CTBP1 p.Pro110=
c.330C>T · rs111349558 · VCV733810
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.43%, sas)
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 -12 | GERP -3.4 |
| Overall | ||
| CADD | 0.215 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.43%
South Asian · 1,200/84,022 alleles
Filtering AF
1.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.33%
Overall
0.109%
1,674/1,542,486 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.43% | 70 |
| Middle Eastern | 0.251% | 399 |
| African / African-American | 0.249% | 402 |
| East Asian | 0.242% | 413 |
| Remaining individualsnot grpmax-eligible | 0.185% | 541 |
| Admixed American | 0.0373% | 2,683 |
| European (non-Finnish) | 0.0041% | 24,395 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0035% | 28,604 |
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.Pro110=
- Coding
- c.330C>T
- MANE Select
- NM_001012614
- dbSNP
- rs111349558
- Type
- single nucleotide variant
- Location
- chr4:1225544 (GRCh38)
- Gene constraint
- LOEUF 0.533 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 84.08 · 11 PDB
- Residue 110
- an α-helix
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-pro110 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown