BOR syndrome: genes and variants
Explore variant evidence for BOR syndrome across 2 analyzed proteins (EYA1, SIX1). Linked ClinVar records include 5 pathogenic or likely pathogenic variants, 60 variants of uncertain significance and 25 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Source labels are pooled across this disease family.
Data updated 2026-10-10. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to BOR 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.
4 ClinVar pathogenic / likely pathogenic and 85 uncertain variants in EYA1 have source records linked to BOR syndrome. Association strength is not clinical gene validity.
SIX1: Homeobox protein SIX1
It regulates developmental programs in the ear, kidney, craniofacial structures, and skeletal muscle together with EYA-family cofactors. Heterozygous pathogenic variants cause branchio-otic or branchio-oto-renal syndrome with hearing loss and variable branchial or renal abnormalities.
1 ClinVar pathogenic / likely pathogenic and 0 uncertain variants in SIX1 have source records linked to BOR syndrome. Association strength is not clinical gene validity.
ClinVar pathogenic and likely pathogenic variants linked to BOR syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| EYA1 R440Q | 440 | Pathogenic / likely pathogenic (★★) | |
| EYA1 S487P | 487 | Pathogenic / likely pathogenic (★) | |
| EYA1 L580R | 580 | Pathogenic / likely pathogenic (★) | |
| EYA1 L483P | 483 | Pathogenic / likely pathogenic (★) | |
| SIX1 Q167R | 167 | Homeobox | Pathogenic / likely pathogenic (★) |
Uncertain variants prioritized for review in BOR syndrome
| 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 also has ClinVar records linked to EYA1 variants; they fall partly in the same places as the BOR syndrome variants (5 pathogenic / likely pathogenic).
- Anterior segment anomalies and cataract also has ClinVar records linked to EYA1 variants; they fall mostly in different places as the BOR syndrome variants (3 pathogenic / likely pathogenic).
- Branchiootic syndrome also has ClinVar records linked to SIX1 variants; they fall mostly in different places as the BOR syndrome variants (11 pathogenic / likely pathogenic).
- Autosomal dominant nonsyndromic hearing loss also has ClinVar records linked to SIX1 variants; they fall mostly in different places as the BOR syndrome variants (8 pathogenic / likely pathogenic).
Diseases related to BOR syndrome
- Branchiootic syndrome, also linked to EYA1 and SIX1
- Rare genetic deafness, also linked to EYA1
- Autosomal dominant nonsyndromic hearing loss, also linked to SIX1
- Branchiootorenal syndrome 1, also linked to EYA1
- Otofaciocervical syndrome, also linked to EYA1
Frequently asked questions
Which genes have records linked to BOR syndrome?
This view contains 2 analyzed proteins: EYA1, SIX1. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 5 pathogenic or likely pathogenic variants, 60 variants of uncertain significance and 25 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 1 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 141 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses 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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