EYA4

gene
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Summary

EYA4 (EYA transcriptional coactivator and phosphatase 4, HGNC:3522) is a protein-coding gene on chromosome 6q23.2, encoding Protein phosphatase EYA4 (O95677). Tyrosine phosphatase that specifically dephosphorylates ‘Tyr-142’ of histone H2AX (H2AXY142ph). ‘Tyr-142’ phosphorylation of histone H2AX plays a central role in DNA repair and acts as a mark that distinguishes between apoptotic and repair responses to genotoxic stress. It is haploinsufficient (ClinGen: sufficient evidence).

This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may act as a transcriptional activator through its protein phosphatase activity, and it may be important for eye development, and for continued function of the mature organ of Corti. Mutations in this gene are associated with postlingual, progressive, autosomal dominant hearing loss at the deafness, autosomal dominant non-syndromic sensorineural 10 locus. The encoded protein is also a putative oncogene that mediates DNA repair, apoptosis, and innate immunity following DNA damage, cellular damage, and viral attack. Defects in this gene are also associated with dilated cardiomyopathy 1J. Alternative splicing results in multiple transcript variants encoding distinct isoforms.

Source: NCBI Gene 2070 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): nonsyndromic genetic hearing loss (Definitive, ClinGen) — +3 more curated relationships
  • GWAS associations: 49
  • Clinical variants (ClinVar): 1,031 total — 48 pathogenic, 31 likely-pathogenic
  • Phenotypes (HPO): 10
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_004100

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3522
Approved symbolEYA4
NameEYA transcriptional coactivator and phosphatase 4
Location6q23.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000112319
Ensembl biotypeprotein_coding
OMIM603550
Entrez2070

Gene structure

Transcript identifiers

Ensembl transcripts: 42 — 22 protein_coding, 16 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000355167, ENST00000355286, ENST00000421413, ENST00000430974, ENST00000431403, ENST00000441015, ENST00000452339, ENST00000497350, ENST00000525614, ENST00000525849, ENST00000531861, ENST00000531901, ENST00000532518, ENST00000682730, ENST00000683175, ENST00000683325, ENST00000683361, ENST00000683421, ENST00000683422, ENST00000683580, ENST00000683664, ENST00000683674, ENST00000683832, ENST00000684040, ENST00000684097, ENST00000684425, ENST00000684513, ENST00000684773, ENST00000706301, ENST00000883053, ENST00000883054, ENST00000883055, ENST00000883056, ENST00000883057, ENST00000883058, ENST00000883059, ENST00000883060, ENST00000883061, ENST00000883062, ENST00000883063, ENST00000883064, ENST00000943593

RefSeq mRNA: 7 — MANE Select: NM_004100 NM_001301012, NM_001301013, NM_001370458, NM_001370459, NM_004100, NM_172103, NM_172105

CCDS: CCDS43506, CCDS5165, CCDS75521, CCDS75523, CCDS94004, CCDS94005

Canonical transcript exons

ENST00000355286 — 20 exons

ExonStartEnd
ENSE00000798773133512878133513038
ENSE00000798774133515321133515435
ENSE00001284413133241357133241749
ENSE00001284455133274716133274813
ENSE00001597576133523056133523177
ENSE00001711375133525154133525254
ENSE00001852704133528725133532128
ENSE00003464008133506106133506195
ENSE00003468302133483032133483115
ENSE00003468388133448111133448179
ENSE00003540255133512721133512779
ENSE00003564780133456556133456648
ENSE00003566031133481463133481599
ENSE00003582680133462335133462477
ENSE00003587571133382392133382441
ENSE00003590926133462621133462764
ENSE00003595413133461114133461180
ENSE00003628601133446630133446754
ENSE00003648898133468566133468731
ENSE00003689200133464779133464858

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 93.60.

FANTOM5 (CAGE): breadth broad, TPM avg 4.7838 / max 188.6831, expressed in 777 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
698423.3256724
698410.5093314
698430.3197143
698440.3008148
698400.165281
698390.163378

Top tissues by expression

279 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
biceps brachiiUBERON:000150793.60gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450292.82gold quality
seminal vesicleUBERON:000099891.81gold quality
gastrocnemiusUBERON:000138891.50gold quality
muscle of legUBERON:000138390.98gold quality
calcaneal tendonUBERON:000370189.24gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451189.08gold quality
muscle organUBERON:000163088.93gold quality
mucosa of paranasal sinusUBERON:000503088.80gold quality
hindlimb stylopod muscleUBERON:000425288.51gold quality
bronchial epithelial cellCL:000232887.99gold quality
heart right ventricleUBERON:000208087.27gold quality
skeletal muscle tissueUBERON:000113486.35gold quality
deltoidUBERON:000147685.49gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.35gold quality
tibialis anteriorUBERON:000138583.17silver quality
muscle tissueUBERON:000238582.55gold quality
quadriceps femorisUBERON:000137781.82gold quality
epithelium of bronchusUBERON:000203181.34gold quality
vastus lateralisUBERON:000137981.32gold quality
right uterine tubeUBERON:000130281.08gold quality
bronchusUBERON:000218580.61gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.02gold quality
olfactory segment of nasal mucosaUBERON:000538678.97gold quality
right atrium auricular regionUBERON:000663178.81gold quality
tendonUBERON:000004378.72gold quality
cardiac atriumUBERON:000208178.29gold quality
myocardiumUBERON:000234977.43gold quality
cardiac ventricleUBERON:000208277.41gold quality
heart left ventricleUBERON:000208477.28gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-ANND-2yes2911.96
E-CURD-119yes29.43
E-ANND-3yes6.09
E-MTAB-5061no3.81
E-GEOD-83139no2.91

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1, RUNX1

miRNA regulators (miRDB)

185 targeting EYA4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-656-3P100.0072.152788
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-8485100.0077.574731
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3163100.0077.238605
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-548AW99.9972.573559
HSA-MIR-511-3P99.9968.851467
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-806899.9873.852376
HSA-MIR-477599.9875.006394
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-570-3P99.9672.414910
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-548AT-5P99.9670.832666

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • Mutation analysis of the EYA4 gene, which maps to 6q22.3, revealed an insertion of 4 bp (1558insTTTG) in affected family members with hereditary hearing impairment (PMID:12477971)
  • Mutation in the transcriptional coactivator EYA4 causes dilated cardiomyopathy and sensorineural hearing loss (PMID:15735644)
  • Results show the first definitive cardiac evaluations of DFNA10 hearing loss to support a correlation of EYA4 mutation with/without the of dilated cardiomyopathy, and will facilitate the counseling of patients with these phenotypes and EYA4 mutations. (PMID:17567890)
  • Study is the first report of a point mutation in EYA4 that is hypothesized to lead to aberrant pre-mRNA splicing and human disease. (PMID:17568404)
  • Mice lacking the orthologous gene have severe hearing deficits, suggesting that some human otitis media susceptibility reflects underlying genetic predisposition in genes such as this one. (PMID:18219393)
  • Findings identify a role of EYA4 and possibly interacting SIX and DACH proteins in MPNSTs and suggest the EYA4 pathway as a rational therapeutic target. (PMID:19901965)
  • EYA4 and hTERT mRNA expression increased with the severity of esophageal pathological changes and may be useful for identifying high-risk endoscopy candidates or for monitoring changes in premalignant esophageal lesions. (PMID:19939248)
  • Serum methylation levels of TAC1, SEPT9, and EYA4 were significant discriminants between stage I colorectal cancer and healthy controls. (PMID:23862763)
  • High methylation of the EYA4 gene is associated with ulcerative colitis with colorectal cancer. (PMID:23867875)
  • Work shows a clear role for EYA4 as a putative tumor suppressor genes in non-small-cell lung cancer. (PMID:24096489)
  • Low EYA4 expression is associated with hepatocellular carcinoma. (PMID:24306662)
  • Results provide molecular and clinical information in order to gain improved understanding of the pathogenesis of DFNA10 protein EYA4 mutations and the genotypephenotype correlations of DFNA10 hearing loss. (PMID:25242383)
  • EYA4 methylation may be identified in stool samples. (PMID:25620232)
  • Autosomal dominant hearing impairment due to a novel EYA4 frameshift mutation:a novel heterozygous frame-shift mutation (c.579_580insTACC, p.(Asp194Tyrfs*52)) in EYA4 was identified that truncates the so-called variable region of the protein. (PMID:25681523)
  • EYA4 mutations are associated with autosomal dominant non-syndromic hearing loss. (PMID:25781927)
  • A novel missense mutation c.1643C>G (p.T548R) in EYA4 may cause autosomal dominant non-syndromic hearing impairment. (PMID:25809937)
  • Exome Sequencing Identifies a Mutation in EYA4 as a Novel Cause of Autosomal Dominant Non-Syndromic Hearing Loss (PMID:25961296)
  • analysis of an EYA4 mutation causing hearing loss in a Chinese DFNA family (PMID:25963406)
  • The identification of a novel EYA4 truncation mutation associated with DFNA10, rather than syndromic hearing loss, supports a previously reported genotype-phenotype correlation in this gene. (PMID:26015337)
  • In a Dutch family with c.464del EYA4 mutation, hearing impairment begins as a mid-frequency hearing impairment in childhood and develops into a high-frequency, moderate hearing impairment later in life. (PMID:26331839)
  • Genetic variations in the EYA4, GRHL2 and DFNA5 genes and their interactions with occupational noise exposure may play an important role in the incidence of noise-induced hearing loss (NIHL). (PMID:26400775)
  • results implicate Eya4/Six1 regulates normal cardiac function via p27/casein kinase-2alpha/histone deacetylase 2 and indicate that mutations within this transcriptional complex and signaling cascade lead to the development of cardiomyopathy. (PMID:26499333)
  • Low expression of EYA4 is associated with oral cancer. (PMID:27015871)
  • Up to now, merely 7 loci have been linked to mid-frequency hearing loss. Only four genetic mid-frequency deafness genes, namely, DFNA10 (EYA4), DFNA8/12 (TECTA), DFNA13 (COL11A2), DFNA44 (CCDC50), have been reported to date. [review] (PMID:27142990)
  • study identified EYA4 gene as targets for AML1-ETO and indicated it as a novel tumor suppressor gene. In addition, we provided evidence that EYA4 gene might be a novel therapeutic target and a potential candidate for treating AML1-ETO+ t (8;21) AML. (PMID:27231175)
  • EYA4 functions as tumor suppressor gene in pancreatic ductal adenocarcinoma via repressing beta-catenin/ID2 activation, and was an independent prognostic factor in PDAC. (PMID:27378242)
  • Loss of EYA4 expression is associated with intrahepatic cholangiocarcinoma. (PMID:27469137)
  • Locus polymorphism of rs3813346 was associated with the risk of developing noise-induced hearing loss in the dominance model, the codominance model and the addictive model. Generalized multiple dimensionality reduction indicated that the combined interaction of the 2 loci-rs3813346 and rs9493627-significantly affected the incidence of noise-induced hearing loss. (PMID:27613755)
  • We discovered two genome-wide significant SNPs. The first was novel and near ISG20. The second was in TRIOBP, a gene previously associated with prelingual nonsyndromic hearing loss. Motivated by our TRIOBP results, we also looked at exons in known hearing loss genes, and identified two additional SNPs, rs2877561 in ILDR1 and rs9493672 in EYA4 (at a significance threshold adjusted for number of SNPs in those regions). (PMID:27764096)
  • EYA4 hypermethylation is associated with colorectal cancer. (PMID:28351398)
  • identified novel EYA4 mutation can be considered responsible of the hearing loss observed in the proband and her father, while a dual molecular diagnosis was reached in the relatives co-segregating the EYA4 and the PAX3 mutations (PMID:29287889)
  • Although the clinical patient outcome of our 38 Colorectal Cancer patients was not associated with EYA4 promoter hypermethylation, the high frequency of this methylation and its high sensitivity and specificity to neoplastic cells may qualify EYA4 promoter methylation as a potential candidate screening marker in Iranian population and may help to improve early detection of CRC. (PMID:29436791)
  • Eyes absent homolog 4 (Drosophila) protein (EYA4) is frequently hypermethylated in esophageal squamous cell carcinoma (ESCC) and may function as a tumor suppressor gene in the development of ESCC. (PMID:29660222)
  • Findings identified eyes absent homolog 4 (EYA4) as a tumor suppressor that disrupts aberrant activation of the nuclear factor kappa B (NF-kappaB)/RAP1 protein signaling pathway and thus orchestrates a physiological impediment to hepatocellular carcinoma (HCC) growth and invasion. (PMID:29764501)
  • Overexpression of EYA4 enhanced glioma cell proliferation, and EYA4 suppressed the expression of p27Kip1 directly in these cells. (PMID:30231237)
  • the novel missense mutation c.1855T>G (p.W619G) in EYA4 causing autosomal dominant non-syndromic hearing impairment in the selected Chinese family, was identified. (PMID:30942159)
  • EYA4 is a novel tumour suppressor in HCC and a new prognostic biomarker and therapeutic target in HCC. (PMID:30957411)
  • Result show that EYA4 expression is regulated by miR626 which targets its 3’UTR in bladder cancer cells. (PMID:31101108)
  • Study reports that EYA4 suppressed hepatocellular carcinoma (HCC) tumor cell growth by reducing the nuclear translocation of beta-catenin by dephosphorylation at Ser552, thereby suppressing the transcription of MYCBP which was induced by beta-catenin/LEF1 binding to the promoter of MYCBP. (PMID:31385398)
  • Prevalence and clinical features of hearing loss caused by EYA4 variants. (PMID:32107406)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioeya4ENSDARG00000012397
mus_musculusEya4ENSMUSG00000010461
rattus_norvegicusEya4ENSRNOG00000016627
drosophila_melanogastereyaFBGN0000320
caenorhabditis_eleganseya-1WBGENE00001377

Paralogs (3): EYA2 (ENSG00000064655), EYA1 (ENSG00000104313), EYA3 (ENSG00000158161)

Protein

Protein identifiers

Protein phosphatase EYA4O95677 (reviewed: O95677)

Alternative names: Eyes absent homolog 4

All UniProt accessions (9): O95677, A0A0S2Z3Q2, A0A0S2Z3V9, A0A804HHY3, A0A804HL00, A0A8C8KDW0, E7ESD5, E9PLN6, F2Z2Y1

UniProt curated annotations — full annotation on UniProt →

Function. Tyrosine phosphatase that specifically dephosphorylates ‘Tyr-142’ of histone H2AX (H2AXY142ph). ‘Tyr-142’ phosphorylation of histone H2AX plays a central role in DNA repair and acts as a mark that distinguishes between apoptotic and repair responses to genotoxic stress. Promotes efficient DNA repair by dephosphorylating H2AX, promoting the recruitment of DNA repair complexes containing MDC1. Its function as histone phosphatase probably explains its role in transcription regulation during organogenesis. May be involved in development of the eye.

Subunit / interactions. Interacts with SIX3; translocates EYA4 from the cytoplasm to the nucleus and promotes activation of their target genes.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Highly expressed in heart and skeletal muscle.

Disease relevance. Deafness, autosomal dominant, 10 (DFNA10) [MIM:601316] 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. The disease is caused by variants affecting the gene represented in this entry. Cardiomyopathy, dilated, 1J (CMD1J) [MIM:605362] A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. CMD1J is characterized by the association of sensorineural hearing loss and dilated cardiomyopathy in the absence of other anomalies. The disease is caused by variants affecting the gene represented in this entry.

Cofactor. Binds 1 Mg(2+) ion per subunit.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the HAD-like hydrolase superfamily. EYA family.

Isoforms (5)

UniProt IDNamesCanonical?
O95677-11yes
O95677-22
O95677-33
O95677-44
O95677-55

RefSeq proteins (7): NP_001287941, NP_001287942, NP_001357387, NP_001357388, NP_004091, NP_742101, NP_742103 (=MANE)

Domains & families (InterPro)

IDNameType
IPR006545EYA_domDomain
IPR028472EYAFamily
IPR038102EYA_dom_sfHomologous_superfamily
IPR042577EYA_dom_metazoanDomain

Pfam: PF00702

Catalyzed reactions (Rhea), 1 shown:

  • O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate (RHEA:10684)

UniProt features (29 total): splice variant 6, sequence variant 6, region of interest 3, binding site 3, compositionally biased region 3, modified residue 2, cross-link 2, active site 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95677-F163.790.41

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 375 (nucleophile); 377 (proton donor)

Ligand- & substrate-binding residues (3): 377; 603; 375

Post-translational modifications (4): 1, 361, 14, 52

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-5693565Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks

MSigDB gene sets: 242 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, CERVERA_SDHB_TARGETS_1_DN, CHANDRAN_METASTASIS_DN, GOBP_REGULATION_OF_DNA_REPAIR, GTGCCTT_MIR506, GOBP_NEGATIVE_REGULATION_OF_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_REGULATION_OF_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_REGULATION_OF_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_ABSENCE_OF_LIGAND, TGTGTGA_MIR377, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_SIGNAL_TRANSDUCTION_IN_ABSENCE_OF_LIGAND, ZIC1_01

GO Biological Process (10): DNA repair (GO:0006281), chromatin organization (GO:0006325), visual perception (GO:0007601), anatomical structure morphogenesis (GO:0009653), cell differentiation (GO:0030154), positive regulation of DNA repair (GO:0045739), inner ear development (GO:0048839), negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240), DNA damage response (GO:0006974), multicellular organism development (GO:0007275)

GO Molecular Function (5): protein tyrosine phosphatase activity (GO:0004725), metal ion binding (GO:0046872), phosphoprotein phosphatase activity (GO:0004721), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
DNA Double Strand Break Response1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
anatomical structure development3
DNA metabolic process1
DNA damage response1
cellular component organization1
sensory perception of light stimulus1
developmental process1
cellular developmental process1
DNA repair1
regulation of DNA repair1
positive regulation of response to stimulus1
positive regulation of DNA metabolic process1
ear development1
extrinsic apoptotic signaling pathway in absence of ligand1
negative regulation of signal transduction in absence of ligand1
negative regulation of extrinsic apoptotic signaling pathway1
regulation of extrinsic apoptotic signaling pathway in absence of ligand1
cellular response to stress1
multicellular organismal process1
phosphoprotein phosphatase activity1
cation binding1
phosphatase activity1
catalytic activity, acting on a protein1
binding1
catalytic activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1382 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EYA4TCF21O43680806
EYA4NLRX1Q86UT6789
EYA4RBM20Q5T481739
EYA4ABCC9O60706703
EYA4TMPOP08918688
EYA4NEXNQ0ZGT2655
EYA4KCNQ4P56696646
EYA4FKTNO75072622
EYA4SIX4Q9UIU6609
EYA4MYBPC3Q14896604
EYA4DSG2Q14126602
EYA4SIX1Q15475602
EYA4CSRP3P50461592
EYA4TCAPO15273589
EYA4SGCDQ92629585
EYA4SGK1O00141585

IntAct

24 interactions, top by confidence:

ABTypeScore
SIX2EYA2psi-mi:“MI:0914”(association)0.530
PFDN2CDC40psi-mi:“MI:0914”(association)0.530
EYA4AATKpsi-mi:“MI:0915”(physical association)0.370
EYA4ERBB3psi-mi:“MI:0915”(physical association)0.370
FOXJ2TCERG1psi-mi:“MI:0914”(association)0.350
PIPRBM47psi-mi:“MI:0914”(association)0.350
SIX5PPM1Gpsi-mi:“MI:0914”(association)0.350
SIX1EYA4psi-mi:“MI:0914”(association)0.350
GATA2BCL9psi-mi:“MI:2364”(proximity)0.270
HNF1BBCL9psi-mi:“MI:2364”(proximity)0.270
SOX15SMCHD1psi-mi:“MI:2364”(proximity)0.270
SP7IGF2BP3psi-mi:“MI:2364”(proximity)0.270
TLX1BCL9psi-mi:“MI:2364”(proximity)0.270
EYA4PPIP5K2psi-mi:“MI:0915”(physical association)0.000
EYA4SEC24Bpsi-mi:“MI:0915”(physical association)0.000
EYA4UBE2D2psi-mi:“MI:0915”(physical association)0.000
EYA4PLECpsi-mi:“MI:0915”(physical association)0.000
EYA4QSER1psi-mi:“MI:0915”(physical association)0.000
EYA4AAK1psi-mi:“MI:0915”(physical association)0.000
EYA4CCDC88Apsi-mi:“MI:0915”(physical association)0.000
EYA4LUZP1psi-mi:“MI:0915”(physical association)0.000
EYA4URGCPpsi-mi:“MI:0915”(physical association)0.000
EYA4DVL3psi-mi:“MI:0915”(physical association)0.000

BioGRID (273): EYA4 (Affinity Capture-MS), EYA4 (Affinity Capture-MS), DCTPP1 (Affinity Capture-MS), ERC1 (Affinity Capture-MS), RPA2 (Affinity Capture-MS), RPA3 (Affinity Capture-MS), SIX2 (Affinity Capture-MS), SIX4 (Affinity Capture-MS), SUPT5H (Affinity Capture-MS), EYA4 (Affinity Capture-MS), DCTPP1 (Affinity Capture-MS), SCO1 (Affinity Capture-MS), EOGT (Affinity Capture-MS), SLC25A15 (Affinity Capture-MS), SCO2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1P8AS03, A3LX75, A5DDB7, D5MCN2, F4IUY8, F4K1Z0, G4NID8, M2TGT8, M2U3Z7, O13987, O17670, O60167, O61708, O74345, O74412, O95677, P25644, P34643, P53297, P97767, Q05672, Q07998, Q08400, Q09750, Q09801, Q10655, Q10667, Q18273, Q20374, Q20870, Q2L4W6, Q3MK94, Q3S405, Q61X54, Q6E3D2, Q6E3D4, Q6FLG1, Q6FSQ6, Q75BK1, Q7ZT82

Diamond homologs: O00167, O08575, O82162, O95677, P97480, P97767, Q05201, Q58DB6, Q99502, Q99504, Q9YH98, Q9YH99, Q9YHA0, Q9YHA1, Q9Z191, O17670

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

1031 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic48
Likely pathogenic31
Uncertain significance533
Likely benign301
Benign52

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1185054NM_004100.5(EYA4):c.964C>T (p.Gln322Ter)Pathogenic
1185589NM_004100.5(EYA4):c.580+2T>CPathogenic
1185629NM_004100.5(EYA4):c.804+2T>APathogenic
1185652NM_004100.5(EYA4):c.804+2delPathogenic
1210331NM_004100.5(EYA4):c.1154C>A (p.Ser385Ter)Pathogenic
1322847NM_004100.5(EYA4):c.1026_1027dup (p.Thr343fs)Pathogenic
1322854NM_004100.5(EYA4):c.1048_1049dup (p.Arg352fs)Pathogenic
1380128NM_004100.5(EYA4):c.832C>T (p.Gln278Ter)Pathogenic
1419206NM_004100.5(EYA4):c.67C>T (p.Gln23Ter)Pathogenic
1808956GRCh37/hg19 6q23.2(chr6:133522860-134541311)x1Pathogenic
1916328NM_004100.5(EYA4):c.223_224del (p.Val75fs)Pathogenic
1965243NM_004100.5(EYA4):c.242G>A (p.Trp81Ter)Pathogenic
2112319NM_004100.5(EYA4):c.1574G>A (p.Trp525Ter)Pathogenic
2126137NM_004100.5(EYA4):c.1472del (p.Leu491fs)Pathogenic
236032NM_004100.5(EYA4):c.441del (p.Tyr148fs)Pathogenic
2425022NC_000006.11:g.(?133782232)(133783922_?)delPathogenic
2445629NM_004100.5(EYA4):c.992dup (p.Ser331fs)Pathogenic
2446670NM_004100.5(EYA4):c.988C>T (p.Gln330Ter)Pathogenic
2743050NM_004100.5(EYA4):c.211G>T (p.Glu71Ter)Pathogenic
2783559NM_004100.5(EYA4):c.579C>G (p.Tyr193Ter)Pathogenic
2833829NM_004100.5(EYA4):c.1776dup (p.Gly593fs)Pathogenic
3239625GRCh37/hg19 6q23.2(chr6:133782252-133804253)x1Pathogenic
3246004NC_000006.11:g.(?133595919)(133595971_?)delPathogenic
3511153NM_004100.5(EYA4):c.279del (p.Met93fs)Pathogenic
3630137NM_004100.5(EYA4):c.222del (p.Val75fs)Pathogenic
3655361NM_004100.5(EYA4):c.13C>T (p.Gln5Ter)Pathogenic
3657058NM_004100.5(EYA4):c.646C>T (p.Gln216Ter)Pathogenic
3668390NM_004100.5(EYA4):c.337_350del (p.Thr112_Gly113insTer)Pathogenic
3685913NM_004100.5(EYA4):c.616_617del (p.Ser206fs)Pathogenic
3772603NM_004100.5(EYA4):c.1269dup (p.Asn424Ter)Pathogenic

SpliceAI

4787 predictions. Top by Δscore:

VariantEffectΔscore
6:133241746:CGAGG:Cdonor_loss1.0000
6:133241747:GAG:Gdonor_gain1.0000
6:133241747:GAGGT:Gdonor_loss1.0000
6:133241748:AGG:Adonor_loss1.0000
6:133241749:GGTG:Gdonor_loss1.0000
6:133241750:G:Cdonor_loss1.0000
6:133241750:G:GGdonor_gain1.0000
6:133274702:T:Gacceptor_gain1.0000
6:133274708:T:Aacceptor_gain1.0000
6:133274711:TTTA:Tacceptor_loss1.0000
6:133274713:TA:Tacceptor_loss1.0000
6:133274714:A:AGacceptor_gain1.0000
6:133274715:G:GAacceptor_gain1.0000
6:133274715:G:Tacceptor_loss1.0000
6:133274715:GAT:Gacceptor_gain1.0000
6:133274715:GATA:Gacceptor_gain1.0000
6:133274809:AATCA:Adonor_gain1.0000
6:133274810:ATCA:Adonor_gain1.0000
6:133274811:TCA:Tdonor_gain1.0000
6:133274813:AGTAA:Adonor_loss1.0000
6:133274814:G:GGdonor_gain1.0000
6:133274815:TA:Tdonor_loss1.0000
6:133274816:AAGTC:Adonor_loss1.0000
6:133398644:T:Gacceptor_gain1.0000
6:133446609:T:TAacceptor_gain1.0000
6:133446612:T:Aacceptor_gain1.0000
6:133446619:T:Aacceptor_gain1.0000
6:133446751:GGAG:Gdonor_gain1.0000
6:133446752:GAGG:Gdonor_gain1.0000
6:133446752:GAGGT:Gdonor_loss1.0000

AlphaMissense

4168 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:133483039:T:CF372S1.000
6:133483042:T:AV373D1.000
6:133483044:T:AW374R1.000
6:133483044:T:CW374R1.000
6:133483045:G:CW374S1.000
6:133483046:G:CW374C1.000
6:133483046:G:TW374C1.000
6:133483048:A:CD375A1.000
6:133483053:G:CD377H1.000
6:133483054:A:CD377A1.000
6:133483054:A:TD377V1.000
6:133483057:A:TE378V1.000
6:133483060:C:TT379I1.000
6:133483071:T:CF383L1.000
6:133483073:T:AF383L1.000
6:133483073:T:GF383L1.000
6:133483074:C:GH384D1.000
6:133483081:T:CL386P1.000
6:133483084:T:AL387H1.000
6:133483084:T:CL387P1.000
6:133506130:G:AG406R1.000
6:133506130:G:CG406R1.000
6:133506131:G:AG406E1.000
6:133506134:T:CL407P1.000
6:133506143:A:TE410V1.000
6:133506144:A:CE410D1.000
6:133506144:A:TE410D1.000
6:133506154:T:CF414L1.000
6:133506155:T:CF414S1.000
6:133506155:T:GF414C1.000

dbSNP variants (sampled 300 via entrez): RS1000002767 (6:133490882 T>C), RS1000023310 (6:133381327 T>G), RS1000027181 (6:133278872 A>G), RS1000031267 (6:133318038 G>A,C), RS1000048055 (6:133333961 A>C), RS1000051989 (6:133318060 C>T), RS1000059224 (6:133260033 A>T), RS1000064526 (6:133405498 A>T), RS1000064572 (6:133299637 G>A,T), RS1000067185 (6:133422850 C>T), RS1000079360 (6:133364644 G>A), RS1000094068 (6:133374729 G>A), RS1000096522 (6:133405799 T>A,C), RS1000098998 (6:133445577 CTTTTTTT>C,CTTT,CTTTT,CTTTTT,CTTTTTT,CTTTTTTTT,CTTTTTTTTT,CTTTTTTTTTT,CTTTTTTTTTTTTT,CTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTGTTTGTTTTTATATTTTCTTTTTTTTTTTTTTTAGTTTTTTTTTCTAGTTTCCTTTCCTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTT), RS1000110115 (6:133511838 A>G)

Disease associations

OMIM: gene MIM:603550 | disease phenotypes: MIM:605362, MIM:601316, MIM:192600, MIM:115200

GenCC curated gene-disease

DiseaseClassificationInheritance
nonsyndromic genetic hearing lossDefinitiveAutosomal dominant
autosomal dominant nonsyndromic hearing loss 10DefinitiveAutosomal dominant
dilated cardiomyopathy 1JModerateAutosomal dominant
autosomal dominant nonsyndromic hearing lossSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
nonsyndromic genetic hearing lossDefinitiveAD
dilated cardiomyopathy 1JLimitedAD

Mondo (12): dilated cardiomyopathy 1J (MONDO:0011541), autosomal dominant nonsyndromic hearing loss 10 (MONDO:0011031), hearing loss disorder (MONDO:0005365), nonsyndromic genetic hearing loss (MONDO:0019497), dilated cardiomyopathy (MONDO:0005021), hypertrophic cardiomyopathy (MONDO:0005045), familial hypertrophic cardiomyopathy (MONDO:0024573), myoepithelial tumor (MONDO:0002380), congestive heart failure (MONDO:0005009), ventricular tachycardia (MONDO:0005477), familial dilated cardiomyopathy (MONDO:0016333), autosomal dominant nonsyndromic hearing loss (MONDO:0019587)

Orphanet (9): Sensorineural deafness with dilated cardiomyopathy (Orphanet:217622), Rare autosomal dominant non-syndromic sensorineural deafness type DFNA (Orphanet:90635), Rare non-syndromic genetic deafness (Orphanet:87884), Dilated cardiomyopathy (Orphanet:217604), Rare genetic deafness (Orphanet:96210), Rare hypertrophic cardiomyopathy (Orphanet:217569), Rare familial disorder with hypertrophic cardiomyopathy (Orphanet:99739), Familial dilated cardiomyopathy (Orphanet:217607), NON RARE IN EUROPE: Familial isolated hypertrophic cardiomyopathy (Orphanet:155)

HPO phenotypes

10 total (11 of 10 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000365Hearing impairment
HP:0000403Recurrent otitis media
HP:0000407Sensorineural hearing impairment
HP:0001635Congestive heart failure
HP:0001644Dilated cardiomyopathy
HP:0001645Sudden cardiac death
HP:0001699Sudden death
HP:0005162Abnormal left ventricular function
HP:0030872Abnormal cardiac ventricular function
HP:0001639Hypertrophic cardiomyopathy

GWAS associations

49 associations (top):

StudyTraitp-value
GCST000189_13Protein quantitative trait loci1.000000e-06
GCST001520_10Response to angiotensin II receptor blocker therapy6.000000e-06
GCST001525_40Visceral fat9.000000e-06
GCST002493_5Bone mineral density (paediatric, skull)2.000000e-12
GCST002493_6Bone mineral density (paediatric, skull)8.000000e-17
GCST004136_25Methadone dose in opioid dependence6.000000e-06
GCST004292_20Glomerular filtration rate (creatinine)4.000000e-09
GCST004505_40Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)1.000000e-07
GCST004508_42Waist-to-hip ratio adjusted for BMI in non-smokers2.000000e-09
GCST006061_215Atrial fibrillation2.000000e-08
GCST006288_135Heel bone mineral density2.000000e-32
GCST006288_136Heel bone mineral density2.000000e-14
GCST006288_464Heel bone mineral density2.000000e-36
GCST006288_465Heel bone mineral density2.000000e-12
GCST006288_559Heel bone mineral density9.000000e-67
GCST006288_560Heel bone mineral density2.000000e-24
GCST006979_394Heel bone mineral density1.000000e-112
GCST006979_395Heel bone mineral density3.000000e-13
GCST006979_396Heel bone mineral density8.000000e-33
GCST007876_89Estimated glomerular filtration rate7.000000e-10
GCST007989_9Facial morphology traits (63 three-dimensional facial segments)6.000000e-12
GCST008058_79Estimated glomerular filtration rate5.000000e-23
GCST008059_72Estimated glomerular filtration rate8.000000e-22
GCST008156_26Hip circumference adjusted for BMI4.000000e-07
GCST008162_107Hip circumference7.000000e-06
GCST009028_4Adverse response to drug8.000000e-07
GCST010173_134Triglyceride levels2.000000e-09
GCST010244_326Triglyceride levels2.000000e-14
GCST011457_18Asthma with severe exacerbations6.000000e-07
GCST012125_6Chronic pain3.000000e-06

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004815alpha macroglobulin measurement
EFO:0007907methadone dose measurement
EFO:0004318smoking behavior
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0009270heel bone mineral density
EFO:0008039BMI-adjusted hip circumference
EFO:0009658adverse effect
EFO:0004530triglyceride measurement
EFO:0004980appendicular lean mass
EFO:0004833neutrophil count

MeSH disease descriptors (10)

DescriptorNameTree numbers
D002311Cardiomyopathy, DilatedC14.280.195.160; C14.280.238.070; C16.320.488.750
D002312Cardiomyopathy, HypertrophicC14.280.238.100; C14.280.484.048.750.070.160
D024741Cardiomyopathy, Hypertrophic, FamilialC14.280.238.100.500; C14.280.484.048.750.070.160.500; C16.320.160
D034381Hearing LossC09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341
D009208MyoepitheliomaC04.557.435.585
D017180Tachycardia, VentricularC14.280.067.845.940; C14.280.123.875.940; C23.550.073.845.940
C565337Cardiomyopathy, Dilated, 1J (supp.)
C563354Deafness, Autosomal Dominant 10 (supp.)
C580334Nonsyndromic Deafness (supp.)
C536231familial dilated cardiomyopathy (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs17301249EYA40.000

CTD chemical–gene interactions

44 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression7
trichostatin Aaffects cotreatment, increases expression3
sodium arseniteaffects methylation, increases expression, affects acetylation2
entinostatdecreases expression, affects cotreatment2
Vorinostataffects cotreatment, increases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Tretinoindecreases expression2
aristolochic acid Idecreases expression1
TAK-243increases sumoylation1
methylmercuric chloridedecreases expression1
methyleugenoldecreases expression1
bisphenol Aincreases expression1
terbufosincreases methylation1
arseniteaffects binding, decreases reaction1
butyraldehydedecreases expression1
perfluorooctanoic acidincreases expression1
manganese chloridedecreases expression1
potassium chromate(VI)decreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
monomethylarsonous acidaffects acetylation, affects methylation1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
(+)-JQ1 compoundincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Arsenic Trioxidedecreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation, decreases methylation1
Carbamazepineaffects expression1

Cellosaurus cell lines

4 cell lines: 4 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E4DXKEIUi004-AInduced pluripotent stem cellFemale
CVCL_E4DYKEIUi005-AInduced pluripotent stem cellMale
CVCL_E4DZKEIUi006-AInduced pluripotent stem cellFemale
CVCL_E4E0KEIUi007-AInduced pluripotent stem cellMale

Clinical trials (associated diseases)

301 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00205881PHASE4COMPLETEDBilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System
NCT00331539PHASE4UNKNOWNRelationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant
NCT00424307PHASE4UNKNOWNBilateral Cochlear Implant Benefit in Young Children
NCT00765635PHASE4COMPLETEDChlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal
NCT03321006PHASE4COMPLETEDTreating Hearing Loss to Improve Mood and Cognition in Older Adults
NCT01499901PHASE3WITHDRAWNComparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children
NCT02561091PHASE3COMPLETEDAM-111 in the Treatment of Acute Inner Ear Hearing Loss
NCT03331627PHASE3COMPLETEDSafety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL
NCT05532657PHASE3ACTIVE_NOT_RECRUITINGACHIEVE Brain Health Follow-Up Study
NCT00013455PHASE2COMPLETEDQuantifying Auditory Perceptual Learning Following Hearing Aid Fitting
NCT00323427PHASE2COMPLETEDClinical Trial of the Living Well With Hearing Loss Workshop
NCT00552786PHASE2COMPLETEDAntioxidation Medication for Noise-induced Hearing Loss
NCT00802425PHASE2COMPLETEDEfficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss
NCT01139281PHASE2COMPLETEDThe Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans
NCT01451853PHASE2UNKNOWNSPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss
NCT01588925PHASE2COMPLETEDHearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT02832128PHASE2COMPLETEDEvaluating Possible Improvement in Speech and Hearing Tests After 28 Days of Dosing of the Study Drug AUT00063 Compared to Placebo (QuicKfire)
NCT04915183PHASE2RECRUITINGAtorvastatin to Reduce Cisplatin-Induced Hearing Loss Among Individuals With Head and Neck Cancer
NCT05258773PHASE2COMPLETEDEvaluation of the Presence of SENS-401 in the Perilymph
NCT06340633PHASE2RECRUITINGSPI-1005 in Adults Receiving Cochlear Implant
NCT00582946PHASE1COMPLETEDWide-Bandwidth Open Canal Hearing Aid For Better Multitalker Speech Understanding
NCT00584155PHASE1WITHDRAWNProtection From Cisplatin Ototoxicity by Lactated Ringers
NCT01206829PHASE1UNKNOWNHearing Impairment, Cognitive Therapy and Coping
NCT01256229PHASE1COMPLETEDOutcomes In Children With Developmental Delay And Deafness
NCT01343394PHASE1WITHDRAWNSafety of Autologous Human Umbilical Cord Blood Mononuclear Fraction to Treat Acquired Hearing Loss in Children
NCT01452607PHASE1COMPLETEDStudy to Evaluate the Safety and Pharmacokinetics of SPI-1005
NCT02259595PHASE1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC
NCT04041440PHASE1COMPLETEDSpeech Recognition Training in Children With Hearing Loss
NCT07218913PHASE1RECRUITINGTesting the Addition of Pedmark to Cisplatin Chemotherapy for Reducing Drug-Induced Ear Damage in Men With Stage II-III Metastatic Testicular Germ Cell Tumors
NCT01802190Not specifiedTERMINATEDPrevalence of POU4F3 and SLC17A8 Mutations
NCT00486577PHASE2/PHASE3COMPLETEDChronic Electrical Stimulation of the Auditory Cortex for Intractable Tinnitus
NCT00789061PHASE2/PHASE3UNKNOWNApplying Proton Pump Inhibitor to Prevent and Treat Acute Fluctuating Hearing Loss in Patients With SLC26A4 Mutation
NCT01423409PHASE2/PHASE3COMPLETEDMulticenter Trial Assessing an Innovative VAS of Pain Among Deaf People
NCT05786378PHASE2/PHASE3UNKNOWNAssessment of The Efficacy of Intratympanic Platelet Rich Plasma for Treatment of Sensorineural Hearing Loss.
NCT01108601PHASE1/PHASE2UNKNOWNTranstympanic Ringer’s Lactate for the Prevention of Cisplatin Ototoxicity
NCT01621256PHASE1/PHASE2COMPLETEDEfficacy, Safety, and Tolerability of Ancrod in Patients With Sudden Hearing Loss
NCT06370351PHASE1/PHASE2RECRUITINGA Phase I/II Clinical Trial with SENS-501 in Children Suffering from Severe to Profound Hearing Loss Due to Otoferlin (OTOF) Mutations
NCT06545175PHASE1/PHASE2RECRUITINGIntracochlear Application of VSF1.01 for the Reduction of Cochlear Implant Surgery Related Trauma
NCT07304024PHASE1/PHASE2RECRUITINGA Treatment for a Form of Age-Related Central Auditory Processing Disorder Consisting of Clemastine Fumarate Plus Engineered Sound