CDKN2C

cyclin dependent kinase inhibitor 2C, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 1:50960744-50974634

Links

ENSG00000123080 ∙ NCBI:1031 ∙ OMIM:603369 ∙ HGNC:1789 ∙ Uniprot:P42773 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDKN2C gene.

• not provided (3 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDKN2C gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	1		2
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in CDKN2C

This is a list of pathogenic ClinVar variants found in the CDKN2C region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-50970386-G-A			Uncertain significance (Apr 01, 2023)
1-50970392-G-T		not specified	Uncertain significance (Jul 11, 2023)
1-50970485-G-T		not specified	Uncertain significance (Dec 11, 2023)
1-50970498-G-T			not provided (-)
1-50973952-C-T			Likely benign (Dec 01, 2023)
1-50973993-C-A		Multiple myeloma	Likely pathogenic (Aug 31, 2019)
1-50974171-G-C		not specified	Uncertain significance (Dec 03, 2021)
1-50974240-C-T			Likely benign (Aug 01, 2023)
1-50974241-G-A		not specified	Likely benign (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDKN2C	protein_coding	protein_coding	ENST00000262662	2	13889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.395	0.568	125746	0	2	125748	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	67	97.0	0.691	0.00000483	1100
Missense in Polyphen		16	34.358	0.46569		422
Synonymous	1.14	33	42.5	0.777	0.00000231	350
Loss of Function	1.66	1	4.99	0.200	2.97e-7	54

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts strongly with CDK6, weakly with CDK4. Inhibits cell growth and proliferation with a correlated dependence on endogenous retinoblastoma protein RB.
• Pathway: Cushing,s syndrome - Homo sapiens (human);Cell cycle - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Signaling Pathways in Glioblastoma;Vitamin D Receptor Pathway;G1 to S cell cycle control;cyclins and cell cycle regulation;Oncogene Induced Senescence;Oxidative Stress Induced Senescence;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;Hedgehog;Cyclin D associated events in G1;G1 Phase;Mitotic G1-G1/S phases;Cellular responses to external stimuli;Cell Cycle;Cell Cycle, Mitotic;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.230

Intolerance Scores

• loftool: 0.321
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.826
• hipred: Y
• hipred_score: 0.696
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.852

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cdkn2c
• Phenotype: neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;G1/S transition of mitotic cell cycle;cell cycle arrest;negative regulation of cell population proliferation;negative regulation of cell growth;negative regulation of phosphorylation;negative regulation of cyclin-dependent protein serine/threonine kinase activity;oligodendrocyte differentiation
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: cyclin-dependent protein serine/threonine kinase inhibitor activity;protein binding;protein kinase binding