CDC14B
cell division cycle 14B, the group of CDC14 phosphatases
Basic information
Region (hg38): 9:96490241-96619843
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 CDC14B 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 | 34 | 35 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 34 | 1 | 0 |
Variants in CDC14B
This is a list of pathogenic ClinVar variants found in the CDC14B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-96503757-C-T | not specified | Uncertain significance (Dec 13, 2021) | ||
| 9-96503770-T-C | not specified | Uncertain significance (Jan 10, 2023) | ||
| 9-96509684-G-C | not specified | Uncertain significance (Apr 24, 2023) | ||
| 9-96509754-G-A | not specified | Uncertain significance (Mar 28, 2023) | ||
| 9-96522581-T-C | not specified | Uncertain significance (Jan 10, 2023) | ||
| 9-96523265-T-G | not specified | Uncertain significance (Aug 13, 2021) | ||
| 9-96523266-C-T | not specified | Uncertain significance (Dec 08, 2023) | ||
| 9-96523329-G-A | not specified | Uncertain significance (Mar 21, 2022) | ||
| 9-96523343-G-A | not specified | Uncertain significance (Mar 29, 2024) | ||
| 9-96523370-T-C | not specified | Likely benign (Jan 08, 2024) | ||
| 9-96523382-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 9-96523687-T-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 9-96534004-G-A | not specified | Uncertain significance (Dec 01, 2022) | ||
| 9-96534016-G-A | not specified | Uncertain significance (Mar 07, 2023) | ||
| 9-96534031-T-C | not specified | Uncertain significance (Jan 05, 2022) | ||
| 9-96534038-C-T | not specified | Uncertain significance (Jul 13, 2021) | ||
| 9-96534058-C-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 9-96534061-T-C | not specified | Uncertain significance (Jul 21, 2021) | ||
| 9-96534149-G-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 9-96534510-T-C | not specified | Uncertain significance (May 09, 2023) | ||
| 9-96534533-T-G | not specified | Uncertain significance (Jun 07, 2023) | ||
| 9-96539085-T-C | not specified | Uncertain significance (May 18, 2022) | ||
| 9-96539112-T-C | not specified | Uncertain significance (Feb 22, 2023) | ||
| 9-96541845-C-T | not specified | Uncertain significance (Aug 19, 2023) | ||
| 9-96541876-T-C | not specified | Uncertain significance (Aug 13, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDC14B | protein_coding | protein_coding | ENST00000375241 | 14 | 129590 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.943 | 0.0569 | 125726 | 0 | 20 | 125746 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 217 | 263 | 0.824 | 0.0000137 | 3288 |
| Missense in Polyphen | 68 | 96.922 | 0.70159 | 1224 | ||
| Synonymous | 0.494 | 85 | 91.0 | 0.934 | 0.00000498 | 898 |
| Loss of Function | 4.07 | 4 | 26.7 | 0.150 | 0.00000131 | 347 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000133 | 0.000132 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Dual-specificity phosphatase involved in DNA damage response. Essential regulator of the G2 DNA damage checkpoint: following DNA damage, translocates to the nucleus and dephosphorylates FZR1/CDH1, a key activator of the anaphase promoting complex/cyclosome (APC/C). Dephosphorylates SIRT2 around early anaphase. Dephosphorylation of FZR1/CDH1 activates the APC/C, leading to the ubiquitination of PLK1, preventing entry into mitosis. Preferentially dephosphorylates proteins modified by proline-directed kinases. {ECO:0000269|PubMed:17488717, ECO:0000269|PubMed:18662541, ECO:0000269|PubMed:9367992}.;
- Pathway
- Cell cycle - Homo sapiens (human);Cell Cycle;Signal Transduction;MAPK6/MAPK4 signaling;MAPK family signaling cascades;PLK1 signaling events
(Consensus)
Recessive Scores
- pRec
- 0.0997
Intolerance Scores
- loftool
- 0.125
- rvis_EVS
- -0.31
- rvis_percentile_EVS
- 31.93
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.822
- ghis
- 0.609
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.923
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdc14b
- Phenotype
- skeleton phenotype; vision/eye phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- cdc14b
- Affected structure
- macula saccule
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- microtubule cytoskeleton organization;mitotic cell cycle;DNA repair;protein dephosphorylation;regulation of exit from mitosis;positive regulation of cytokinesis;peptidyl-tyrosine dephosphorylation;mitotic cell cycle arrest;signal transduction involved in G2 DNA damage checkpoint;positive regulation of ubiquitin protein ligase activity
- Cellular component
- spindle pole;nucleus;nucleoplasm;nucleolus;cytoplasm;centrosome;mitotic spindle
- Molecular function
- protein serine/threonine phosphatase activity;protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity