rs11547328

chr12-57751648-G-Achr12-57751648-G-Cchr12-57751648-G-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000075.4(CDK4):c.70C>T(p.Arg24Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,882 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R24L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CDK4 NM_000075.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:9 O:1
• Conservation: PhyloP100: 7.90

Genes affected

CDK4 (HGNC:1773): (cyclin dependent kinase 4) The protein encoded by this gene is a member of the Ser/Thr protein kinase family. This protein is highly similar to the gene products of S. cerevisiae cdc28 and S. pombe cdc2. It is a catalytic subunit of the protein kinase complex that is important for cell cycle G1 phase progression. The activity of this kinase is restricted to the G1-S phase, which is controlled by the regulatory subunits D-type cyclins and CDK inhibitor p16(INK4a). This kinase was shown to be responsible for the phosphorylation of retinoblastoma gene product (Rb). Mutations in this gene as well as in its related proteins including D-type cyclins, p16(INK4a) and Rb were all found to be associated with tumorigenesis of a variety of cancers. Multiple polyadenylation sites of this gene have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a strand (size 4) in uniprot entity CDK4_HUMAN there are 6 pathogenic changes around while only 0 benign (100%) in NM_000075.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr12-57751647-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 16929.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.965
• PP5: Variant 12-57751648-G-A is Pathogenic according to our data. Variant chr12-57751648-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 16928.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-57751648-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK4	NM_000075.4	c.70C>T	p.Arg24Cys	missense_variant	2/8	ENST00000257904.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK4	ENST00000257904.11	c.70C>T	p.Arg24Cys	missense_variant	2/8	1	NM_000075.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251466 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135904

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS 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: 1461882 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727248

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 27, 2023	The p.R24C pathogenic mutation (also known as c.70C>T), located in coding exon 1 of the CDK4 gene, results from a C to T substitution at nucleotide position 70. The arginine at codon 24 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been reported in the literature to segregate with melanoma in six different families (Zuo L et al. Nat. Genet., 1996 Jan;12:97-9; Puntervoll HE et al. J. Med. Genet., 2013 Apr;50:264-70). Additionally, this variant has been shown to disrupt p16INK4a binding and inhibition of CDK4, which results in an increase in CDK4 kinase activity (Wölfel T et al. Science, 1995 Sep;269:1281-4). Mouse in vivo studies demonstrated that mice with this variant showed significantly increased susceptibility to the development of CDK4 related tumors (Rane SG et al. Mol. Cell. Biol., 2002 Jan;22:644-56). This amino acid position is highly 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 30, 2020	This missense variant replaces arginine with cysteine at codon 24 of the CDK4 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). Experimental functional studies have shown that this variant impairs interaction with CDKN2A (p16-INK4a) preventing inhibition by p16-INK4a and allowing for unregulated CDK4 kinase activity, cell cycle progression and cellular transformation (PMID: 11756559, 7652577, 9228064). This variant has been reported in individuals affected with melanoma (PMID: 8528263, 22804906 23384855) and has been shown to segregate with disease (PMID: 23384855, 8528263). This variant has been identified in 1/251466 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Familial melanoma Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Sep 06, 2022	ClinVar contains an entry for this variant (Variation ID: 16928). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Experimental studies have shown that this missense change affects CDK4 function (PMID: 7652577, 11756559). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This missense change has been observed in individual(s) with melanoma (PMID: 8528263, 23384855). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs11547328, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 24 of the CDK4 protein (p.Arg24Cys). -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 15, 2017	Variant summary: The CDK4 c.70C>T (p.Arg24Cys) variant involves the alteration of a conserved nucleotide and is located in protein kinase domain of the protein (InterPro). 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 1/121378 control chromosomes from ExAC at a frequency of 0.0000082, which does not exceed the estimated maximal expected allele frequency of a pathogenic CDK4 variant (0.00002). This variant has been reported in six unrelated cutaneous malignant melanoma families including evidence of cosegregation with disease (Zuo_1996, Ghiorzo_2012, Puntervoll_2013). In vivo mice-model study shows the recapitulation of melanoma phenotype (Rane_2002). The codon p.Arg24 is a mutational hot-spot in which another mutation p.Arg24His is known to be pathogenic. Multiple clinical diagnostic laboratories in ClinVar have classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -

Melanoma, cutaneous malignant, susceptibility to, 3 Pathogenic:1 Other:1

risk factor, no assertion criteria provided	literature only	OMIM	Jan 01, 1996	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	May 26, 2016	- -

Multiple myeloma Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Database of Curated Mutations (DoCM)

May 31, 2016

- -

Lung adenocarcinoma Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Database of Curated Mutations (DoCM)

May 31, 2016

- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Apr 26, 2016

This pathogenic variant is denoted CDK4 c.70C>T at the cDNA level, p.Arg24Cys (R24C) at the protein level, and results in the change of an Arginine to a Cysteine (CGT>TGT). This variant has been reported to segregate with melanoma in several melanoma families (Zuo 1996, Puntervoll 2013). Functional studies have shown that this variant disrupts binding with CDKN2A, resulting in resistance to CDKN2A inhibition and increased CDK4 kinase activity (Wolfel 1995, Rane 2002). CDK4 Arg24Cys was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Arginine and Cysteine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CDK4 Arg24Cys occurs at a position that is conserved across species and is located in the protein kinase domain (UniProt). In silico analyses are inconsistent regarding the effect this pathogenic variant may have on protein structure and function. Based on currently available evidence, we consider this variant to be pathogenic. -

Malignant melanoma of skin Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Database of Curated Mutations (DoCM)

May 31, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.71
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Pathogenic	0.14
Cadd	Pathogenic	34
Dann	Uncertain	1.0
DEOGEN2	Benign	0.30	T;D;.;T;.
Eigen	Uncertain	0.26
Eigen_PC	Uncertain	0.32
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.94	D;D;D;D;D
M_CAP	Uncertain	0.086	D
MetaRNN	Pathogenic	0.97	D;D;D;D;D
MetaSVM	Benign	-0.79	T
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.74	T
PROVEAN	Pathogenic	-6.7	D;D;D;D;D
REVEL	Uncertain	0.58
Sift	Uncertain	0.016	D;D;D;D;D
Sift4G	Uncertain	0.045	D;T;D;.;.
Polyphen		0.74	.;P;.;.;.
Vest4		0.94
MutPred		0.90		Loss of disorder (P = 0.0238);Loss of disorder (P = 0.0238);Loss of disorder (P = 0.0238);Loss of disorder (P = 0.0238);Loss of disorder (P = 0.0238);
MVP		0.91
MPC		1.2
ClinPred		0.98	D
GERP RS		4.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Varity_R		0.80
gMVP		0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.20		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.20		Position offset: -14

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

Publications

LitVar

Other links and lift over

dbSNP: rs11547328; hg19: chr12-58145431; COSMIC: COSV56984534; COSMIC: COSV56984534;