BBX p.Ala60=
c.180C>T · rs150018279 · VCV714946
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.314%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.32 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.6 | GERP -4.1 |
| Overall | ||
| CADD | 1.147 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.314%
European (non-Finnish) · 3,709/1,179,642 alleles
Filtering AF
0.306%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.303%
Overall
0.253%
4,075/1,613,476 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.314% | 318 |
| Remaining individualsnot grpmax-eligible | 0.234% | 428 |
| South Asian | 0.0956% | 1,046 |
| Finnishnot grpmax-eligible | 0.0703% | 1,422 |
| Middle Eastern | 0.0661% | 1,513 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0608% | 1,643 |
| Admixed American | 0.0517% | 1,935 |
| African / African-American | 0.0467% | 2,142 |
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
- BBX
- Protein
- p.Ala60=
- Coding
- c.180C>T
- MANE Select
- NM_001142568
- dbSNP
- rs150018279
- Type
- single nucleotide variant
- Location
- chr3:107716624 (GRCh38)
- Gene constraint
- LOEUF 0.359 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.79
- Residue 60
- the 'disordered' region
Similar variants
- BBX p.Ala442Thr Benign ★★ same type
- BBX p.Ala892= Benign ★★ same type
- BBX p.Ala139Thr Uncertain significance ★ ⚠ same type
- BBX p.Ala143Gly Uncertain significance ★ ⚠ same type
- BBX p.Ala269Pro Uncertain significance ★ ⚠ same type
- BBX p.Ala354Thr Uncertain significance ★ ⚠ same type
- BBX p.Ala375Thr Uncertain significance ★ ⚠ same type
- BBX p.Ala592Thr 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/bbx-p-ala60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown