BLTP1 p.Ser1787=
c.5361A>G · rs73844502 · VCV1253905
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.02%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.009 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.7 | GERP -3.8 |
| Overall | ||
| CADD | 6.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.02%
African / African-American · 6,011/74,950 alleles
Filtering AF
7.85%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.78%
Overall
1.2%
19,326/1,613,304 alleles · common
exomes 15,028/1,461,244 · genomes 4,298/152,060 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.02% | 12 |
| South Asian | 3% | 33 |
| Ashkenazi Jewishnot grpmax-eligible | 1.56% | 64 |
| Middle Eastern | 1.53% | 65 |
| Remaining individualsnot grpmax-eligible | 1.42% | 71 |
| Admixed American | 1.07% | 93 |
| European (non-Finnish) | 0.712% | 140 |
| Finnishnot grpmax-eligible | 0.116% | 865 |
| East Asian | 0.0691% | 1,447 |
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.Ser1787=
- Coding
- c.5361A>G
- MANE Select
- NM_001384125
- dbSNP
- rs73844502
- Type
- single nucleotide variant
- Location
- chr4:122247206 (GRCh38)
- Residue 1787
- a UniProt-annotated variant site (in alkkucs)
Similar variants
- 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
- BLTP1 p.Arg3665Gln 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-ser1787 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown