BLTP1 p.Pro3595=
c.10785G>A · rs563545352 · VCV2655066
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0714%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.016 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.29 | |
| Overall | ||
| CADD | 9.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0714%
East Asian · 32/44,838 alleles
Filtering AF
0.0519%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0453%
Overall
0.0049%
79/1,613,020 alleles · ultra-rare
exomes 64/1,460,770 · genomes 15/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0714% | 1,401 |
| Middle Eastern | 0.0165% | 6,046 |
| Admixed American | 0.01% | 9,982 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,489 |
| European (non-Finnish) | 0.0028% | 35,741 |
| African / African-American | 0.00133% | 74,976 |
| South Asian | 0.0011% | 90,954 |
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.Pro3595=
- Coding
- c.10785G>A
- MANE Select
- NM_001384125
- dbSNP
- rs563545352
- Type
- single nucleotide variant
- Location
- chr4:122316776 (GRCh38)
- Residue 3595
- a UniProt-annotated variant site (in alkkucs)
Similar variants
- BLTP1 p.Pro3595Leu 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-pro3595 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown