CLCN2 p.Cys69Phe
c.206_207delinsTT · rs2474262975 · VCV2195347
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -2.6 |
| Regional constraint | o/e 0.87 | unconstrained · MANE · 15 kb · p 6e-06 · regional, not allelic |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CLCN2
- Protein
- p.Cys69Phe
- Coding
- c.206_207delinsTT
- MANE Select
- NM_004366
- dbSNP
- rs2474262975
- Type
- Indel
- Location
- chr3:184358988 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.82 · 8 PDB
Similar variants
- CLCN2 p.Cys69Ter Likely pathogenic ★ same residue
- CLCN2 p.Cys69= Likely benign ★ same residue
- CLCN2 c.2271+1_2271+2delinsCA Likely pathogenic ★ same type
- CLCN2 p.Ser375fs Pathogenic ★ 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/clcn2-p-cys69phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown