CTBP2 p.Ala426=
c.1278G>A · rs76963654 · VCV776551
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.203%, eas)
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 -3.4 | GERP -5.1 |
| Overall | ||
| CADD | 4.237 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.203%
East Asian · 91/44,874 alleles
Filtering AF
0.169%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.157%
Overall
0.00899%
145/1,613,380 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.203% | 493 |
| Admixed American | 0.0617% | 1,622 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,452 |
| European (non-Finnish) | 0.00136% | 73,737 |
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
- CTBP2
- Protein
- p.Ala426=
- Coding
- c.1278G>A
- MANE Select
- NM_001329
- dbSNP
- rs76963654
- Type
- single nucleotide variant
- Location
- chr10:124989578 (GRCh38)
- Gene constraint
- LOEUF 0.522 · pLI 0.82 (gnomAD)
- Structure
- AlphaFold pLDDT 83.67 · 5 PDB
- Residue 426
- the 'disordered' region
Similar variants
- CTBP2 c.58+11873C>T Benign ★★ same type
- CTBP2 c.58+11963C>T Benign ★★ same type
- CTBP2 c.58+12441C>T Benign ★★ same type
- CTBP2 c.58+12475A>C Benign ★★ same type
- CTBP2 p.Pro309= Benign ★★ same type
- ZRANB1 p.Arg669Trp Uncertain significance ★ ⚠ same type
- ZRANB1 p.Arg670Trp Uncertain significance ★ ⚠ same type
- ZRANB1 p.Arg688Gln 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/ctbp2-p-ala426 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown