BUB1B p.Val106=
c.318A>G · rs186580106 · VCV1728621
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0213%, afr)
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 2.1 | GERP -4.8, phastCons 1 |
| Overall | ||
| CADD | 7.474 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0213%
African / African-American · 16/75,050 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0109%
Overall
0.00198%
32/1,613,472 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0213% | 4,691 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| European (non-Finnish) | 0.00127% | 78,629 |
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.Val106=
- Coding
- c.318A>G
- MANE Select
- NM_001211
- dbSNP
- rs186580106
- Type
- single nucleotide variant
- Location
- chr15:40170615 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.62 · 9 PDB
- Residue 106
- the bub1 n-terminal domain; an α-helix
Similar variants
- BUB1B p.Val106Ala Uncertain significance ★★ ⚠ same residue
- BUB1B p.Val106Ile Likely benign ★ 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
- BUB1B p.Gln267Ter 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-val106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown