CLCN5 p.Val593del
c.1773TGT[1] · rs2519444458 · VCV2499136
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
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 2.7 | GERP 2, phastCons 1 |
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
- CLCN5
- Protein
- p.Val593del
- Coding
- c.1773TGT[1]
- MANE Select
- NM_001127898
- dbSNP
- rs2519444458
- Type
- Microsatellite
- Location
- chrX:50090143 (GRCh38)
- Structure
- AlphaFold pLDDT 80.48 · 2 PDB
Similar variants
- CLCN5 p.Cys462fs Pathogenic ★★ same type
- CLCN5 p.Ala535Ter Likely pathogenic ★ same type
- CLCN5 p.Asn174_Ser175insTer Pathogenic ★ same type
- CLCN5 p.Asp762fs Likely pathogenic ★ same type
- CLCN5 p.Cys471_Asp472delinsTer Pathogenic ★ same type
- CLCN5 p.Leu333del Uncertain significance ★ same type
- CLCN5 c.1744+216CT[3] Benign ★ same type
- CLCN5 p.Cys160fs 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/clcn5-p-val593del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown