CUL7 p.Ala20=
c.60C>T · rs1764530830 · VCV911605
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
3M syndrome 1
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 -1.4 | GERP -0.65 |
| Overall | ||
| CADD | 10.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,042 alleles
Overall
6.2e-05%
1/1,612,310 alleles · very rare
exomes 1/1,459,952 · genomes 0/152,358 · joint denominator
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.Ala20=
- Coding
- c.60C>T
- MANE Select
- NM_014780
- dbSNP
- rs1764530830
- Type
- single nucleotide variant
- Location
- chr6:43052729 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.11 · 2 PDB
- Residue 20
- a β-strand
Similar variants
- CUL7 c.2397+1G>A Likely pathogenic ★★ same condition
- CUL7 c.2660+1G>C Pathogenic ★★ same condition
- CUL7 c.3356-2A>C Likely pathogenic ★★ same condition
- CUL7 p.Arg1440Ter Pathogenic/Likely pathogenic ★★ same condition
- CUL7 p.Arg1445Ter Pathogenic ★★ same condition
- CUL7 p.Arg1573Ter Pathogenic ★★ same condition
- CUL7 p.Arg382Ter Pathogenic ★★ same condition
- CUL7 p.Arg550Ter Pathogenic/Likely pathogenic ★★ same condition
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-ala20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown