BMPER p.Thr437=
c.1311C>T · rs760041868 · VCV911318
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 -14 | GERP -4.4 |
| Overall | ||
| CADD | 3.496 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,002 alleles
Overall
6.84e-05%
1/1,461,738 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
- BMPER
- Protein
- p.Thr437=
- Coding
- c.1311C>T
- MANE Select
- NM_001365308
- dbSNP
- rs760041868
- Type
- single nucleotide variant
- Location
- chr7:34079089 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
- Residue 437
- a disulfide bond; the vwfd 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-thr437 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown