CDC23
cell division cycle 23, the group of Anaphase promoting complex |Tetratricopeptide repeat domain containing
Basic information
Region (hg38): 5:138187649-138213343
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 CDC23 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 | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 11 | 1 | 1 |
Variants in CDC23
This is a list of pathogenic ClinVar variants found in the CDC23 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-138189027-G-A | not specified | Uncertain significance (May 24, 2024) | ||
| 5-138189030-T-C | not specified | Uncertain significance (Jul 09, 2021) | ||
| 5-138189082-T-C | not specified | Uncertain significance (Mar 23, 2023) | ||
| 5-138189633-A-G | Benign (Jul 13, 2018) | |||
| 5-138189661-C-A | not specified | Uncertain significance (Dec 07, 2021) | ||
| 5-138189748-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
| 5-138192259-C-T | Benign (Jul 13, 2018) | |||
| 5-138192285-G-A | not specified | Uncertain significance (Feb 14, 2023) | ||
| 5-138198744-C-A | not specified | Uncertain significance (Jan 08, 2024) | ||
| 5-138201365-G-A | not specified | Uncertain significance (Nov 06, 2023) | ||
| 5-138206576-A-T | not specified | Uncertain significance (Apr 18, 2023) | ||
| 5-138206597-C-T | not specified | Uncertain significance (Feb 16, 2023) | ||
| 5-138206633-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
| 5-138213038-G-A | not specified | Uncertain significance (May 12, 2024) | ||
| 5-138213246-T-A | not specified | Uncertain significance (Jul 14, 2022) | ||
| 5-138213292-C-A | not specified | Likely benign (Mar 30, 2022) | ||
| 5-138213294-T-C | not specified | Likely benign (May 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDC23 | protein_coding | protein_coding | ENST00000394886 | 16 | 25694 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.992 | 0.00825 | 125732 | 0 | 12 | 125744 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.78 | 190 | 333 | 0.571 | 0.0000178 | 3893 |
| Missense in Polyphen | 19 | 82.492 | 0.23033 | 902 | ||
| Synonymous | 0.392 | 121 | 127 | 0.956 | 0.00000676 | 1125 |
| Loss of Function | 4.82 | 5 | 36.4 | 0.137 | 0.00000175 | 459 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000876 | 0.0000876 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. {ECO:0000269|PubMed:18485873}.;
- Pathway
- Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Ubiquitin mediated proteolysis - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;Inactivation of APC/C via direct inhibition of the APC/C complex;Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;DNA Replication;Switching of origins to a post-replicative state;Class I MHC mediated antigen processing & presentation;Synthesis of DNA;S Phase;Cellular responses to external stimuli;TGF_beta_Receptor;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Regulation of APC/C activators between G1/S and early anaphase;Phosphorylation of the APC/C;CDK-mediated phosphorylation and removal of Cdc6;Cdc20:Phospho-APC/C mediated degradation of Cyclin A;APC-Cdc20 mediated degradation of Nek2A;APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint;APC/C:Cdc20 mediated degradation of Cyclin B;APC/C:Cdc20 mediated degradation of Securin;APC/C:Cdc20 mediated degradation of mitotic proteins;Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins;Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase;APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1;Autodegradation of Cdh1 by Cdh1:APC/C;APC/C-mediated degradation of cell cycle proteins;Regulation of mitotic cell cycle;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.141
Intolerance Scores
- loftool
- 0.234
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.51
Haploinsufficiency Scores
- pHI
- 0.808
- hipred
- Y
- hipred_score
- 0.714
- ghis
- 0.660
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.810
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdc23
- Phenotype
Gene ontology
- Biological process
- mitotic cell cycle;ubiquitin-dependent protein catabolic process;mitotic metaphase plate congression;metaphase/anaphase transition of mitotic cell cycle;regulation of exit from mitosis;regulation of mitotic metaphase/anaphase transition;anaphase-promoting complex-dependent catabolic process;cell division;protein K11-linked ubiquitination;regulation of mitotic cell cycle phase transition
- Cellular component
- nucleoplasm;anaphase-promoting complex;cytosol
- Molecular function
- ubiquitin-protein transferase activity;protein binding