BUB3 p.Thr113=
c.339T>C · rs1844369167 · VCV1731000
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 0.012 | GERP 0.41, phastCons 0.92 |
| Overall | ||
| CADD | 10.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,008 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,614,032 alleles · very rare
exomes 2/1,461,828 · genomes 1/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,008 |
| European (non-Finnish) | 0.000169% | 590,005 |
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.Thr113=
- Coding
- c.339T>C
- MANE Select
- NM_004725
- dbSNP
- rs1844369167
- Type
- single nucleotide variant
- Location
- chr10:123157802 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.10
Similar variants
- 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
- BUB3 p.Ala239Gly Uncertain significance ★ ⚠ same type
- BUB3 p.Ala292Val 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-thr113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown