BMPER p.Pro487=
c.1461G>A · rs77064045 · VCV1660034
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0121%, sas)
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 | GERP -4.6 |
| Overall | ||
| CADD | 4.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0121%
South Asian · 11/91,062 alleles
Filtering AF
0.00676%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00522%
Overall
0.00109%
16/1,461,842 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0121% | 8,278 |
| East Asian | 0.00223% | 44,868 |
| European (non-Finnish) | 0.000339% | 294,986 |
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
- BMPER
- Protein
- p.Pro487=
- Coding
- c.1461G>A
- MANE Select
- NM_001365308
- dbSNP
- rs77064045
- Type
- single nucleotide variant
- Location
- chr7:34085808 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
- Residue 487
- a disulfide bond; the vwfd domain
Similar variants
- BMPER p.Pro487Leu Uncertain significance ★★ ⚠ same residue
- BMPER p.Arg241Ter Likely pathogenic ★★ same type
- BMPER p.Gln309Ter Pathogenic ★★ same type
- BMPER p.Ala39Ser Uncertain significance ★★ ⚠ same type
- BMPER p.Ala486Val Uncertain significance ★★ ⚠ same type
- BMPER p.Arg131Cys Uncertain significance ★★ ⚠ same type
- BMPER p.Arg16Ser Uncertain significance ★★ ⚠ same type
- BMPER p.Arg332His 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/bmper-p-pro487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown