rs137854598

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 10P and 1B. PM1PM2PM5PP3_StrongBS2_Supporting

The NM_000077.5(CDKN2A):​c.305C>T​(p.Ala102Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,452,980 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. A102E) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

CDKN2A
NM_000077.5 missense

Scores

7
9
2

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:3

Conservation

PhyloP100: 9.22

Publications

27 publications found
Variant links:
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 Gene-Disease associations (from GenCC):
  • melanoma, cutaneous malignant, susceptibility to, 2
    Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
  • melanoma-pancreatic cancer syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
  • familial atypical multiple mole melanoma syndrome
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • melanoma and neural system tumor syndrome
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_pathogenic. The variant received 9 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 chr9-21971054-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 9418.We mark this variant Likely_pathogenic, oryginal submission is: [Conflicting_classifications_of_pathogenicity].
PP3
MetaRNN computational evidence supports a deleterious effect, 0.971
BS2
High AC in GnomAdExome4 at 5 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDKN2ANM_000077.5 linkc.305C>T p.Ala102Val missense_variant Exon 2 of 3 ENST00000304494.10 NP_000068.1 P42771-1K7PML8
CDKN2ANM_058195.4 linkc.348C>T p.Gly116Gly synonymous_variant Exon 2 of 3 ENST00000579755.2 NP_478102.2 Q8N726-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDKN2AENST00000304494.10 linkc.305C>T p.Ala102Val missense_variant Exon 2 of 3 1 NM_000077.5 ENSP00000307101.5 P42771-1
CDKN2AENST00000579755.2 linkc.348C>T p.Gly116Gly synonymous_variant Exon 2 of 3 1 NM_058195.4 ENSP00000462950.1 Q8N726-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000344
AC:
5
AN:
1452980
Hom.:
0
Cov.:
31
AF XY:
0.00000691
AC XY:
5
AN XY:
723124
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33422
American (AMR)
AF:
0.00
AC:
0
AN:
44622
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26044
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39672
South Asian (SAS)
AF:
0.0000581
AC:
5
AN:
86112
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46444
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5212
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1111286
Other (OTH)
AF:
0.00
AC:
0
AN:
60166
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Uncertain:1
Jan 04, 2024
GeneDx
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 9053859, 16354195, 16234564, 31026031, 26681309, 25064638, 37611275) -

Hereditary cancer-predisposing syndrome Uncertain:1
May 28, 2025
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The p.A102V variant (also known as c.305C>T), located in coding exon 2 of the CDKN2A gene, results from a C to T substitution at nucleotide position 305. The alanine at codon 102 is replaced by valine, an amino acid with similar properties. Of note, this variant is also known as c.348C>T (p.G116G)in the p14(ARF) isoform. This alteration was identified in an individual diagnosed with melanoma (Potrony M et al. J. Am. Acad. Dermatol., 2014 Nov;71:888-95). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. -

Familial melanoma Uncertain:1
Dec 02, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

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 alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 102 of the CDKN2A (p16INK4a) protein (p.Ala102Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with melanoma (PMID: 26681309). This variant is also known as c.348C>T (Silent) in the CDKN2A (p14ARF) transcript. ClinVar contains an entry for this variant (Variation ID: 234071). 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. 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
Pathogenic
0.64
BayesDel_addAF
Pathogenic
0.32
D
BayesDel_noAF
Pathogenic
0.22
CADD
Uncertain
25
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.46
T;T;.;.;.;.;T;.
Eigen
Uncertain
0.63
Eigen_PC
Uncertain
0.63
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.94
D;D;.;D;.;D;D;D
M_CAP
Pathogenic
0.87
D
MetaRNN
Pathogenic
0.97
D;D;D;D;D;D;D;D
MetaSVM
Uncertain
0.069
D
PhyloP100
9.2
PrimateAI
Benign
0.45
T
PROVEAN
Uncertain
-3.6
D;.;.;D;.;.;.;.
REVEL
Pathogenic
0.68
Sift
Uncertain
0.0010
D;.;.;D;.;.;.;.
Sift4G
Uncertain
0.050
T;D;D;D;D;D;D;D
Polyphen
1.0
D;.;.;.;.;.;.;.
Vest4
0.79
MutPred
0.78
Gain of MoRF binding (P = 0.1079);Gain of MoRF binding (P = 0.1079);.;Gain of MoRF binding (P = 0.1079);.;.;.;.;
MVP
1.0
MPC
1.2
ClinPred
0.98
D
GERP RS
5.9
PromoterAI
-0.0022
Neutral
Varity_R
0.56
gMVP
0.77
Mutation Taster
=0/100
disease causing

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

Other links and lift over

dbSNP: rs137854598; hg19: chr9-21971053; COSMIC: COSV58689032; COSMIC: COSV58689032; API