CDKN2D
cyclin dependent kinase inhibitor 2D, the group of Ankyrin repeat domain containing
Basic information
Region (hg38): 19:10566460-10569059
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 CDKN2D 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 | 0 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
Variants in CDKN2D
This is a list of pathogenic ClinVar variants found in the CDKN2D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-10567123-C-T | not specified | Uncertain significance (Oct 27, 2021) | ||
| 19-10567132-A-C | not specified | Uncertain significance (Nov 07, 2023) | ||
| 19-10567150-C-G | not specified | Uncertain significance (Nov 25, 2024) | ||
| 19-10567177-C-G | not specified | Uncertain significance (Mar 01, 2023) | ||
| 19-10567240-C-T | not specified | Uncertain significance (Mar 14, 2023) | ||
| 19-10567255-C-T | not specified | Uncertain significance (Nov 03, 2023) | ||
| 19-10567339-C-T | not specified | Uncertain significance (Nov 26, 2024) | ||
| 19-10567390-C-T | not specified | Uncertain significance (Jan 18, 2022) | ||
| 19-10568587-C-G | not specified | Uncertain significance (Jan 03, 2024) | ||
| 19-10568596-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
| 19-10568644-C-T | not specified | Uncertain significance (Apr 14, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDKN2D | protein_coding | protein_coding | ENST00000393599 | 2 | 2598 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.495 | 0.436 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.13 | 62 | 92.7 | 0.669 | 0.00000537 | 1038 |
| Missense in Polyphen | 18 | 32.34 | 0.55659 | 345 | ||
| Synonymous | 0.847 | 35 | 42.0 | 0.834 | 0.00000272 | 381 |
| Loss of Function | 1.27 | 0 | 1.89 | 0.00 | 8.02e-8 | 26 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Interacts strongly with CDK4 and CDK6 and inhibits them. {ECO:0000269|PubMed:7739548, ECO:0000269|PubMed:8741839}.;
- Pathway
- Cell cycle - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);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;cell cycle: g2/m checkpoint;Cellular responses to external stimuli;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.181
Intolerance Scores
- loftool
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.265
- hipred
- Y
- hipred_score
- 0.620
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.975
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdkn2d
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); neoplasm; 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); hearing/vestibular/ear phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;G1/S transition of mitotic cell cycle;DNA synthesis involved in DNA repair;cell cycle arrest;sensory perception of sound;negative regulation of cell population proliferation;response to UV;negative regulation of cell growth;response to retinoic acid;response to vitamin D;negative regulation of phosphorylation;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of cyclin-dependent protein serine/threonine kinase activity;autophagic cell death;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage;negative regulation of cell cycle G1/S phase transition
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;cyclin D2-CDK4 complex
- Molecular function
- cyclin-dependent protein serine/threonine kinase inhibitor activity;protein binding;protein kinase binding