BLTP1 p.Pro304=
c.912G>A · rs143187683 · VCV786522
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.78%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.227 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.83 | GERP -3.8, phastCons 0.97 |
| Overall | ||
| CADD | 10.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.78%
African / African-American · 1,332/74,936 alleles
Filtering AF
1.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.67%
Overall
0.101%
1,629/1,612,030 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.78% | 56 |
| Admixed American | 0.178% | 560 |
| Remaining individualsnot grpmax-eligible | 0.144% | 693 |
| Middle Eastern | 0.0661% | 1,514 |
| Finnishnot grpmax-eligible | 0.0203% | 4,918 |
| South Asian | 0.0121% | 8,268 |
| European (non-Finnish) | 0.00594% | 16,836 |
| East Asian | 0.00447% | 22,393 |
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.Pro304=
- Coding
- c.912G>A
- MANE Select
- NM_001384125
- dbSNP
- rs143187683
- Type
- single nucleotide variant
- Location
- chr4:122192239 (GRCh38)
Similar variants
- BLTP1 p.Pro304Leu Uncertain significance ★★ same residue
- BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same type
- BLTP1 c.1498+4A>G Uncertain significance ★★ same type
- BLTP1 p.Ala2332Thr Uncertain significance ★★ ⚠ same type
- BLTP1 p.Arg1317His Uncertain significance ★★ same type
- BLTP1 p.Arg1791Lys Uncertain significance ★★ ⚠ same type
- BLTP1 p.Arg2095His Uncertain significance ★★ same type
- BLTP1 p.Arg2279Cys 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/bltp1-p-pro304 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown