BLTP3B p.Leu491=
c.1471C>T · rs143906625 · VCV774217
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.26%, nfe)
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 2.6 | GERP -0.085, phastCons 1 |
| Overall | ||
| CADD | 2.938 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.26%
European (non-Finnish) · 14,815/1,178,804 alleles
Filtering AF
1.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.23%
Overall
1.05%
16,923/1,607,824 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.26% | 80 |
| Ashkenazi Jewishnot grpmax-eligible | 1.15% | 87 |
| Remaining individualsnot grpmax-eligible | 0.971% | 103 |
| Admixed American | 0.818% | 122 |
| Middle Eastern | 0.546% | 183 |
| Finnishnot grpmax-eligible | 0.339% | 295 |
| South Asian | 0.307% | 325 |
| Amishnot grpmax-eligible | 0.219% | 456 |
| African / African-American | 0.215% | 464 |
| East Asian | 0.00674% | 14,829 |
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
- BLTP3B
- Protein
- p.Leu491=
- Coding
- c.1471C>T
- MANE Select
- NM_015054
- dbSNP
- rs143906625
- Type
- single nucleotide variant
- Location
- chr12:100072750 (GRCh38)
- Structure
- AlphaFold pLDDT 67.53
Similar variants
- BLTP3B p.Ala109Val Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala1162Thr Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala1272Ser Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala231Ser Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala231Thr Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala257Gly Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala66Thr Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala847Val Uncertain significance ★ ⚠ same type
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/bltp3b-p-leu491 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown