Otofaciocervical syndrome: genes and variants
Otofaciocervical syndrome is linked to 1 analyzed protein (EYA1). 1 DNA variants are known to cause it; 41 more are uncertain, and 1 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Also known as: otofaciocervical syndrome 1
Genes linked to Otofaciocervical syndrome
EYA1: Protein phosphatase EYA1
It functions as a transcriptional coactivator and phosphatase in developmental programs that form the ear, kidney, and craniofacial structures. Haploinsufficiency causes branchio-oto-renal spectrum disorders with hearing loss, branchial anomalies, and variable renal malformations.
1 disease-causing and 41 uncertain variants in EYA1 are linked to Otofaciocervical syndrome.
Known disease-causing variants in Otofaciocervical syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| EYA1 R440Q | 440 | Disease-causing (★★) |
Uncertain variants in Otofaciocervical syndrome that look disease-causing
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| EYA1 R440W | 440 | Uncertain (★★) | +6: in a 3D region that tolerates change poorly (1R); R440Q at the same position is pathogenic; REVEL 0.783 |
Same protein, different disease
- Branchiootorenal syndrome 1 is also caused by EYA1 variants; they fall mostly in different places as the Otofaciocervical syndrome variants (5 disease-causing).
- Melnick-Fraser syndrome is also caused by EYA1 variants; they fall mostly in different places as the Otofaciocervical syndrome variants (4 disease-causing).
- Anterior segment anomalies and cataract is also caused by EYA1 variants; they fall mostly in different places as the Otofaciocervical syndrome variants (3 disease-causing).
Diseases related to Otofaciocervical syndrome
- Rare genetic deafness, also linked to EYA1
- Branchiootic syndrome, also linked to EYA1
- Melnick-Fraser syndrome, also linked to EYA1
- Branchiootorenal syndrome 1, also linked to EYA1
Frequently asked questions
Which genes are linked to Otofaciocervical syndrome?
In CATVariant, Otofaciocervical syndrome is linked to 1 analyzed protein: EYA1 (Protein phosphatase EYA1).
How many genetic variants are linked to Otofaciocervical syndrome?
54 variants: 1 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 41 are of uncertain significance or have conflicting reports.
Which uncertain variants in Otofaciocervical syndrome look disease-causing?
1 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example EYA1 R440W. These are leads for expert review, not diagnoses.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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