SLC19A3 p.Ala330fs
c.989del · VCV3631810
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
biotin-responsive basal ganglia disease
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 6 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.47 | GERP -3.8, phastCons 0.74 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- SLC19A3
- Protein
- p.Ala330fs
- Coding
- c.989del
- MANE Select
- NM_025243
- Type
- Deletion
- Location
- chr2:227696072 (GRCh38)
- Gene constraint
- LOEUF 0.968 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.96 · 19 PDB
- Residue 330
- an α-helix
Disease context
biotin-responsive basal ganglia disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Thiamine-responsive encephalopathy (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent
Similar variants
- SLC19A3 p.Ala330Asp Uncertain significance ★ ⚠ same residue
- SLC19A3 p.Ala330= Likely benign ★ same residue
- SLC19A3 p.His200fs Pathogenic ★★ same condition
- SLC19A3 p.Leu161fs Pathogenic/Likely pathogenic ★★ same condition
- SLC19A3 p.Lys208fs Pathogenic/Likely pathogenic ★★ same condition
- SLC19A3 p.Tyr38fs Pathogenic/Likely pathogenic ★★ same condition
- SLC19A3 p.Val299fs Pathogenic ★★ same condition
- SLC19A3 p.Val58fs Pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/slc19a3-p-ala330fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown