BLTP3B p.Gln213=
c.639A>G · rs144893873 · VCV784308
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.38%, afr)
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 -2.2 | GERP -4.8 |
| Overall | ||
| CADD | 5.986 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.38%
African / African-American · 1,036/75,018 alleles
Filtering AF
1.31%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.28%
Overall
0.0778%
1,255/1,612,792 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.38% | 72 |
| Admixed American | 0.197% | 507 |
| Remaining individualsnot grpmax-eligible | 0.0769% | 1,301 |
| Middle Eastern | 0.0496% | 2,015 |
| European (non-Finnish) | 0.0039% | 25,641 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,570 |
| South Asian | 0.0033% | 30,257 |
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.Gln213=
- Coding
- c.639A>G
- MANE Select
- NM_015054
- dbSNP
- rs144893873
- Type
- single nucleotide variant
- Location
- chr12:100097395 (GRCh38)
- Structure
- AlphaFold pLDDT 67.53
Similar variants
- BLTP3B p.Leu491= Benign ★★ same type
- 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
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-gln213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown