BUB1B p.Arg416=
c.1246C>A · rs755579898 · VCV1759593
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0516%, sas)
Conditions
2
Inborn genetic diseases
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 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 13.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0516%
South Asian · 47/91,056 alleles
Filtering AF
0.0399%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0357%
Overall
0.00297%
48/1,613,938 alleles · ultra-rare
exomes 48/1,461,730 · genomes 0/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0516% | 1,937 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,496 |
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
- BUB1B
- Protein
- p.Arg416=
- Coding
- c.1246C>A
- MANE Select
- NM_001211
- dbSNP
- rs755579898
- Type
- single nucleotide variant
- Location
- chr15:40196732 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.62 · 9 PDB
Similar variants
- BUB1B p.Arg416Trp Uncertain significance ★★ ⚠ same residue
- BUB1B p.Arg416Gln Uncertain significance ★ ⚠ same residue
- BUB1B p.Arg416Leu Uncertain significance ★ ⚠ same residue
- BUB1B p.Arg114Ter Pathogenic ★★ same condition
- BUB1B p.Arg120Ter Pathogenic ★★ same condition
- BUB1B p.Arg194Ter Pathogenic/Likely pathogenic ★★ same condition
- BUB1B p.Arg199Ter Pathogenic/Likely pathogenic ★★ same condition
- BUB1B p.Arg67Ter Pathogenic/Likely pathogenic ★★ 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/bub1b-p-arg416 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown