CUX1 p.Pro438=
c.1314G>C · rs782792685 · VCV2673121
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -0.43, phastCons 1 |
| Overall | ||
| CADD | 6.851 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
African / African-American · 5/74,840 alleles
Filtering AF
0.00318%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00287%
Overall
0.00366%
59/1,612,160 alleles · very rare
exomes 47/1,460,108 · genomes 12/152,052 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00668% | 14,968 |
| European (non-Finnish) | 0.00416% | 24,056 |
| South Asian | 0.0033% | 30,335 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,189 |
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
- CUX1
- Protein
- p.Pro438=
- Coding
- c.1314G>C
- MANE Select
- NM_181552
- dbSNP
- rs782792685
- Type
- single nucleotide variant
- Location
- chr7:102196725 (GRCh38)
- Gene constraint
- LOEUF 0.277 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.84 · 3 PDB
- Residue 438
- the 'disordered' region
Similar variants
- CUX1 c.1451-2A>G Likely pathogenic ★★ same type
- CUX1 c.1681-1G>A Pathogenic/Likely pathogenic ★★ same type
- CUX1 p.Arg661Ter Pathogenic/Likely pathogenic ★★ same type
- CUX1 p.Gln862Ter Pathogenic/Likely pathogenic ★★ same type
- CUX1 p.Glu866Ter Pathogenic/Likely pathogenic ★★ same type
- CUX1 p.Trp1188Ter Pathogenic ★★ same type
- CUX1 p.Ala1433Val Uncertain significance ★★ ⚠ same type
- CUX1 p.Ala454Val 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/cux1-p-pro438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown