CTBP1 p.Pro12=
c.36C>A · rs572177087 · VCV1957184
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.97e-05%)
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 4.7 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 10.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.97e-05%
Overall
6.97e-05%
1/1,435,136 alleles · very rare
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.Pro12=
- Coding
- c.36C>A
- MANE Select
- NM_001012614
- dbSNP
- rs572177087
- Type
- single nucleotide variant
- Location
- chr4:1238309 (GRCh38)
- Gene constraint
- LOEUF 0.533 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 84.08 · 11 PDB
- Residue 12
- the 'interaction with glis2 1' region
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-pro12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown