CBX2 p.Ser438=
c.1314T>C · rs532091014 · VCV729346
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.235%, sas)
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 -20 | GERP -2.4 |
| Overall | ||
| CADD | 0.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.235%
South Asian · 213/90,804 alleles
Filtering AF
0.209%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.199%
Overall
0.0147%
237/1,610,882 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.235% | 426 |
| Middle Eastern | 0.116% | 865 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,796 |
| East Asian | 0.00223% | 44,772 |
| Admixed American | 0.00167% | 59,714 |
| African / African-American | 0.00133% | 74,940 |
| European (non-Finnish) | 8.48e-05% | 1,179,140 |
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.Ser438=
- Coding
- c.1314T>C
- MANE Select
- NM_005189
- dbSNP
- rs532091014
- Type
- single nucleotide variant
- Location
- chr17:79784757 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.29 · 3 PDB
- Residue 438
- the 'disordered' region
Similar variants
- CBX2 p.Ser438Ile Uncertain significance ★ ⚠ same residue
- 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
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-ser438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown