BUB1B p.Pro299=
c.897C>A · rs374307209 · VCV1765304
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000932%, nfe)
Conditions
1
mosaic variegated aneuploidy syndrome 1
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 -2.6 | GERP -4.7 |
| Overall | ||
| CADD | 3.869 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000932%
European (non-Finnish) · 11/1,180,044 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000682%
11/1,614,066 alleles · very rare
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.Pro299=
- Coding
- c.897C>A
- MANE Select
- NM_001211
- dbSNP
- rs374307209
- Type
- single nucleotide variant
- Location
- chr15:40185310 (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.Pro299Ala Uncertain significance ★★ ⚠ same residue
- BUB1B p.Pro299Leu 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
- 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-pro299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown