CUL7 p.Pro1064=
c.3192C>A · VCV3708232
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 0.22 | GERP 0.59, phastCons 0.88 |
| Overall | ||
| CADD | 3.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,078 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00149%
24/1,609,512 alleles · ultra-rare
exomes 21/1,457,336 · genomes 3/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,078 |
| African / African-American | 0.00534% | 18,718 |
| Admixed American | 0.00506% | 19,763 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,328 |
| European (non-Finnish) | 0.00127% | 78,510 |
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
- CUL7
- Protein
- p.Pro1064=
- Coding
- c.3192C>A
- MANE Select
- NM_014780
- Type
- single nucleotide variant
- Location
- chr6:43043611 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.11 · 2 PDB
- Residue 1064
- an α-helix
Similar variants
- CUL7 c.2397+1G>A Likely pathogenic ★★ same type
- CUL7 c.2398-2A>G Likely pathogenic ★★ same type
- CUL7 c.2660+1G>C Pathogenic ★★ same type
- CUL7 c.3356-2A>C Likely pathogenic ★★ same type
- CUL7 p.Arg1440Ter Pathogenic/Likely pathogenic ★★ same type
- CUL7 p.Arg1445Ter Pathogenic ★★ same type
- CUL7 p.Arg1573Ter Pathogenic ★★ same type
- CUL7 p.Arg382Ter Pathogenic ★★ 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/cul7-p-pro1064 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown