BMPER p.Glu288=
c.864G>A · rs1475153405 · VCV3046943
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
1
BMPER-related disorder
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 -0.4 | GERP -4.1, phastCons 0.005 |
| Overall | ||
| CADD | 4.099 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,002 alleles
Overall
0.000124%
2/1,614,028 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,002 |
| European (non-Finnish) | 8.47e-05% | 1,180,044 |
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.Glu288=
- Coding
- c.864G>A
- MANE Select
- NM_001365308
- dbSNP
- rs1475153405
- Type
- single nucleotide variant
- Location
- chr7:34055240 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
- Residue 288
- the vwfc 4 domain
Disease context
BMPER-related disorder
Similar variants
- BMPER p.Glu288Asp Uncertain significance ★ ⚠ same residue
- BMPER p.Glu288Gln Uncertain significance ★ ⚠ same residue
- BMPER c.219+1G>C Likely pathogenic same condition
- BMPER c.133+8A>T Likely benign same condition
- BMPER c.-1G>C Likely benign same condition
- BMPER c.*10C>T Likely benign same condition
- BMPER p.Arg241Ter Likely pathogenic ★★ same type
- BMPER p.Gln309Ter Pathogenic ★★ 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-glu288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown