BLTP1 p.Leu397=
c.1189T>C · rs768283793 · VCV3030203
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0339%, eas)
Conditions
1
BLTP1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.042 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -0.072, phastCons 0.99 |
| Overall | ||
| CADD | 8.488 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0339%
East Asian · 15/44,312 alleles
Filtering AF
0.0208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0168%
Overall
0.00107%
17/1,581,682 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0339% | 2,954 |
| Remaining individualsnot grpmax-eligible | 0.00327% | 30,621 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BLTP1
- Protein
- p.Leu397=
- Coding
- c.1189T>C
- MANE Select
- NM_001384125
- dbSNP
- rs768283793
- Type
- single nucleotide variant
- Location
- chr4:122196771 (GRCh38)
Disease context
BLTP1-related disorder
Similar variants
- BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same condition
- BLTP1 p.His3063Arg Uncertain significance ★★ same condition
- BLTP1 c.10312+2T>C Likely pathogenic ★ same condition
- BLTP1 c.11513+1G>C Likely pathogenic ★ same condition
- BLTP1 c.5184+1G>T Likely pathogenic ★ same condition
- BLTP1 p.Arg3190Ter Likely pathogenic ★ same condition
- BLTP1 p.Phe3799Ser Uncertain significance ★ same condition
- BLTP1 p.Val1878Ala Uncertain significance ⚠ 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/bltp1-p-leu397 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown