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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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EYA1
EYA transcriptional coactivator and phosphatase 1
Chromosome 8 Β· 8q13.3
NCBI Gene: 2138Ensembl: ENSG00000104313.20HGNC: HGNC:3519UniProt: A0A2R8Y6K4
109PubMed Papers
24Diseases
0Drugs
203Pathogenic Variants
FUNCTIONAL ROLE
DNA RepairHighly ConstrainedTranscription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cytoplasmnuclear bodyprotein bindinghistone H2AXY142 phosphatase activityBOR syndromebranchiootic syndrome 1branchio-oto-renal syndromeBranchio-otic syndrome
✦AI Summary

EYA1 is a dual-function protein that acts as both a tyrosine phosphatase and transcriptional coactivator critical for organogenesis. As a phosphatase, EYA1 dephosphorylates histone H2AX at tyrosine 142, promoting efficient DNA repair and distinguishing repair responses from apoptotic pathways 1. As a transcriptional coactivator, EYA1 partners with SIX1 and related SIX family members in a regulatory network essential for craniofacial, skeletal, renal, and ear development 2. EYA1 is particularly important for inner ear development and sensory function, with specific enhancer elements (CNE16.39 and CNE16.45) driving tissue-specific expression in the inner ear sensory regions 3. Pathogenic EYA1 variants cause Branchio-oto-renal (BOR) syndrome, an autosomal dominant disorder accounting for approximately 40% of BOR cases 3. BOR syndrome presents with branchial arch anomalies, hearing impairment, ear malformations, and renal defects 45. EYA1 variants also associate with anterior segment anomalies and otofaciocervical syndrome. Prenatal presentation may include amniotic fluid abnormalities and cardiac defects, with variants in the conserved Eya Homologous Region affecting protein stability and phenotypic severity 6. In pediatric CAKUT cohorts, EYA1 variants represent significant genetic risk factors for progression to kidney failure 7.

Sources cited
1
EYA1 dephosphorylates histone H2AX at Tyr-142 and promotes DNA repair; this phosphorylation distinguishes repair from apoptotic responses
PMID: 19234442
2
EYA1 and SIX1 act in a regulatory network required for development of organs affected in BOR syndrome; EYA1 is a transcriptional coactivator
PMID: 17238186
3
EYA1 accounts for over 40% of BOR syndrome cases; specific enhancer elements (CNE16.39 and CNE16.45) drive inner ear-specific expression
PMID: 38228108
4
BOR syndrome is caused by mutations in EYA1 gene with autosomal dominant inheritance; features include branchial, otologic, and renal manifestations
PMID: 9777487
5
EYA1 is a human homologue of Drosophila eyes absent gene; mutations cause BOR syndrome characterized by branchial, ear, hearing, and renal anomalies
PMID: 14696767
6
EYA1 variants in the Eya Homologous Region affect protein stability and phenotypic severity; prenatal cases show amniotic fluid anomalies and cardiac abnormalities
PMID: 39394648
7
EYA1 variants are independent prognostic factors for kidney failure in pediatric CAKUT cohorts
PMID: 36549658
Disease Associationsβ“˜24
BOR syndromeOpen Targets
0.84Strong
branchiootic syndrome 1Open Targets
0.70Strong
branchio-oto-renal syndromeOpen Targets
0.69Moderate
Branchio-otic syndromeOpen Targets
0.69Moderate
otofaciocervical syndrome 1Open Targets
0.66Moderate
otofaciocervical syndromeOpen Targets
0.64Moderate
neurodegenerative diseaseOpen Targets
0.54Moderate
Rare genetic deafnessOpen Targets
0.53Moderate
genetic disorderOpen Targets
0.47Moderate
type 2 diabetes mellitusOpen Targets
0.42Moderate
branchiooculofacial syndromeOpen Targets
0.41Moderate
hearing lossOpen Targets
0.40Weak
smoking behaviorOpen Targets
0.39Weak
non-alcoholic fatty liver diseaseOpen Targets
0.39Weak
branchiootic syndromeOpen Targets
0.38Weak
Preauricular pitOpen Targets
0.37Weak
hyperparathyroidismOpen Targets
0.35Weak
open-angle glaucomaOpen Targets
0.35Weak
glaucomaOpen Targets
0.34Weak
bilateral renal agenesisOpen Targets
0.34Weak
Anterior segment anomalies with or without cataractUniProt
Branchiootic syndrome 1UniProt
Branchiootorenal syndrome 1UniProt
Otofaciocervical syndrome 1UniProt
Pathogenic Variants203
NM_000503.6(EYA1):c.1051-2A>GPathogenic
Melnick-Fraser syndrome|Branchiootorenal syndrome 1
β˜…β˜…β˜†β˜†2026
NM_000503.6(EYA1):c.1289G>A (p.Trp430Ter)Pathogenic
not provided|Monogenic hearing loss|Melnick-Fraser syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 430
NM_000503.6(EYA1):c.922C>T (p.Arg308Ter)Pathogenic
Branchiootorenal syndrome 1|Rare genetic deafness|Melnick-Fraser syndrome|not provided|EYA1-related disorder|Branchiootorenal syndrome 1;Otofaciocervical syndrome 1;Branchiootic syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 308
NM_000503.6(EYA1):c.966+5G>APathogenic
Branchiootorenal syndrome 1|not provided|Melnick-Fraser syndrome
β˜…β˜…β˜†β˜†2025
NM_000503.6(EYA1):c.637C>T (p.Gln213Ter)Pathogenic
Melnick-Fraser syndrome|Branchiootic syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 213
NM_000503.6(EYA1):c.1361-1G>APathogenic
Branchiootic syndrome 1|Melnick-Fraser syndrome
β˜…β˜…β˜†β˜†2025
NM_000503.6(EYA1):c.1081C>T (p.Arg361Ter)Pathogenic
Branchiootic syndrome 1|Branchiootorenal syndrome 1|not provided|Melnick-Fraser syndrome|Inborn genetic diseases|EYA1-related disorder|Branchiootorenal syndrome 1;Otofaciocervical syndrome 1;Branchiootic syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 361
NM_000503.6(EYA1):c.889C>T (p.Arg297Ter)Pathogenic
not provided|Melnick-Fraser syndrome|Branchiootic syndrome 1|Branchiootic syndrome 1;Branchiootorenal syndrome 1;Otofaciocervical syndrome 1|EYA1-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 297
NM_000503.6(EYA1):c.1697dup (p.His567fs)Pathogenic
Melnick-Fraser syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 567
NM_000503.6(EYA1):c.1344C>A (p.Tyr448Ter)Pathogenic
Melnick-Fraser syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 448
NM_000503.6(EYA1):c.1199+1G>APathogenic
Branchiootorenal syndrome 1|Melnick-Fraser syndrome
β˜…β˜…β˜†β˜†2025
NM_000503.6(EYA1):c.1254_1255del (p.Cys419fs)Pathogenic
not provided|Branchiootic syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 419
NM_000503.6(EYA1):c.1319G>A (p.Arg440Gln)Pathogenic
Branchiootorenal syndrome 1|Rare genetic deafness|Branchiooculofacial syndrome|Melnick-Fraser syndrome|Branchiootic syndrome 1|EYA1-related disorder|Branchiootorenal syndrome 1;Otofaciocervical syndrome 1;Branchiootic syndrome 1
β˜…β˜…β˜†β˜†2024β†’ Residue 440
NM_000503.6(EYA1):c.229C>T (p.Arg77Ter)Pathogenic
Melnick-Fraser syndrome|not provided|Branchiootorenal syndrome 1;Branchiootic syndrome 1;Otofaciocervical syndrome 1
β˜…β˜…β˜†β˜†2024β†’ Residue 77
NM_000503.6(EYA1):c.1189C>T (p.Gln397Ter)Pathogenic
not provided|Melnick-Fraser syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 397
NM_000503.6(EYA1):c.1698+1G>TPathogenic
Melnick-Fraser syndrome|Branchiootorenal syndrome 1
β˜…β˜…β˜†β˜†2024
NM_000503.6(EYA1):c.1200-1G>APathogenic
Melnick-Fraser syndrome|not provided
β˜…β˜…β˜†β˜†2024
NM_000503.6(EYA1):c.602C>G (p.Ser201Ter)Pathogenic
not provided|Melnick-Fraser syndrome|EYA1-related disorder
β˜…β˜…β˜†β˜†2023β†’ Residue 201
NM_000503.6(EYA1):c.1044T>G (p.Tyr348Ter)Pathogenic
Branchiootorenal syndrome 1|Melnick-Fraser syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 348
NM_000503.6(EYA1):c.880C>T (p.Arg294Ter)Pathogenic
Melnick-Fraser syndrome|not provided|Inborn genetic diseases|Branchiootorenal syndrome 1
β˜…β˜…β˜†β˜†2023β†’ Residue 294
View on ClinVar β†—
Related Genes
TLX1Protein interaction95%SIX5Protein interaction94%DACH1Protein interaction88%SIX4Protein interaction88%SIX2Protein interaction86%PAX3Protein interaction86%
Tissue Expression6 tissues
Brain
100%
Heart
55%
Bone Marrow
1%
Lung
1%
Ovary
0%
Liver
0%
Gene Interaction Network
Click a node to explore
EYA1TLX1SIX5DACH1SIX4SIX2PAX3
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q0P517
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.29Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.18 [0.11–0.29]
RankingsWhere EYA1 stands among ~20K protein-coding genes
  • #4,356of 20,598
    Most Researched109 Β· top quartile
  • #332of 5,498
    Most Pathogenic Variants203 Β· top 10%
  • #1,070of 17,882
    Most Constrained (LOEUF)0.29 Β· top 10%
Genes detectedEYA1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Prenatal Phenotypic Analysis of Branchio-Oto-Renal Spectrum Disorder Attributable to EYA1 Gene Pathogenic Variants and Systematic Literature Review.
PMID: 39394648
Prenat Diagn Β· 2024
1.00
2
Branchio-oto-renal syndrome.
PMID: 17238186
Am J Med Genet A Β· 2007
0.90
3
Branchio-oto-renal syndrome.
PMID: 9777487
J Commun Disord Β· 1998
0.80
4
Prenatal whole-exome sequencing for fetal structural anomalies: a retrospective analysis of 145 Chinese cases.
PMID: 37880672
BMC Med Genomics Β· 2023
0.70
5
Genetic spectrum of CAKUT and risk factors for kidney failure: a pediatric multicenter cohort study.
PMID: 36549658
Nephrol Dial Transplant Β· 2022
0.60