BUB3 p.Thr290=
c.870G>A · rs1844441145 · VCV1764401
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 -6.7 | GERP -5.2 |
| Overall | ||
| CADD | 2.642 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,030 alleles
Overall
0.000205%
3/1,461,656 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,030 |
| South Asian | 0.0011% | 91,032 |
| European (non-Finnish) | 8.47e-05% | 1,179,958 |
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
- BUB3
- Protein
- p.Thr290=
- Coding
- c.870G>A
- MANE Select
- NM_004725
- dbSNP
- rs1844441145
- Type
- single nucleotide variant
- Location
- chr10:123162727 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.10
Similar variants
- BUB3 p.Thr290Ala Uncertain significance ★ ⚠ same residue
- BUB3 p.Thr290Met Uncertain significance ★ ⚠ same residue
- BUB3 p.Arg314= Likely benign ★★ same type
- BUB3 p.Ser197= Likely benign ★★ same type
- BUB3 p.Ser198= Likely benign ★★ same type
- BUB3 p.Ala131Val Uncertain significance ★ ⚠ same type
- BUB3 p.Ala155Val Uncertain significance ★ ⚠ same type
- BUB3 p.Ala187Gly 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/bub3-p-thr290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown