CBX4 p.Arg70=
c.210G>C · rs73422118 · VCV722969
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.507%, 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 -0.48 | GERP -4, phastCons 0.037 |
| Overall | ||
| CADD | 9.283 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.507%
African / African-American · 380/74,984 alleles
Filtering AF
0.465%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.448%
Overall
0.0273%
441/1,613,242 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.507% | 197 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,155 |
| Admixed American | 0.0333% | 3,000 |
| Middle Eastern | 0.0165% | 6,058 |
| European (non-Finnish) | 0.000932% | 107,260 |
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
- CBX4
- Protein
- p.Arg70=
- Coding
- c.210G>C
- MANE Select
- NM_003655
- dbSNP
- rs73422118
- Type
- single nucleotide variant
- Location
- chr17:79835682 (GRCh38)
- Gene constraint
- LOEUF 0.48 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 55.01 · 3 PDB
- Residue 70
- the 'interaction with bmi1' region; the 'involved in interaction with h3c15 and h3c1' region
Similar variants
- CBX4 p.Arg70Gln Uncertain significance ★ ⚠ same residue
- CBX4 p.Ala138Val Uncertain significance ★ ⚠ same type
- CBX4 p.Ala236Val Uncertain significance ★ ⚠ same type
- CBX4 p.Ala298Val Uncertain significance ★ ⚠ same type
- CBX4 p.Ala314Pro Uncertain significance ★ ⚠ same type
- CBX4 p.Ala316Ser Uncertain significance ★ ⚠ same type
- CBX4 p.Ala316Thr Uncertain significance ★ ⚠ same type
- CBX4 p.Ala323Glu 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/cbx4-p-arg70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown