CBX2 p.Pro143=
c.429G>A · rs150943047 · VCV769928
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.44%, 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 -1.9 | GERP -3.3 |
| Overall | ||
| CADD | 9.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.44%
African / African-American · 1,083/75,018 alleles
Filtering AF
1.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.34%
Overall
0.41%
6,624/1,613,944 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.44% | 69 |
| Admixed American | 0.603% | 166 |
| Remaining individualsnot grpmax-eligible | 0.461% | 217 |
| European (non-Finnish) | 0.411% | 243 |
| Middle Eastern | 0.115% | 866 |
| Finnishnot grpmax-eligible | 0.0454% | 2,204 |
| South Asian | 0.00439% | 22,769 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| East Asian | 0.00223% | 44,866 |
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
- CBX2
- Protein
- p.Pro143=
- Coding
- c.429G>A
- MANE Select
- NM_005189
- dbSNP
- rs150943047
- Type
- single nucleotide variant
- Location
- chr17:79783872 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.29 · 3 PDB
- Residue 143
- the 'disordered' region
Similar variants
- CBX2 c.288+52G>T Uncertain significance ★★ same type
- CBX2 p.Arg137His Uncertain significance ★★ ⚠ same type
- CBX2 p.Gln349His Uncertain significance ★★ ⚠ same type
- CBX2 p.Gly133Ser Uncertain significance ★★ ⚠ same type
- CBX2 p.Gly287Arg Uncertain significance ★★ ⚠ same type
- CBX2 p.Gly332Asp Uncertain significance ★★ ⚠ same type
- CBX2 p.Met260Val Uncertain significance ★★ ⚠ same type
- CBX2 p.Met404Leu 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/cbx2-p-pro143 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown