CUL7 p.Ser1256=
c.3768C>T · rs138763036 · VCV735879
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.351%, 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 -1.8 | GERP -3.7 |
| Overall | ||
| CADD | 3.894 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.351%
African / African-American · 263/75,030 alleles
Filtering AF
0.316%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.302%
Overall
0.0223%
360/1,613,292 alleles · rare
exomes 207/1,460,956 · genomes 153/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.351% | 285 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,124 |
| Middle Eastern | 0.0165% | 6,060 |
| Admixed American | 0.0117% | 8,559 |
| South Asian | 0.0066% | 15,145 |
| European (non-Finnish) | 0.00534% | 18,724 |
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.Ser1256=
- Coding
- c.3768C>T
- MANE Select
- NM_014780
- dbSNP
- rs138763036
- Type
- single nucleotide variant
- Location
- chr6:43040953 (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-ser1256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown