CDC34
cell division cycle 34, ubiqiutin conjugating enzyme, the group of Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 19:531760-542092
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 CDC34 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 0 |
Variants in CDC34
This is a list of pathogenic ClinVar variants found in the CDC34 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-531935-G-T | not specified | Uncertain significance (Apr 26, 2024) | ||
| 19-531939-G-A | not specified | Uncertain significance (May 08, 2024) | ||
| 19-532062-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| 19-536279-G-A | not specified | Uncertain significance (Nov 08, 2022) | ||
| 19-537099-A-G | not specified | Uncertain significance (Nov 03, 2023) | ||
| 19-537126-G-A | not specified | Uncertain significance (Dec 13, 2022) | ||
| 19-541368-C-T | not specified | Uncertain significance (Jan 07, 2022) | ||
| 19-541406-G-A | not specified | Uncertain significance (Aug 01, 2023) | ||
| 19-541428-C-T | not specified | Uncertain significance (Mar 31, 2023) | ||
| 19-541439-G-A | not specified | Uncertain significance (Nov 18, 2022) | ||
| 19-541487-G-A | not specified | Uncertain significance (Jul 26, 2022) | ||
| 19-541496-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 19-541519-C-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 19-541520-G-A | not specified | Uncertain significance (Nov 08, 2021) | ||
| 19-541539-C-T | not specified | Uncertain significance (Mar 21, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDC34 | protein_coding | protein_coding | ENST00000215574 | 5 | 10384 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.956 | 0.0437 | 125719 | 0 | 2 | 125721 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.83 | 85 | 148 | 0.576 | 0.0000100 | 1517 |
| Missense in Polyphen | 24 | 52.337 | 0.45857 | 559 | ||
| Synonymous | -1.84 | 90 | 70.4 | 1.28 | 0.00000603 | 447 |
| Loss of Function | 2.90 | 0 | 9.80 | 0.00 | 4.17e-7 | 122 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| 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 | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys- 48'-linked polyubiquitination (PubMed:22496338). Cooperates with the E2 UBCH5C and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation. Performs ubiquitin chain elongation building ubiquitin chains from the UBE2D3-primed NFKBIA-linked ubiquitin. UBE2D3 acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin. Cooperates with the SCF(SKP2) E3 ligase complex to regulate cell proliferation through ubiquitination and degradation of MYBL2 and KIP1. Involved in ubiquitin conjugation and degradation of CREM isoform ICERIIgamma and ATF15 resulting in abrogation of ICERIIgamma- and ATF5-mediated repression of cAMP-induced transcription during both meiotic and mitotic cell cycles. Involved in the regulation of the cell cycle G2/M phase through its targeting of the WEE1 kinase for ubiquitination and degradation. Also involved in the degradation of beta-catenin. Is target of human herpes virus 1 protein ICP0, leading to ICP0- dependent dynamic interaction with proteasomes (PubMed:10329681, PubMed:10373550, PubMed:10871850, PubMed:11675391, PubMed:12037680, PubMed:15652359, PubMed:17461777, PubMed:17698585, PubMed:19112177, PubMed:19126550, PubMed:19945379, PubMed:20061386, PubMed:20347421). {ECO:0000269|PubMed:10329681, ECO:0000269|PubMed:10373550, ECO:0000269|PubMed:10871850, ECO:0000269|PubMed:11675391, ECO:0000269|PubMed:12037680, ECO:0000269|PubMed:15652359, ECO:0000269|PubMed:17461777, ECO:0000269|PubMed:17698585, ECO:0000269|PubMed:19112177, ECO:0000269|PubMed:19126550, ECO:0000269|PubMed:19945379, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:20347421, ECO:0000269|PubMed:22496338}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Vitamin D Receptor Pathway;cyclin e destruction pathway;e2f1 destruction pathway;Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Protein ubiquitination;TNFalpha
(Consensus)
Intolerance Scores
- loftool
- 0.434
- rvis_EVS
- -0.65
- rvis_percentile_EVS
- 16.36
Haploinsufficiency Scores
- pHI
- 0.238
- hipred
- Y
- hipred_score
- 0.713
- ghis
- 0.562
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.850
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdc34
- 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); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;protein polyubiquitination;DNA replication initiation;cellular protein modification process;ubiquitin-dependent protein catabolic process;protein ubiquitination;cellular response to interferon-beta;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of neuron apoptotic process;negative regulation of cAMP-mediated signaling;response to growth factor;protein K48-linked ubiquitination;positive regulation of inclusion body assembly
- Cellular component
- nucleus;nucleoplasm;cytosol;nuclear speck
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin conjugating enzyme activity