9-21971058-C-G

Position:

• chr9-21971058-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PM1 PM5 PP3 BS2

The NM_000077.5(CDKN2A):​c.301G>C​(p.Gly101Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000482 in 1,452,982 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 Uncertain significance (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G101W) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:6
• Conservation: PhyloP100: 0.816

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 Uncertain_significance. Variant got 1 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, 17 uncertain in NM_000077.5
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr9-21971058-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 9412.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.811
• BS2: High AC in GnomAdExome4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKN2A	NM_000077.5	c.301G>C	p.Gly101Arg	missense_variant	2/3	ENST00000304494.10
CDKN2A	NM_058195.4	c.344G>C	p.Arg115Pro	missense_variant	2/3	ENST00000579755.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2A	ENST00000304494.10	c.301G>C	p.Gly101Arg	missense_variant	2/3	1	NM_000077.5	P2
CDKN2A	ENST00000579755.2	c.344G>C	p.Arg115Pro	missense_variant	2/3	1	NM_058195.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000853 AC: 2 AN: 234468 Hom.: 0 AF XY: 0.0000155 AC XY: 2 AN XY: 128882

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000329

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000944

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000482 AC: 7 AN: 1452982 Hom.: 0 Cov.: 31 AF XY: 0.00000415 AC XY: 3 AN XY: 723122

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: 0.0000464

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

ExAC AF: 0.0000167 AC: 2

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 25, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jun 03, 2015	This variant is denoted CDKN2A c.301G>C at the cDNA level, p.Gly101Arg (G101R) at the protein level, and results in the change of a Glycine to an Arginine (GGG>CGG). This variant was observed in a case of familial melanoma (Nikolaou 2011). An alternate base change, CDKN2A c.301G>A, which leads to the same amino acid change observed in this case, Gly101Arg, has been observed in a familial pancreatic cancer family, and was found in functional assays to behave similar to wild-type with regard to cell-cycle arrest and loss of function (Miller 2011, Zhen 2014, Greenblatt 2003). CDKN2A Gly101Arg 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 Glycine and Arginine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CDKN2A Gly101Arg occurs at a position that is conserved in mammals, with Arginine being the naturally occurring amino acid at this position in one vertebrate, and is located in the ANK 3 repeat (UniProt). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available information, it is unclear whether CDKN2A Gly101Arg is pathogenic or benign. We consider it to be a variant of uncertain significance. -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 29, 2023	The p.G101R variant (also known as c.301G>C), located in coding exon 2 of the CDKN2A gene, results from a G to C substitution at nucleotide position 301. The glycine at codon 101 is replaced by arginine, an amino acid with dissimilar properties. This alteration has been reported in a Greek proband with a personal and family history of melanoma (Nikolaou V et al, Br. J. Dermatol. 2011 Dec; 165(6):1219-22), in three patients with multiple primary melanomas from a cohort of 587 patients with either multiple- or single-primary melanomas from Italy (Bruno W et al. J Am Acad Dermatol, 2016 Feb;74:325-32), and in a cohort of 296 breast cancer patients from India who were tested with a 30-gene panel (Kaur RP et al. Med Oncol, 2018 Apr;35:81). Functional studies have shown this alteration exhibits cell cycle arrest activity similar to wildtype (Greenblatt MS et al. Oncogene, 2003 Feb;22:1150-63; Miller PJ et al. Hum. Mutat., 2011 Aug;32:900-11). In addition, one of the most common CDKN2A mutations (p.G101W) has been described at this same position (Hussussian CJ et al. Nat. Genet. 1994;8:15-21,Vinarsky V et al. Head Neck 2009;31:1524-7). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 01, 2023	The CDKN2A gene encodes two different proteins, p16INK4a and p14ARF ( https://www.ncbi.nlm.nih.gov/books/NBK7030/ ). This missense variant replaces glycine with arginine at codon 101 of the CDKN2A (p16INK4A) protein. Computational prediction tool suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >=0.7, PMID: 27666373). However, functional studies have shown that this variant induces cell cycle arrest similarly to wild-type p16INK4a protein (PMID: 12606942, 21462282). This variant has been reported in at least one individual affected with single primary melanoma (PMID: 21801156, 29774366), in an individual affected with pancreatic cancer (PMID: 25356972), and in 3 individuals affected with multiple primary melanoma (PMID: 26775776). This variant has been identified in 2/234468 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different missense variant occurring at the same position, p.Gly101Trp, is known to be pathogenic (Clinvar variation ID: 9412), indicating glycine at this position is important for the p16INK4a protein function. Although there is a suspicion that this variant may be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Melanoma and neural system tumor syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Baylor Genetics

Feb 06, 2024

- -

Familial melanoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Jul 25, 2023

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. This variant disrupts the p.Gly101 amino acid residue in CDKN2A (p16INK4a). Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10869234, 11807902, 14679123, 15146471, 21462282, 21801156). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change does not substantially affect CDKN2A (p16INK4a) function (PMID: 12606942, 21462282, 35001868). 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. ClinVar contains an entry for this variant (Variation ID: 216274). This variant is also known as c.344G>C (p.Arg115Pro) in the CDKN2A (p14ARF) transcript. This missense change has been observed in individual(s) with melanoma and pancreatic cancer (PMID: 21801156, 25356972, 29774366). This variant is present in population databases (rs104894094, gnomAD 0.003%). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 101 of the CDKN2A (p16INK4a) protein (p.Gly101Arg). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.62
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	-0.060
CADD	Uncertain	24
DANN	Uncertain	0.98
DEOGEN2	Uncertain	0.55	D;T;.;.;.;.;T;.
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.96	D;D;.;D;.;D;D;D
M_CAP	Pathogenic	0.32	D
MetaRNN	Pathogenic	0.81	D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.31	D
MutationTaster	Benign	0.84	D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.53	T
PROVEAN	Pathogenic	-5.9	D;.;.;D;.;.;.;.
REVEL	Pathogenic	0.73
Sift	Benign	0.032	D;.;.;D;.;.;.;.
Sift4G	Uncertain	0.033	D;D;T;D;T;T;T;T
Polyphen		1.0	D;.;.;.;.;.;.;.
Vest4		0.55
MutPred		0.78		Gain of methylation at G101 (P = 0.0294);Gain of methylation at G101 (P = 0.0294);.;Gain of methylation at G101 (P = 0.0294);.;.;.;.;
MVP		0.99
MPC		1.3
ClinPred		0.70	D
GERP RS		5.9
Varity_R		0.37
gMVP		0.88

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: rs104894094; hg19: chr9-21971057;