9-21971160-C-G

Position:

• chr9-21971160-C-G

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1 PM2 PM5 PP3_Strong PP5

The NM_000077.5(CDKN2A):​c.199G>C​(p.Gly67Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000277 in 1,442,608 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G67S) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3 U:2
• Conservation: PhyloP100: 5.57

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 11 ACMG points.

• 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 chr9-21971160-C-T is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.981
• PP5: Variant 9-21971160-C-G is Pathogenic according to our data. Variant chr9-21971160-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 216272.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Likely_pathogenic=2}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2A	NM_000077.5	c.199G>C	p.Gly67Arg	missense_variant	2/3	ENST00000304494.10	NP_000068.1
CDKN2A	NM_058195.4	c.242G>C	p.Arg81Pro	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.199G>C	p.Gly67Arg	missense_variant	2/3	1	NM_000077.5	ENSP00000307101.5
CDKN2A	ENST00000579755.2	c.242G>C	p.Arg81Pro	missense_variant	2/3	1	NM_058195.4	ENSP00000462950.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000469 AC: 1 AN: 213440 Hom.: 0 AF XY: 0.00000840 AC XY: 1 AN XY: 119108

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000300

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: 0.00000277 AC: 4 AN: 1442608 Hom.: 0 Cov.: 31 AF XY: 0.00000279 AC XY: 2 AN XY: 717748

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000227

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: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:3 Uncertain:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 31, 2023	The CDKN2A locus encodes two different gene products, p16INK4a and p14ARF (https://www.ncbi.nlm.nih.gov/books/NBK7030/). This missense variant replaces glycine with arginine at codon 67 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). Functional studies have reported inconclusive results with the mutant protein showing partial loss of CDK4 binding activity and normal to moderately impaired cell cycle control (PMID: 19260062, 21462282, 33322357). This variant has been reported in seven individuals with melanoma with positive family history of melanoma or pancreatic cancer (PMID: 10390011, 19260062, 21462282, 33322357) and in an individual with familial pancreatic cancer (PMID: 22368299). This variant is rare in the general population and has been identified in 1/213440 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although the impact of this variant on p16INK4a protein function is not clearly understood, the available clinical evidence indicates that this variant is likely disease-causing. Therefore, this variant is classified as Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 26, 2023	The p.G67R variant (also known as c.199G>C), located in coding exon 2 of the CDKN2A gene, results from a G to C substitution at nucleotide position 199. The glycine at codon 67 is replaced by arginine, an amino acid with dissimilar properties. The p.G67 residue lies within a highly conserved region adjacent to the helix-turn-helix motif generated by the 2nd ankyrin repeat. This alteration has been reported in multiple individuals and families with melanoma and/or pancreatic cancer (Newton Bishop JA et al. Br. J. Cancer 1999 Apr; 80(1-2):295-300; Ghiorzo P et al. J. Med. Genet. 2012 Mar; 49(3):164-70; Kannengiesser C et al. Hum. Mutat. 2009 Apr; 30(4):564-74; De Simone P et al. Int J Mol Sci 2020 Dec;21(24); Lang J et al. Br J Dermatol 2005 Dec;153(6):1121-5). This alteration has been observed in at least one individual with a personal and/or family history that is consistent with CDKN2A-related disease (Ambry internal data). A CDK4 binding assay demonstrated reduced binding activity for p.G67R at approximately 60% (Kannengiesser C et al. Hum Mutat. 2009 Apr;30(4):564-74), however assays of cellular proliferation have reported this variant as inconclusive or neutral (Miller PJ et al. Hum. Mutat. 2011 Aug; 32(8):900-11; Kimura H et al. Elife. 2022 Jan;11). Bayesian calculations by Miller et al. suggest that this alteration is a likely pathogenic variant. Based on internal structural analysis, p.G67R is structurally destabilizing (Ambry internal data). 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. -

CDKN2A-related disorder Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 23, 2024

The CDKN2A c.199G>C variant is predicted to result in the amino acid substitution p.Gly67Arg. This variant has been reported in multiple individuals with melanoma (Figure 1, Newton Bishop et al. 1999. PubMed ID: 10390011; Table 1, Kannengiesser et al. 2009. PubMed ID: 19260062) and it has also been reported with a CDKN2A loss-of-function variant in a family with pancreatic cancer and melanoma (Table 2, Ghiorzo et al. 2012. PubMed ID: 22368299). This variant is reported in 0.0030% of alleles in individuals of Latino descent in gnomAD. The results of functional studies of this variant have been inconclusive (Figure 2, Kannengiesser et al. 2009. PubMed ID: 19260062; Figure S3, Kimura et al. 2022. PubMed ID: 35001868). This variant is interpreted as likely pathogenic by two submitters and as uncertain by the third submitter (https://www.ncbi.nlm.nih.gov/clinvar/variation/216272/). In summary, this variant is interpreted as likely pathogenic. -

Melanoma and neural system tumor syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 08, 2024

- -

Familial melanoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

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 glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 67 of the CDKN2A (p16INK4a) protein (p.Gly67Arg). This variant is present in population databases (no rsID available, gnomAD 0.003%). This missense change has been observed in individual(s) with cutaneous melanoma and/or pancreatic cancer, however it does not appear to segregate with disease in at lease one of these families (PMID: 10390011, 15146471, 16307646, 16905682, 17047042, 19260062, 21462282, 21507037, 22368299, 22841127). This variant is also known as c.242G>C (p.Arg81Pro) in the p14ARF transcript. ClinVar contains an entry for this variant (Variation ID: 216272). 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 are conflicting or provide insufficient evidence to determine the effect of this variant on CDKN2A (p16INK4a) function (PMID: 19260062, 35001868). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.50
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Uncertain	-0.010
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.55	D;T;.;.;.;.;T;.
Eigen	Uncertain	0.59
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.99	D;D;.;D;.;D;D;D
M_CAP	Pathogenic	0.62	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.18	D
PrimateAI	Uncertain	0.72	T
PROVEAN	Pathogenic	-7.6	D;.;.;D;.;.;.;.
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;.;.;D;.;.;.;.
Sift4G	Pathogenic	0.0010	D;D;D;D;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.;.;.
Vest4		0.77
MutPred		0.87		Loss of catalytic residue at G67 (P = 0.0769);Loss of catalytic residue at G67 (P = 0.0769);.;Loss of catalytic residue at G67 (P = 0.0769);.;.;.;.;
MVP		0.99
MPC		1.3
ClinPred		0.94	D
GERP RS		5.8
Varity_R		0.50
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs758389471; hg19: chr9-21971159;