BMPER p.Arg555=
c.1665G>A · rs763105833 · VCV1899738
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 1.1 | GERP -2.7, phastCons 0.99 |
| Overall | ||
| CADD | 5.592 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,984 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000248%
4/1,613,838 alleles · very rare
exomes 2/1,461,884 · genomes 2/151,954 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,995 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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.Arg555=
- Coding
- c.1665G>A
- MANE Select
- NM_001365308
- dbSNP
- rs763105833
- Type
- single nucleotide variant
- Location
- chr7:34086012 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
- Residue 555
- a UniProt-annotated variant site (in)
Similar variants
- BMPER p.Arg555Trp Benign/Likely benign ★★ 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-arg555 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown