BLTP2 p.Leu963=
c.2887C>T · rs138833748 · VCV781856
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.2%, amr)
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 1.9 | GERP -0.27, phastCons 0.99 |
| Overall | ||
| CADD | 4.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.2%
Admixed American · 1,318/60,030 alleles
Filtering AF
2.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.06%
Overall
0.0875%
1,413/1,614,218 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 2.2% | 46 |
| Remaining individualsnot grpmax-eligible | 0.0736% | 1,359 |
| African / African-American | 0.052% | 1,924 |
| European (non-Finnish) | 0.000847% | 118,004 |
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
- BLTP2
- Protein
- p.Leu963=
- Coding
- c.2887C>T
- MANE Select
- NM_014680
- dbSNP
- rs138833748
- Type
- single nucleotide variant
- Location
- chr17:28634700 (GRCh38)
- Structure
- AlphaFold pLDDT 71.37
Similar variants
- BLTP2 p.Ala1395Ser Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala1564Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala1826Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala248Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala324Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala393Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala539Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala694Gly 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/bltp2-p-leu963 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown