Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2: genes and variants
Explore variant evidence for Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 across 1 analyzed protein (SETX). Linked ClinVar records include 17 pathogenic or likely pathogenic variants, 302 variants of uncertain significance and 275 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.
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Genes linked to Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2
SETX: Helicase senataxin
It resolves RNA-DNA hybrids and supports transcription termination, RNA processing, and genome stability, particularly in long-lived neurons. Different pathogenic mechanisms cause ataxia with oculomotor apraxia type 2 or juvenile amyotrophic lateral sclerosis type 4.
17 ClinVar pathogenic / likely pathogenic and 577 uncertain variants in SETX have source records linked to Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2. Association strength is not clinical gene validity.
Where Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 variants cluster
- SETX UPF1-type SF1B helicase ATP-binding (positions 1933–2254): 7 of 17 ClinVar pathogenic / likely pathogenic variants, 3.4× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SETX L1976R | 1976 | UPF1-type SF1B helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| SETX L389S | 389 | Pathogenic / likely pathogenic (★★) | |
| SETX T8M | 8 | Pathogenic / likely pathogenic (★★) | |
| SETX R332W | 332 | Pathogenic / likely pathogenic (★★) | |
| SETX V2013G | 2013 | UPF1-type SF1B helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| SETX D2207V | 2207 | UPF1-type SF1B helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SETX R2232C | 2232 | UPF1-type SF1B helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SETX L1981R | 1981 | UPF1-type SF1B helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SETX C2006Y | 2006 | UPF1-type SF1B helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SETX L495P | 495 | Pathogenic / likely pathogenic (★) | |
| SETX G240D | 240 | Pathogenic / likely pathogenic (★) | |
| SETX G2036R | 2036 | UPF1-type SF1B helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SETX R1294C | 1294 | Pathogenic / likely pathogenic | |
| SETX F1083L | 1083 | Pathogenic / likely pathogenic | |
| SETX M274I | 274 | Pathogenic / likely pathogenic | |
| SETX N603D | 603 | Pathogenic / likely pathogenic | |
| SETX Q653K | 653 | Pathogenic / likely pathogenic |
Which prediction tools work for Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- PolyPhen-2: 92 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CATVariant: 91 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 90 out of 100
- CADD: 89 out of 100
- phyloP: 86 out of 100
- REVEL: 86 out of 100 (learned from overlapping clinical labels, so this is optimistic)
Diseases related to Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2
- Amyotrophic lateral sclerosis, also linked to SETX
- Spastic ataxia, also linked to SETX
Frequently asked questions
Which genes have records linked to Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2?
This view contains 1 analyzed proteins: SETX. 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 17 pathogenic or likely pathogenic variants, 302 variants of uncertain significance and 275 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. 0 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 805 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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