BPI p.Pro150=
c.450C>T · rs2515875439 · VCV2652317
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 -4.3 | GERP -4.5 |
| Overall | ||
| CADD | 0.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,014 alleles
Overall
6.84e-05%
1/1,461,848 alleles · very rare
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
- BPI
- Protein
- p.Pro150=
- Coding
- c.450C>T
- MANE Select
- NM_001725
- dbSNP
- rs2515875439
- Type
- single nucleotide variant
- Location
- chr20:38310566 (GRCh38)
- Gene constraint
- LOEUF 1.011 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.70 · 2 PDB
- Residue 150
- the 'n-terminal barrel' region; a β-strand
Similar variants
- BPI c.664+7G>T Benign ★★ same type
- BPI p.Ala12Val Benign ★★ same type
- BPI p.Ala192Val Benign ★★ same type
- BPI p.Ala333Thr Likely benign ★★ ⚠ same type
- BPI p.Ala8Thr Benign ★★ same type
- BPI p.Ala8Val Benign ★★ same type
- BPI p.Arg86Cys Benign ★★ ⚠ same type
- BPI p.Glu136Gln Benign ★★ 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/bpi-p-pro150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown