Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.4 | GERP -2.6, phastCons 0.99 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CLIC2
- Coding
- c.*19=
- MANE Select
- NM_001289
- dbSNP
- rs559165
- Type
- single nucleotide variant
- Location
- chrX:155277884 (GRCh38)
- Structure
- AlphaFold pLDDT 93.28 · 3 PDB
Similar variants
- CLIC2 c.57+10C>T Benign/Likely benign ★★ same type
- CLIC2 p.Pro160Ala Benign/Likely benign ★★ same type
- CLIC2 c.582+6T>C Uncertain significance ★ same type
- CLIC2 p.Ala131Thr Uncertain significance ★ ⚠ same type
- CLIC2 p.Arg170Gly Uncertain significance ★ ⚠ same type
- CLIC2 p.Arg214His Conflicting classifications of pathogenicity ★ ⚠ same type
- CLIC2 p.Arg222Cys Uncertain significance ★ ⚠ same type
- CLIC2 p.Arg35Cys 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/clic2-c-star-19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown