CUX2 p.Arg793=
c.2379C>T · rs112401949 · VCV790125
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.27%, 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 -12 | GERP -2.1 |
| Overall | ||
| CADD | 7.208 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.27%
African / African-American · 2,451/74,976 alleles
Filtering AF
3.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.12%
Overall
0.18%
2,881/1,597,976 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.27% | 31 |
| Admixed American | 0.27% | 370 |
| Remaining individualsnot grpmax-eligible | 0.25% | 400 |
| Middle Eastern | 0.132% | 757 |
| South Asian | 0.00879% | 11,382 |
| European (non-Finnish) | 0.00814% | 12,282 |
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
- CUX2
- Protein
- p.Arg793=
- Coding
- c.2379C>T
- MANE Select
- NM_015267
- dbSNP
- rs112401949
- Type
- single nucleotide variant
- Location
- chr12:111320388 (GRCh38)
- Gene constraint
- LOEUF 0.383 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99 · 3 PDB
Similar variants
- CUX2 p.Arg793Cys Uncertain significance ★ ⚠ same residue
- CUX2 p.Arg793Ser Uncertain significance ★ ⚠ same residue
- CUX2 p.Glu590Lys Pathogenic/Likely pathogenic ★★ same type
- CUX2 p.Ala302Ser Uncertain significance ★★ ⚠ same type
- CUX2 p.Ala336Thr Uncertain significance ★★ ⚠ same type
- CUX2 p.Ala544Val Uncertain significance ★★ ⚠ same type
- CUX2 p.Arg312Gln Uncertain significance ★★ ⚠ same type
- CUX2 p.Arg599Ser 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/cux2-p-arg793 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown