BMPER p.Ile643=
c.1929C>T · rs754018099 · VCV1931074
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0253%, sas)
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 1.5 | GERP 0.017, phastCons 1 |
| Overall | ||
| CADD | 4.502 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0253%
South Asian · 23/91,076 alleles
Filtering AF
0.0172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0146%
Overall
0.00155%
25/1,613,934 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0253% | 3,960 |
| Admixed American | 0.00333% | 29,994 |
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.Ile643=
- Coding
- c.1929C>T
- MANE Select
- NM_001365308
- dbSNP
- rs754018099
- Type
- single nucleotide variant
- Location
- chr7:34153144 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
- Residue 643
- the til domain
Similar variants
- BMPER p.Ile643Phe Uncertain significance ★★ ⚠ same residue
- BMPER p.Ile643Val 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
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-ile643 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown