BTD p.Leu478=
c.1434G>A · rs2471522272 · VCV2801766
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
biotinidase deficiency
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP 0.48, phastCons 0.53 |
| Overall | ||
| CADD | 6.827 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BTD
- Protein
- p.Leu478=
- Coding
- c.1434G>A
- MANE Select
- NM_001370658
- dbSNP
- rs2471522272
- Type
- single nucleotide variant
- Location
- chr3:15645350 (GRCh38)
- Gene constraint
- LOEUF 1.22 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.77
Disease context
biotinidase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Biotinidase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- BTD p.Leu478fs Pathogenic ★★ same residue
- BTD p.Leu478Met Uncertain significance ★ ⚠ same residue
- BTD c.1330G>C Pathogenic ★★ same condition
- BTD c.249+1G>T Likely pathogenic ★★ same condition
- BTD c.400-2A>G Likely pathogenic ★★ same condition
- BTD c.-17+2T>C Pathogenic/Likely pathogenic ★★ same condition
- BTD p.Ala142Val Pathogenic/Likely pathogenic ★★ same condition
- BTD p.Ala217Thr Pathogenic/Likely 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/btd-p-leu478 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown