BMPER p.His453=
c.1359C>T · rs1259590354 · VCV2993219
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00891%, eas)
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 -0.57 | GERP -3.2, phastCons 0.009 |
| Overall | ||
| CADD | 6.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,880 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000248%
4/1,613,904 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.His453=
- Coding
- c.1359C>T
- MANE Select
- NM_001365308
- dbSNP
- rs1259590354
- Type
- single nucleotide variant
- Location
- chr7:34079137 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
- Residue 453
- a disulfide bond; the vwfd domain
Similar variants
- 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
- BMPER p.Arg410His 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-his453 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown