rs1131691186

chr9-21974761-C-Achr9-21974761-C-Gchr9-21974761-C-T

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.67G>T(p.Gly23Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. G23D) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:1
• Conservation: PhyloP100: 3.55

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 4 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
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr9-21974760-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 420108.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.967
• PP5: Variant 9-21974761-C-A is Pathogenic according to our data. Variant chr9-21974761-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 429109.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=4, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKN2A	NM_000077.5	c.67G>T	p.Gly23Cys	missense_variant	1/3	ENST00000304494.10
CDKN2A	NM_058195.4	c.194-3553G>T		intron_variant		ENST00000579755.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2A	ENST00000304494.10	c.67G>T	p.Gly23Cys	missense_variant	1/3	1	NM_000077.5	P2
CDKN2A	ENST00000579755.2	c.194-3553G>T		intron_variant		1	NM_058195.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial melanoma Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 30, 2023	Variant summary: CDKN2A c.67G>T (p.Gly23Cys) results in a non-conservative amino acid change in 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 235382 control chromosomes. c.67G>T has been reported in the literature in at least one individual affected with multiple primary melanoma (e.g., Blackwood_2012, Miller_2011). At least one publication reported experimental evidence evaluating an impact on protein function, and demonstrated that this variant results in increased cellular proliferation, indicating a loss of p16 (INK4A) function (e.g., Scaini_2014). The following publications have been ascertained in the context of this evaluation (PMID: 12001124, 21462282, 24659262). Three submitters have reported clinical-significance assessments for this variant to ClinVar after 2014; two submitters classified the variant as likely pathogenic and one submitter classified the variant as uncertain significance. Additionally, several other different missense variants affecting the same codon, including p.Gly23Arg, p.Gly23Ser, and p.Gly23Asp, have been reported in affected individuals (PMIDs: 17992122, 9425228, 32482799) and experimental studies suggest that several of these missense variants disupt protein function (PMID: 24659262). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jul 17, 2023	This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 23 of the CDKN2A (p16INK4a) protein (p.Gly23Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with melanoma (PMID: 12001124, 21462282; Invitae). ClinVar contains an entry for this variant (Variation ID: 429109). 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: 24659262). This variant disrupts the p.Gly23 amino acid residue in CDKN2A (p16INK4a). Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9425228, 17992122, 19260062, 19712690, 20340136, 21462282, 24659262). 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. -

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jul 15, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 11, 2023	The p.G23C variant (also known as c.67G>T), located in coding exon 1 of the CDKN2A gene, results from a G to T substitution at nucleotide position 67. The glycine at codon 23 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant has been detected in multiple individuals with personal and family histories of melanoma (Blackwood MA et al. Cancer 2002 Apr; 94(8):2248-55; Ambry internal data). This variant is predicted to be likely deleterious using a combination of in silico analyses and results of a proliferation assay consistent with loss of protein function (Scaini MC et al. Hum. Mutat. 2014 Jul;35(7):828-40). In addition, structural analysis predicts that the p.G23C variant results in severe perturbation of the protein, likely resulting in misfolding and loss of binding (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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. -

Melanoma and neural system tumor syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Jun 01, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.81
BayesDel_addAF	Pathogenic	0.38	D
BayesDel_noAF	Pathogenic	0.31
Cadd	Pathogenic	26
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.56	D;T;.
Eigen	Pathogenic	0.84
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.92	D;D;D
M_CAP	Pathogenic	0.76	D
MetaRNN	Pathogenic	0.97	D;D;D
MetaSVM	Uncertain	0.63	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.74	T
PROVEAN	Pathogenic	-7.5	D;.;D
REVEL	Pathogenic	0.73
Sift	Pathogenic	0.0	D;.;D
Sift4G	Pathogenic	0.0	D;D;D
Polyphen		1.0	D;.;.
Vest4		0.88
MutPred		0.68		Loss of methylation at R22 (P = 0.0439);Loss of methylation at R22 (P = 0.0439);Loss of methylation at R22 (P = 0.0439);
MVP		0.96
MPC		1.2
ClinPred		0.99	D
GERP RS		4.9
Varity_R		0.73
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1131691186; hg19: chr9-21974760; COSMIC: COSV100446547; COSMIC: COSV100446547;