9-21974686-G-T

Position:

• chr9-21974686-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_000077.5(CDKN2A):​c.142C>A​(p.Pro48Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,714 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P48L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 0.410

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 16 ACMG points.

• PM1: In a turn (size 2) in uniprot entity CDN2A_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) 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 chrnull-null-null-null is described in UniProt as null.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.909
• PP5: Variant 9-21974686-G-T is Pathogenic according to our data. Variant chr9-21974686-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 188286.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-21974686-G-T is described in Lovd as [Likely_pathogenic]. Variant chr9-21974686-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2A	NM_000077.5	c.142C>A	p.Pro48Thr	missense_variant	1/3	ENST00000304494.10	NP_000068.1
CDKN2A	NM_058195.4	c.194-3478C>A		intron_variant		ENST00000579755.2	NP_478102.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2A	ENST00000304494.10	c.142C>A	p.Pro48Thr	missense_variant	1/3	1	NM_000077.5	ENSP00000307101	P2
CDKN2A	ENST00000579755.2	c.194-3478C>A		intron_variant		1	NM_058195.4	ENSP00000462950

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461714 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727164

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jun 10, 2021	The p.P48T pathogenic mutation (also known as c.142C>A), located in coding exon 1 of the CDKN2A gene, results from a C to A substitution at nucleotide position 142. The proline at codon 48 is replaced by threonine, an amino acid with highly similar properties. This mutation was reported in a large Italian kindred with cutaneous melanoma, including a proband with multiple melanomas; p.P48T segregated with disease in 3 of 3 affected relatives tested (Della Torre G et al. Br J Cancer, 2001 Sep;85:836-44). This mutation has been identified in multiple Italian and Brazilian individuals with personal and family histories of cutaneous melanoma and/or pancreatic cancer (Moore PS et al. Hum Mutat, 2000 Nov;16:447-8; Foppiani L et al. Eur J Endocrinol, 2008 Mar;158:417-22; Menin C et al. Pigment Cell Melanoma Res, 2011 Aug;24:728-30; Bruno W et al. J Am Acad Dermatol, 2016 Feb;74:325-32; de Ávila AL et al. Fam Cancer, 2014 Dec;13:645-9; Puig S et al. Genet Med, 2016 07;18:727-36). One Hungarian patient with atypical mole syndrome and multiple primary melanomas diagnosed at age 30 was actually found to be homozygous for this mutation; his parents were confirmed heterozygous and remained unaffected in their 60s (Széll M et al. Melanoma Res, 2007 Aug;17:251-4). Functional assays have been consistent in p.P48T showing normal CDK4 and CDK6 binding but abnormal cell cycle growth arrest (Della Torre G et al. Br J Cancer, 2001 Sep;85:836-44; Miller PJ et al. Hum Mutat, 2011 Aug;32:900-11). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 06, 2022	The CDKN2A locus encodes two different gene products, p16INK4a and p14ARF (https://www.ncbi.nlm.nih.gov/books/NBK7030/). This missense variant replaces proline with threonine at codon 48 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). A functional study has shown the mutant protein to exhibit normal ability to interact with CDK4 and CDK6 protein but show mildly impaired ability to control cell cycle (PMID: 11556834). This variant has been reported in over twenty individuals and families affected with melanoma (PMID: 11058911, 11556834, 11556834, 16470311, 17625456, 18299477, 18363633, 21672182, 21893440, 22841127, 25023876, 26775776, 30274933, 34664323). In one family, this variant segregated with melanoma in 6 of 12 carriers ; unaffected carriers in this family ranged in age from 23 to 50 years (PMID: 11556834). This variant has also been observed in an individual affected with pancreatic cancer with a first-degree relative also affected with pancreatic cancer (PMID: 11058911). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). While the variant impact on gene function is not clearly understood, the available clinical evidence indicate that this variant is associated with disease. Therefore, this variant is classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 09, 2020	The CDKN2A c.142C>A p.(Pro48Thr) missense variant has been identified in multiple individuals and families with different cancer phenotypes (Moore et al. (2000); Della Torre et al. (2001); Széll et al. (2007; de Avila et al. (2014); Dalmasso et al. (2019)) This variant is not observed in version 2.1.1 of the Genome Aggregation Database. Functional studies by Della Torre et al. (2001) revealed that while the p.(Pro48Thr) variant did not affect binding to CDK4 or CDK6, the variant protein displayed a diminished ability to inhibit cell growth as compared to wild type when expressed in human fibroblasts. The authors also indicate that the variant may cause a defect in the arrest of the cell cycle. Moore et al. (2000) suggest that the p.(Pro48Thr) variant, which occurs in the first four-residue helix of the second ankyrin repeat, may alter the protein's structure or binding properties. Della Torre et al. (2001) note that this region of the protein is important for inhibitory activity. Two additional variants occurring at the same amino acid, p.(Pro48Leu) and p.(Pro48Arg), have been reported in individuals with cancer phenotypes (Platz et al. (1997); Debniak et al. 2008). Based on the collective evidence the c.142C>A p.(Pro48Thr) variant is classified as pathogenic for CDKN2A-related cancer susceptibility. -

Familial melanoma Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 10, 2024

This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 48 of the CDKN2A (p16INK4a) protein (p.Pro48Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of familial atypical multiple mole melanoma syndrome (PMID: 11058911, 11556834, 17625456, 28830827). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 188286). 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: 11556834). This variant disrupts the p.Pro48 amino acid residue in CDKN2A (p16INK4a). Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9168184, 10338331, 10491434, 21462282). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.81
BayesDel_addAF	Pathogenic	0.26	D
BayesDel_noAF	Pathogenic	0.14
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.45	T;T;.
Eigen	Benign	-0.17
Eigen_PC	Benign	-0.42
FATHMM_MKL	Benign	0.47	N
LIST_S2	Benign	0.80	T;T;T
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.91	D;D;D
MetaSVM	Pathogenic	1.0	D
MutationTaster	Benign	1.0	D;D;D;D;D;N;N;N;N
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-4.0	D;.;D
REVEL	Pathogenic	0.69
Sift	Benign	0.050	D;.;T
Sift4G	Uncertain	0.0070	D;D;D
Polyphen		0.88	P;.;.
Vest4		0.62
MutPred		0.76		Gain of phosphorylation at P48 (P = 0.0424);Gain of phosphorylation at P48 (P = 0.0424);Gain of phosphorylation at P48 (P = 0.0424);
MVP		1.0
MPC		1.3
ClinPred		0.89	D
GERP RS		-1.1
Varity_R		0.60
gMVP		0.95

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: rs786204195; hg19: chr9-21974685;