CTBP1 p.Pro406=
c.1218G>C · rs369644553 · VCV2654547
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.211%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.058 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -8.3 | GERP -3.4 |
| Overall | ||
| CADD | 0.436 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.211%
European (non-Finnish) · 459/217,796 alleles
Filtering AF
0.195%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.189%
Overall
0.141%
574/407,226 alleles · rare
exomes 567/270,392 · genomes 7/136,834 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.211% | 475 |
| Middle Eastern | 0.179% | 560 |
| Remaining individualsnot grpmax-eligible | 0.171% | 586 |
| East Asian | 0.124% | 804 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0694% | 1,441 |
| Admixed American | 0.0667% | 1,498 |
| South Asian | 0.0628% | 1,592 |
| African / African-American | 0.0377% | 2,655 |
| Finnishnot grpmax-eligible | 0.012% | 8,338 |
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.Pro406=
- Coding
- c.1218G>C
- MANE Select
- NM_001012614
- dbSNP
- rs369644553
- Type
- single nucleotide variant
- Location
- chr4:1212312 (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-pro406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown