9-21974679-T-C

Variant names:

• chr9-21974679-T-C
• rs587778189
• NM_000077.5:c.149A>G

Variant summary

Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_000077.5(CDKN2A):​c.149A>G​(p.Gln50Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000684 in 1,461,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. 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. Q50H) 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, splice_region
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: 4.65
• Publications: 26 publications found

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

ENSG00000264545 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 16 ACMG points.

• PM1: In a hotspot region, there are 11 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 44 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 chr9-21974678-C-G is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 1045852.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.866
• PP5: Variant 9-21974679-T-C is Pathogenic according to our data. Variant chr9-21974679-T-C is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 232304.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000077.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2A	NM_000077.5	MANE Select	c.149A>G	p.Gln50Arg	missense splice_region	Exon 1 of 3	NP_000068.1
	CDKN2A	NM_058195.4	MANE Plus Clinical	c.194-3471A>G		intron	N/A	NP_478102.2
	CDKN2A	NM_058197.5		c.149A>G	p.Gln50Arg	missense	Exon 1 of 3	NP_478104.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2A	ENST00000304494.10	TSL:1 MANE Select	c.149A>G	p.Gln50Arg	missense splice_region	Exon 1 of 3	ENSP00000307101.5
	CDKN2A	ENST00000498124.1	TSL:1	c.149A>G	p.Gln50Arg	missense splice_region	Exon 1 of 4	ENSP00000418915.1
	CDKN2A	ENST00000380151.3	TSL:1	n.149A>G		non_coding_transcript_exon	Exon 1 of 3	ENSP00000369496.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000401 AC: 1 AN: 249628 AF XY: 0.00000740

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461702 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727142

African (AFR) AF: 0.00 AC: 0 AN: 33478

American (AMR) AF: 0.0000224 AC: 1 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53248

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1112002

Other (OTH) AF: 0.00 AC: 0 AN: 60394

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Nov 21, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Q50R pathogenic mutation (also known as c.149A>G), located in coding exon 1 of the CDKN2A gene, results from an A to G substitution at nucleotide position 149. The glutamine at codon 50 is replaced by arginine, an amino acid with highly similar properties. This alteration has been detected in numerous melanoma and pancreatic cancer cohorts (Walker GJ et al. Hum. Mol. Genet. 1995 Oct;4:1845-52; Box NF et al. Am. J. Hum. Genet. 2001 Oct;69:765-73; Pollock PM et al. Genes Chromosomes Cancer. 2001 Sep;32:89-94; Zhen DB et al. Genet. Med. 2015 Jul;17:569-77; Bruno W et al. Oncotarget. 2018 Jun;9:28798; Ambry internal data). It was also found to segregate with melanoma in at least six melanoma-affected individuals in one family (Walker GJ et al. Hum. Mol. Genet. 1995 Oct;4:1845-52; Box NF et al. Am. J. Hum. Genet. 2001 Oct;69:765-73). Based on internal structural analysis, this amino acid substitution is anticipated to result in a significant decrease in structural stability (Russo AA et al. Nature. 1998 Sep;395:237-43; Ambry internal data). A different substitution at the same position (CDKN2A c.149A>C, p.Q50P) shows both a splice defect and defective CDK4 binding by the native protein harboring only the missense change (Loo JC et al. Oncogene. 2003 Sep; 22(41):6387-94). This amino acid position is highly conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

Feb 21, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces glutamine with arginine at codon 50 in the ankyrin repeat 2 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). Functional studies showed that this variant affected cell cycle control and failed to suppress cell proliferation (PMID: 35001868). Splice site prediction tools suggest that this variant may impact RNA splicing, although this prediction has not been investigated in RNA studies. This variant has been reported in individuals and families affected with melanoma (PMID: 11477665, 12072543, 16905682, 26681309, 26775776, 28830827, 29464027, 32455486; Cardelli 2020, dissertation, University of L'Aquila; Haghighat, et al. P-07, CGA-IGC 2022) and familial pancreatic cancer (PMID 25356972). This variant has been shown to segregate with disease in six related individuals affected with melanoma (PMID: 8595405). This variant has been identified in 1/249628 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Notably, a different nucleotide substitution at the same position, c.149A>C (p.Gln50Pro), has been observed in individuals affected with melanoma (Clinvar Variation ID: 187713) and shown to affect RNA splicing and p16INK4A protein function (PMID: 14508519). Based on the available evidence, this variant is classified as Pathogenic.

Familial melanoma Pathogenic:2

Mar 31, 2020

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CDKN2A c.149A>G (p.Gln50Arg) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 249628 control chromosomes. c.149A>G has been reported in the literature in individuals affected with melanoma (Walker_1995, Pollock_2001, Puig_2016, Bruno_2016) and familial pancreatic cancer (Zhen_2015). In one family, 6 transmissions of the variant allele and 1 transmission of the reference allele to affected individuals was reported (Walker_1995). These data indicate that the variant is likely to be associated with disease. Co-occurrence with a pathogenic variant has been reported (CHEK2 c.1283C>T, p.Ser428Phe), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Based on the evidence outlined above, the variant was classified as likely pathogenic.

Dec 17, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 50 of the CDKN2A (p16INK4a) protein (p.Gln50Arg). This variant is present in population databases (no rsID available, gnomAD 0.003%). This missense change has been observed in individual(s) with melanoma and/or pancreatic cancer (PMID: 8595405, 11477665, 11500805, 25356972, 26775776). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 232304). 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: 8573142, 35001868). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

Melanoma and neural system tumor syndrome Pathogenic:1

Feb 29, 2024

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not provided Pathogenic:1

Nov 24, 2024

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Observed in individuals with melanoma or pancreatic cancer and segregated with disease in at least one family (PMID: 8595405, 11477665, 12072543, 15146471, 16905682, 25356972, 26775776); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 21462282, 9461066, 18573309, 11500805, 23178718, 11477665, 15146471, 25356972, 12072543, 16905682, 10596908, 11687599, 9917418, 8595405, 28830827, 26775776, 9751050, 9823374, 26619011, 26681309, 8573142, 9653180, 9529249, 16173922, 8723678, 35001868, 37611275)

Melanoma-pancreatic cancer syndrome Pathogenic:1

Feb 09, 2023

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 35001868]. This variant is expected to disrupt protein structure [Myriad internal data]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 8595405, 11477665, 26775776, 25356972].

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.27
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.45	T
Eigen	Uncertain	0.32
Eigen_PC	Uncertain	0.30
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.78	T
M_CAP	Pathogenic	0.42	D
MetaRNN	Pathogenic	0.87	D
MetaSVM	Uncertain	-0.21	T
PhyloP100		4.6
PrimateAI	Uncertain	0.67	T
PROVEAN	Uncertain	-3.5	D
REVEL	Pathogenic	0.67
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.010	D
Polyphen		1.0	D
Vest4		0.80
MutPred		0.63		Gain of MoRF binding (P = 0.0204)
MVP		0.91
MPC		1.3
ClinPred		0.97	D
GERP RS		4.9
PromoterAI		-0.15	Neutral
Varity_R		0.72
gMVP		0.98
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
Splicevardb		2.0
SpliceAI score (max)		0.13		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587778189; hg19: chr9-21974678; COSMIC: COSV58683689; COSMIC: COSV58683689;