CTBP1 p.Pro402=
c.1206T>A · rs369652853 · VCV750794
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.101%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.186 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -3.4 |
| Overall | ||
| CADD | 0.758 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.101%
European (non-Finnish) · 1,142/1,127,694 alleles
Filtering AF
0.0963%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0944%
Overall
0.0793%
1,194/1,506,040 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.101% | 987 |
| Remaining individualsnot grpmax-eligible | 0.0328% | 3,047 |
| Finnishnot grpmax-eligible | 0.0303% | 3,295 |
| Admixed American | 0.0164% | 6,096 |
| African / African-American | 0.0101% | 9,885 |
| South Asian | 0.00126% | 79,344 |
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
- CTBP1
- Protein
- p.Pro402=
- Coding
- c.1206T>A
- MANE Select
- NM_001012614
- dbSNP
- rs369652853
- Type
- single nucleotide variant
- Location
- chr4:1212324 (GRCh38)
- Gene constraint
- LOEUF 0.533 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 84.08 · 11 PDB
Similar variants
- CTBP1 p.Arg331Trp Pathogenic ★★ ⚠ same type
- CTBP1 c.-205C>G Uncertain significance ★★ ⚠ same type
- CTBP1 p.Ala384Pro Uncertain significance ★★ ⚠ same type
- CTBP1 p.Ala404Val Uncertain significance ★★ ⚠ same type
- CTBP1 p.Arg173Cys Uncertain significance ★★ ⚠ same type
- CTBP1 p.Gln137His Uncertain significance ★★ ⚠ same type
- CTBP1 p.Gly399Ser Uncertain significance ★★ ⚠ same type
- CTBP1 p.Pro292Ser 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/ctbp1-p-pro402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown