286, 28979722, 20653773, 32113160, 34072659, 33322357) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jan 26, 2021	This variant has been reported as individuals and families with melanoma and pancreatic cancer in the published literature (PMID: 9425228 (1998), 22841127 (2012), 26681309 (2016), 29506128 (2018), 29543703 (2018), and 32113160 (2020)). A peer-reviewed experimental study has reported a damaging effect of the variant on p16 protein function (PMID: 12700603 (2003)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is disease causing and damaging. Based on the available information, this variant is classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Aug 03, 2023	The CDKN2A locus encodes two different gene products, p16INK4a and p14ARF (https://www.ncbi.nlm.nih.gov/books/NBK7030/). This missense variant replaces valine with glycine at codon 59 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 the mutant protein to exhibit defective binding to CDK4 and CDK6, and reduced ability to suppress cell proliferation (PMID: 12700603, 19260062). This variant has been observed in many individuals and families affected with melanoma (PMID: 9036865, 9425228, 10874641, 12700603, 14646620, 19260062, 19571771, 20653773, 21893440, 22841127, 25780468, 26681309, 29543703, 32455486, 35566480) and shown to segregate with melanoma in three unrelated families (PMID: 12700603). This variant has also been reported in an individual affected with familial pancreatic cancer (PMID: 32113160). This variant has been identified in 1/219096 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 20, 2022	The p.V59G variant (also known as c.176T>G), located in coding exon 2 of the CDKN2A gene, results from a T to G substitution at nucleotide position 176. The valine at codon 59 is replaced by glycine, an amino acid with dissimilar properties. This alteration has been reported in several families with multiple cases of melanoma and/or pancreatic cancer (Puig S et al. J. Clin. Oncol. 2005 May;23:3043-51; Pedace L et al. Cancer Epidemiol. 2011 Dec;35:e116-20; Nagore E et al. Melanoma Res. 2009 Aug;19:211-4; Goldstein AM et al. J. Med. Genet. 2007 Feb;44:99-106; Earl J et a. EBioMedicine 2020 Mar;53:102675; De Simone P et al. Int J Mol Sci, 2020 Dec;21:). One study described this alteration in four families with multiple cases of melanoma and determined that it may be a founder mutation of Mediterranean origin (Yakobson E et al. Eur. J. Hum. Genet. 2003 Apr;11:288-96). Based on the results of protein&ndash;protein interaction and cell proliferation assays, the authors concluded that this alteration likely impairs p16 protein function, but may be only a moderate dysfunction mutation. Notably, there were several unaffected p.V59G carriers identified in these four families. In addition, one individual diagnosed with melanoma at age 36 was found to be homozygous for this alteration (Yakobson E et al. Eur. J. Hum. Genet. 2003 Apr;11:288-96). This alteration has also been reported in pancreatic cancer patients (Lowery MA et al. J. Natl. Cancer Inst., 2018 10;110:1067-1074; Earl J et al. EBioMedicine, 2020 Mar;53:102675), including in a patient with a rare tumor type of adenosquamous pancreatic carcinoma (ASPC) (Mart&iacute;nez de Juan F et al. World J Gastrointest Oncol. 2017 Sep;9:390-396). 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. -

Familial melanoma Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 18, 2022	Variant summary: CDKN2A c.176T>G (p.Val59Gly) results in a non-conservative amino acid change located in the second ankyrin repeat domain (Soufir_1998) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.6e-06 in 219096 control chromosomes. c.176T>G has been reported in the literature in multiple individuals from families affected with sporadic/Cutaneous Malignant Melanoma ((example, Piccinin_1997, Soufir_1998, Yakobson_2003, Puig_2005, Casula_2007, de Torre_2010, De Unamuno_2018). 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 in-vitro (example, Yakobson_2003). The most pronounced variant effect results in moderate levels of dysfunction as measured by ability to interact with CDK4 and CDK6 as well as its ability to inhibit the proliferation of human diploid fibroblasts. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 18, 2023	This sequence change replaces valine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 59 of the CDKN2A (p16INK4a) protein (p.Val59Gly). This variant is present in population databases (rs104894099, gnomAD 0.003%). This missense change has been observed in individuals with melanoma (PMID: 9425228, 12700603, 15146471, 19571771, 19799798, 20653773, 21893440, 22841127, 26681309). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 9423). 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: 12700603). For these reasons, this variant has been classified as Pathogenic. -

Melanoma, cutaneous malignant, susceptibility to, 2 Pathogenic:1 Other:1

risk factor, no assertion criteria provided	literature only	OMIM	Apr 01, 2003	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jul 20, 2022	- -

Melanoma and neural system tumor syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Jan 13, 2023

- -

Melanoma and neural system tumor syndrome;C1835044:Melanoma, cutaneous malignant, susceptibility to, 2;C1838547:Melanoma-pancreatic cancer syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Dec 17, 2021

- -

Melanoma-pancreatic cancer syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Counsyl

Aug 10, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.64
BayesDel_addAF	Uncertain	0.035	T
BayesDel_noAF	Benign	-0.10
Cadd	Uncertain	24
Dann	Benign	0.94
DEOGEN2	Benign	0.0071	T;T
Eigen	Benign	0.18
Eigen_PC	Benign	0.20
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Benign	0.070	D
MetaRNN	Benign	0.27	T;T
MetaSVM	Benign	-0.86	T
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;N;N;N
Sift4G	Benign	0.43	T;T
Vest4		0.31
MVP		0.99
ClinPred		0.81	D
GERP RS		4.7

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: rs104894099; hg19: chr9-21971182; COSMIC: COSV58728660; COSMIC: COSV58728660;