BLTP2 p.Gln239=
c.717A>G · rs747117448 · VCV744319
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, 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 0.009 | GERP -2, phastCons 0.84 |
| Overall | ||
| CADD | 7.575 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
Admixed American · 16/60,006 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00118%
19/1,614,038 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0267% | 3,750 |
| East Asian | 0.00223% | 44,900 |
| South Asian | 0.0011% | 91,092 |
| European (non-Finnish) | 8.47e-05% | 1,179,976 |
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.Gln239=
- Coding
- c.717A>G
- MANE Select
- NM_014680
- dbSNP
- rs747117448
- Type
- single nucleotide variant
- Location
- chr17:28641938 (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-gln239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown