CIZ1 p.Pro232=
c.696G>A · rs45579839 · VCV413830
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.27%, eas)
Conditions
1
dystonic disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.86 | GERP -5 |
| Overall | ||
| CADD | 5.738 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.27%
East Asian · 1,018/44,864 alleles
Filtering AF
2.15%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.11%
Overall
0.114%
1,838/1,613,958 alleles · low-frequency
exomes 1,636/1,461,752 · genomes 202/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.27% | 44 |
| Admixed American | 0.875% | 114 |
| Middle Eastern | 0.247% | 404 |
| Remaining individualsnot grpmax-eligible | 0.102% | 977 |
| South Asian | 0.0681% | 1,469 |
| African / African-American | 0.0267% | 3,750 |
| European (non-Finnish) | 0.0113% | 8,872 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
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
- CIZ1
- Protein
- p.Pro232=
- Coding
- c.696G>A
- MANE Select
- NM_001131016
- dbSNP
- rs45579839
- Type
- single nucleotide variant
- Location
- chr9:128180510 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.51 · 1 PDB
- Residue 232
- the 'disordered' region
Similar variants
- CIZ1 p.Pro232Leu Uncertain significance ★ ⚠ same residue
- CIZ1 p.Ala128Ser Uncertain significance ★★ ⚠ same condition
- CIZ1 p.Ala345Val Uncertain significance ★★ ⚠ same condition
- CIZ1 p.Ala523Ser Uncertain significance ★★ ⚠ same condition
- CIZ1 p.Ala833Gly Uncertain significance ★★ ⚠ same condition
- CIZ1 p.Arg286Gln Uncertain significance ★★ ⚠ same condition
- CIZ1 p.Arg571His Uncertain significance ★★ ⚠ same condition
- CIZ1 p.Arg640Gln Uncertain significance ★★ ⚠ same condition
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/ciz1-p-pro232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown