CUL7 p.Ser1056=
c.3168C>T · rs201565396 · VCV2882721
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.103%, eas)
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 -0.66 | GERP -3.7, phastCons 0.001 |
| Overall | ||
| CADD | 0.656 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
East Asian · 46/44,682 alleles
Filtering AF
0.0793%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0709%
Overall
0.00311%
50/1,609,226 alleles · rare
exomes 42/1,456,926 · genomes 8/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.103% | 971 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,150 |
| European (non-Finnish) | 0.00017% | 587,990 |
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.Ser1056=
- Coding
- c.3168C>T
- MANE Select
- NM_014780
- dbSNP
- rs201565396
- Type
- single nucleotide variant
- Location
- chr6:43044756 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.11 · 2 PDB
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-ser1056 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown