9-21971037-C-T

Position:

• chr9-21971037-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.322G>A​(p.Asp108Asn) variant causes a missense change. 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. D108Y) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:2 O:1
• Conservation: PhyloP100: 5.54

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 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 17 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 chr9-21971037-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 182423.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Likely_pathogenic=1}.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.957
• PP5: Variant 9-21971037-C-T is Pathogenic according to our data. Variant chr9-21971037-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 216275.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, not_provided=1, Pathogenic=1, Likely_pathogenic=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKN2A	NM_000077.5	c.322G>A	p.Asp108Asn	missense_variant	2/3	ENST00000304494.10
CDKN2A	NM_058195.4	c.365G>A	p.Arg122Gln	missense_variant	2/3	ENST00000579755.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2A	ENST00000304494.10	c.322G>A	p.Asp108Asn	missense_variant	2/3	1	NM_000077.5	P2
CDKN2A	ENST00000579755.2	c.365G>A	p.Arg122Gln	missense_variant	2/3	1	NM_058195.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000138 AC: 2 AN: 1453704 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 723436

Gnomad4 AFR exome AF: 0.0000299

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: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:2 Other:1

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	May 23, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 14, 2022	The p.D108N variant (also known as c.322G>A), located in coding exon 2 of the CDKN2A gene, results from a G to A substitution at nucleotide position 322. The aspartic acid at codon 108 is replaced by asparagine, an amino acid with highly similar properties. This variant has been detected in multiple familial melanoma cohorts; however, in one family two of the four affected members did not carry the variant, and in another family one member also carried another pathogenic variant CDKN2A p.M53T (Flores JF et al. Oncogene. 1997 Dec;15:2999-3005; Aitken J et al. J. Natl. Cancer Inst. 1999 Mar;91:446-52; Bishop DT et al. J. Natl. Cancer Inst. 2002 Jun;94:894-903; Begg CB et al. J. Natl. Cancer Inst. 2005 Oct;97:1507-15; Goldstein AM et al. Cancer Res. 2006 Oct;66:9818-28; Berwick M et al. Cancer Epidemiol. Biomarkers Prev. 2006 Aug;15:1520-5; Orlow I et al. J. Invest. Dermatol. 2007 May;127:1234-43; Goldstein AM et al. J. Med. Genet. 2007 Feb;44:99-106; Huot TJ et al. Mol. Cell. Biol. 2002 Dec;22:8135-43; Miller PJ et al. Hum. Mutat. 2011 Aug;32:900-11). Two functional studies agree that this variant has an intermediate defect in binding to CDK4, however, they disagree about whether there is a defect in CDK6 binding (Huot TJ et al. Mol. Cell. Biol. 2002 Dec;22:8135-43; Hallett ST et al. Cell Rep. 2017 Oct;21:1386-1398). One of these studies also reports that this variant causes a significant reduction in protein stability, however, this concept was not recapitulated in other functional studies with tagged-exogenous material (Hallett ST et al. Cell Rep. 2017 Oct;21:1386-1398; Huot TJ et al. Mol. Cell. Biol. 2002 Dec;22:8135-43, respectively). Lastly, another functional study showed that cell cycle arrest was not affected by this variant (Miller PJ et al. Hum. Mutat. 2011 Aug;32:900-11). CDKN2A p.D108N sits at the interface with other binding partners, including CDK4/6 and it is anticipated to result in a decrease in protein-protein interactions (Russo AA et al. Nature. 1998 Sep;395:237-43; 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, 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. -

not provided Uncertain:1 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Apr 06, 2015	This variant is denoted CDKN2A c.322G>A at the cDNA level, p.Asp108Asn (D108N) at the protein level, and results in the change of an Aspartic Acid to an Asparagine (GAT>AAT). This variant has been reported in several high-risk melanoma families (Flores 1997, Bishop 2002, Begg 2005, Goldstein 2006, Goldstein 2007, Aoude 2015). Additionally, Huot et al. (2002) identified CDKN2A Asp108Asn in an individual found to harbor a second CDKN2A variant (suspected biallelic). While an in vitro assay completed by Huot et al. (2002) showed that this variant results in a reduced ability to bind CDK4 and CDK6 compared to wild-type, another in vitro assay completed by Miller et al. (2011) showed the this variants retains cell cycle arrest function comparable to wild-type. CDKN2A Asp108Asn was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Aspartic Acid and Asparagine differ in some properties, this is considered a semi-conservative amino acid substitution. CDKN2A Asp108Asn occurs at a position that is conserved across species and is not located in a known functional domain (UniProt). In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available information, it is unclear whether CDKN2A Asp108Asn is pathogenic or benign. We consider it to be a variant of uncertain significance. -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpretted as Uncertain significance and reported on 06-22-2019 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Familial melanoma Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 02, 2023

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 aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 108 of the CDKN2A (p16INK4a) protein (p.Asp108Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with melanoma (PMID: 9416844, 16234564, 21462282; Invitae). It has also been observed to segregate with disease in related individuals. This variant is also known as c.365G>A (p.Arg122Gln) in the CDKN2A (p14ARF) transcript. ClinVar contains an entry for this variant (Variation ID: 216275). 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: 12417717, 21462282, 29091774). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	-0.050
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.51	D;T;.;.;.;.;T;.
Eigen	Uncertain	0.60
Eigen_PC	Uncertain	0.63
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.89	D;D;.;D;.;D;D;D
M_CAP	Pathogenic	0.66	D
MetaRNN	Pathogenic	0.96	D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.087	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.55	T
PROVEAN	Uncertain	-4.3	D;.;.;D;.;.;.;.
REVEL	Pathogenic	0.68
Sift	Benign	0.052	T;.;.;D;.;.;.;.
Sift4G	Benign	0.066	T;T;D;T;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.;.;.
Vest4		0.72
MutPred		0.81		Gain of MoRF binding (P = 0.0396);Gain of MoRF binding (P = 0.0396);.;Gain of MoRF binding (P = 0.0396);.;.;.;.;
MVP		0.97
MPC		1.2
ClinPred		0.91	D
GERP RS		5.9
Varity_R		0.65
gMVP		0.76

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: rs121913381; hg19: chr9-21971036; COSMIC: COSV58690777; COSMIC: COSV58690777;