CDKN2C
cyclin dependent kinase inhibitor 2C, the group of Ankyrin repeat domain containing
Basic information
Region (hg38): 1:50960745-50974634
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 3 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 3 | 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:
| 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:
- 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