Biotin-responsive basal ganglia disease: genes and variants
Explore variant evidence for Biotin-responsive basal ganglia disease across 1 analyzed protein (SLC19A3). Linked ClinVar records include 11 pathogenic or likely pathogenic variants, 188 variants of uncertain significance and 30 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. Counts refer to the selected disease label.
Data updated 2026-10-11. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Biotin-responsive basal ganglia disease
SLC19A3: Thiamine transporter 2
A high-affinity thiamine transporter that helps supply vitamin B1 to cells, including the brain. Variants can cause biotin-thiamine-responsive basal ganglia disease.
11 ClinVar pathogenic / likely pathogenic and 218 uncertain variants in SLC19A3 have source records linked to Biotin-responsive basal ganglia disease. Association strength is not clinical gene validity.
Where Biotin-responsive basal ganglia disease variants cluster
- SLC19A3 Transmembrane (positions 317–337): 3 of 11 ClinVar pathogenic / likely pathogenic variants, 6.4× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Biotin-responsive basal ganglia disease
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SLC19A3 W94R | 94 | Transmembrane | Pathogenic / likely pathogenic (★★) |
| SLC19A3 M1L | 1 | Cytoplasmic | Pathogenic / likely pathogenic (★★) |
| SLC19A3 S181P | 181 | Transmembrane | Pathogenic / likely pathogenic (★★) |
| SLC19A3 G23R | 23 | Transmembrane | Pathogenic / likely pathogenic (★) |
| SLC19A3 T422P | 422 | Transmembrane | Pathogenic / likely pathogenic (★) |
| SLC19A3 G317E | 317 | Transmembrane | Pathogenic / likely pathogenic (★) |
| SLC19A3 E320Q | 320 | Transmembrane | Pathogenic / likely pathogenic |
| SLC19A3 K44E | 44 | Extracellular | Pathogenic / likely pathogenic |
| SLC19A3 W284R | 284 | Transmembrane | Pathogenic / likely pathogenic |
| SLC19A3 L66P | 66 | Transmembrane | Pathogenic / likely pathogenic |
| SLC19A3 A321V | 321 | Transmembrane | Pathogenic / likely pathogenic |
Which prediction tools work for Biotin-responsive basal ganglia disease
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- AlphaMissense: 99 out of 100
- PolyPhen-2: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- ESM1b (LLR): 95 out of 100
- CATVariant: 94 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 91 out of 100
Frequently asked questions
Which genes have records linked to Biotin-responsive basal ganglia disease?
This view contains 1 analyzed proteins: SLC19A3. 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 11 pathogenic or likely pathogenic variants, 188 variants of uncertain significance and 30 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 263 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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