BUB1 p.Ala826=
c.2478C>T · rs55731145 · VCV779305
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.04%, 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 3.3 | phastCons 1 |
| Overall | ||
| CADD | 9.468 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.04%
South Asian · 940/90,684 alleles
Filtering AF
0.982%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.96%
Overall
0.16%
2,562/1,605,272 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.04% | 96 |
| Middle Eastern | 0.777% | 129 |
| Remaining individualsnot grpmax-eligible | 0.159% | 630 |
| Ashkenazi Jewishnot grpmax-eligible | 0.129% | 778 |
| European (non-Finnish) | 0.113% | 886 |
| Admixed American | 0.111% | 905 |
| Finnishnot grpmax-eligible | 0.0425% | 2,351 |
| African / African-American | 0.02% | 4,997 |
| East Asian | 0.00446% | 22,440 |
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
- BUB1
- Protein
- p.Ala826=
- Coding
- c.2478C>T
- MANE Select
- NM_004336
- dbSNP
- rs55731145
- Type
- single nucleotide variant
- Location
- chr2:110641789 (GRCh38)
- Gene constraint
- LOEUF 0.727 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.91 · 11 PDB
- Residue 826
- the protein kinase domain
Similar variants
- BUB1 p.Ala826Pro Uncertain significance ★ ⚠ same residue
- BUB1 p.Ala826Val Uncertain significance ★ ⚠ same residue
- BUB1 c.1698+1G>T Uncertain significance ★★ same type
- BUB1 p.Ala281Thr Uncertain significance ★★ ⚠ same type
- BUB1 p.Ala283Thr Uncertain significance ★★ ⚠ same type
- BUB1 p.Ala499Val Uncertain significance ★★ ⚠ same type
- BUB1 p.Ala502Ser Uncertain significance ★★ ⚠ same type
- BUB1 p.Ala630Gly 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/bub1-p-ala826 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown