CDC14A

protein-coding

cell 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]

Previous symbols:
  • DFNB32

MANE transcript

NM_003672.4

Inheritance

AR

ClinVar variants

P:21U:119B:63

Top phenotype

Deafness, autosomal recessive 32, with or without immotile sperm

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr1:100,325,629-100,520,277

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~194.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hearing loss, autosomal recessiveSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019588

Submitter: Orphanet

hearing impairment and infertile male syndromeSTRONG

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.

autosomal recessive nonsyndromic hearing loss 32LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0012091

Submitter: Ambry Genetics

autosomal recessive nonsyndromic deafness 105STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014849

Submitter: Labcorp Genetics (formerly Invitae)

nonsyndromic genetic hearing lossDEFINITIVE

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)

Deafness, autosomal recessive 32, with or without immotile spermAR

Manifestation: Audiologic/Otolaryngologic; Genitourinary

Intervention: Audiologic/Otolaryngologic

Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development

Refs: 27259055; 29293958Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDC14A variants in ClinVar

9 Conditions Cataloged
not providedTotal: 210
Inborn genetic diseasesTotal: 69
not specifiedTotal: 39
CDC14A-related disorderTotal: 26
Autosomal recessive nonsyndromic hearing loss 32Total: 16
Ear malformationTotal: 2
Monogenic hearing lossTotal: 2
Rare genetic deafnessTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
42
clinvar
6
clinvar
52
missense
4
clinvar
111
clinvar
14
clinvar
1
clinvar
130
nonsense
5
clinvar
4
clinvar
1
clinvar
10
start loss
0
frameshift
3
clinvar
2
clinvar
2
clinvar
7
splice donor/acceptor (+/-2bp)
3
clinvar
1
clinvar
4
Total813119567203

Highest pathogenic variant AF is 0.000029119188

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003672.4RefSeqNP_003663.216MANE Select
ENST00000336454.5EnsemblENSP00000336739.316MANE Select
NM_001319210.2RefSeqNP_001306139.116Standard
NM_001319211.2RefSeqNP_001306140.113Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
cdc14aaDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4943093340.9240.00001724066
Missense (PolyPhen)5885.3650.679441077
Synonymous-1.261471291.140.000006931194
Loss of Function2.621733.30.5100.00000188413

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000430.00037rare
Latino/Admixed American0.000350.00035rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.0000580.000054rare
Finnish0.0000920.000092rare
European (Non-Finnish)0.000170.00017rare
South Asian0.000240.00023rare
Other0.000510.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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