CBX2 p.Ser42=
c.126C>T · VCV3630388
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.258%, 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 0.82 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 15.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.258%
African / African-American · 194/75,056 alleles
Filtering AF
0.229%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.217%
Overall
0.0303%
489/1,613,836 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.258% | 387 |
| Middle Eastern | 0.198% | 504 |
| Admixed American | 0.158% | 632 |
| Ashkenazi Jewishnot grpmax-eligible | 0.139% | 722 |
| Remaining individualsnot grpmax-eligible | 0.072% | 1,389 |
| European (non-Finnish) | 0.00856% | 11,683 |
| South Asian | 0.0011% | 91,036 |
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.Ser42=
- Coding
- c.126C>T
- MANE Select
- NM_005189
- Type
- single nucleotide variant
- Location
- chr17:79779371 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.29 · 3 PDB
- Residue 42
- the chromo domain; a β-strand; the 'involved in the interaction with h3c15 and h3c1' 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-ser42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown