CDC14A
protein-codingcell division cycle 14A, the group of CDC14 phosphatases
Gene summary
The protein encoded by this gene is a member of the dual specificity protein tyrosine phosphatase family. It is highly similar to Saccharomyces cerevisiae Cdc14, a protein tyrosine phosphatase involved in the exit of cell mitosis and initiation of DNA replication, suggesting a role in cell cycle control. This protein has been shown to interact with, and dephosphorylate tumor suppressor protein p53, and is thought to regulate the function of p53. Alternative splicing of this gene results in several transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]
- DFNB32
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~194.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0019588
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0100069
Submitter: ClinGen
The *CDC14A* gene was first associated with autosomal recessive hearing impairment and infertile male syndrome (HIIMS) in 2017 (Imtiaz et al., PMID: 29293958). In five families reported with HIIMS, females homozygous for *CDC14A* variants had prelingual sensorineural hearing loss, and homozygous males had hearing loss and infertility (PMID: 29293958). Three families segregated truncating variants predicted to affect all isoforms of the gene. Two families had two different missense variants in the dual-specificity phosphatase domain of *CDC14A*. One additional family had a third missense variant in this domain, but the fertility status of the affected males could not be determined. This gene-disease relationship is supported by expression studies and animal models (PMIDs: 27259055, 29293958). There are four mouse models for this syndrome, including one with a predicted deleterious missense variant in the phosphatase domain generated by CRISPR/Cas9 (PMID: 29293958). Of note, this gene has also been implicated in autosomal recessive nonsyndromic hearing loss which has been assessed separately. In summary, there is strong evidence to support the association between *CDC14A* and autosomal recessive hearing impairment and infertile male syndrome. Additional reports in humans are needed to reach a definitive classification. This gene-disease pair was originally classified as Strong by the ClinGen Hearing Loss Working Group on 2/26/2018 as per SOP v5. It was reevaluated on 6/1/2023. As of June 2023, this record underwent an update in scoring to be consistent with SOP v9. No new evidence has been reviewed or added. As a result of this reevaluation, the classification did not change.
Inheritance Pattern: AR
Disease ID:MONDO:0012091
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014849
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0019497
Submitter: ClinGen
CDC14A was first reported in relation to autosomal recessive nonsyndromic hearing loss in 2016 (Delmaghani et al., PMID 27259055). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in molecular mechanisms. Therefore, the following disease entities have been split into two disease entities, hearing impairment and infertility in males syndrome (OMIM:608653) and autosomal recessive nonsyndromic hearing loss (OMIM:601071). The split curation for autosomal recessive hearing impairment and infertility in males syndrome (HIIMS) has been curated separately. For males, fertility is directly associated with the location of variants within this gene. Variants that preserve the function of the NM_033313.2 transcript result in nonsyndromic hearing loss instead of HIIMS, while variants that truncate this transcript are expected to result in HIIMS. Six homozygous variants (nonsense, missense, and frameshift) that have been reported in 18 probands in 5 publications (PMIDs: 29293958, 36056583, 33187236, 32231217, 27259055) are included in this curation. This gene-disease association is also supported by animal models (PMIDs: 29293958, 27259055) that demonstrate hearing loss associated with CDC14A heterozygotes. The models also indicate an effect on the length of the kinocilia in inner-ear hair cells, which can impact the differentiation of the auditory sensory cells’ hair bundles. This gene-disease pair was originally evaluated by the Hearing Loss GCEP on 2/26/2018. It was re-evaluated on 1/15/2025. As a result of this reevaluation, the classification changed from limited to definitive, due to the addition of genetic evidence and experimental evidence (PMIDs: 36056583, 33187236, 32231217, 27259055). In summary, CDC14A is definitively associated with autosomal recessive nonsyndromic hearing loss. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Hearing Loss GCEP on the meeting date 1/15/2025 (SOP Version 11).
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Genitourinary
Intervention: Audiologic/Otolaryngologic
Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CDC14A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003672.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 42 | 6 | 52 | ||
| missense | 4 | 111 | 14 | 1 | 130 | |
| nonsense | 5 | 4 | 1 | 10 | ||
| start loss | 0 | |||||
| frameshift | 3 | 2 | 2 | 7 | ||
| splice donor/acceptor (+/-2bp) | 3 | 1 | 4 | |||
| Total | 8 | 13 | 119 | 56 | 7 | 203 |
Highest pathogenic variant AF is 0.000029119188
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003663.2 | 16 | MANE Select | |
| Ensembl | ENSP00000336739.3 | 16 | MANE Select | |
| RefSeq | NP_001306139.1 | 16 | Standard | |
| RefSeq | NP_001306140.1 | 13 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cdc14aa | Danio rerio | Structure: whole organism Quality: increased curvature abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell cycle - Homo sapiens (human)
- Cell Cycle
- Signal Transduction
- MAPK6/MAPK4 signaling
- MAPK family signaling cascades
Biological Process
- microtubule cytoskeleton organization
- mitotic cell cycle
- regulation of exit from mitosis
- sensory perception of sound
- cell population proliferation
Molecular Function
- phosphoprotein phosphatase activity
- protein serine/threonine phosphatase activity
- protein tyrosine phosphatase activity
- protein binding
- protein tyrosine/serine/threonine phosphatase activity
Cellular Component
- spindle pole
- nucleoplasm
- nucleolus
- cytoplasm
- centrosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000361544
- Coding exons
- 15
- Length
- 175250
- Individuals with no LoFs
- 125696
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 52
- Defined
- 125748
- p
- 0.000207
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.494 | 309 | 334 | 0.924 | 0.0000172 | 4066 |
| Missense (PolyPhen) | 58 | 85.365 | 0.67944 | 1077 | ||
| Synonymous | -1.26 | 147 | 129 | 1.14 | 0.00000693 | 1194 |
| Loss of Function | 2.62 | 17 | 33.3 | 0.510 | 0.00000188 | 413 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00037 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.000058 | 0.000054 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00024 | 0.00023 | rare |
| Other | 0.00051 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Dual-specificity phosphatase. Required for centrosome separation and productive cytokinesis during cell division. Dephosphorylates SIRT2 around early anaphase. May dephosphorylate the APC subunit FZR1/CDH1, thereby promoting APC-FZR1 dependent degradation of mitotic cyclins and subsequent exit from mitosis. {ECO:0000269|PubMed:11901424, ECO:0000269|PubMed:12134069, ECO:0000269|PubMed:17488717, ECO:0000269|PubMed:9367992}.;
- Disease
- DISEASE: Deafness, autosomal recessive, 105 (DFNB105) [MIM:616958]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:27259055}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- LoFtool
- 0.708
- RVIS EVS
- -0.4
- RVIS percentile EVS
- 26.93
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.443
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |