BMPER p.Ala258=
c.774T>G · rs117988035 · VCV360104
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.19%, mid)
Conditions
1
diaphanospondylodysostosis
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 -4.7 | GERP -4.3 |
| Overall | ||
| CADD | 0.068 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.19%
Middle Eastern · 193/6,056 alleles
Filtering AF
2.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.68%
Overall
1.17%
18,818/1,613,166 alleles · low-frequency
exomes 17,414/1,460,832 · genomes 1,404/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 3.19% | 31 |
| Remaining individualsnot grpmax-eligible | 1.31% | 77 |
| European (non-Finnish) | 1.27% | 78 |
| Finnishnot grpmax-eligible | 1.25% | 80 |
| South Asian | 1.14% | 87 |
| Admixed American | 0.915% | 109 |
| Ashkenazi Jewishnot grpmax-eligible | 0.794% | 126 |
| African / African-American | 0.212% | 472 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| East Asian | 0.00446% | 22,438 |
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.Ala258=
- Coding
- c.774T>G
- MANE Select
- NM_001365308
- dbSNP
- rs117988035
- Type
- single nucleotide variant
- Location
- chr7:34051958 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
- Residue 258
- the vwfc 4 domain
Similar variants
- BMPER p.Arg241Ter Likely pathogenic ★★ same condition
- BMPER p.Gln309Ter Pathogenic ★★ same condition
- BMPER p.Ala39Ser Uncertain significance ★★ ⚠ same condition
- BMPER p.Ala486Val Uncertain significance ★★ ⚠ same condition
- BMPER p.Arg131Cys Uncertain significance ★★ ⚠ same condition
- BMPER p.Arg505His Uncertain significance ★★ same condition
- BMPER p.Arg582Gln Uncertain significance ★★ ⚠ same condition
- BMPER p.Arg582Trp Uncertain significance ★★ same condition
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-ala258 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown