CLCN5 p.Ser273=
c.819= · rs34464675 · VCV368476
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Dent disease type 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 -5.9, phastCons 0.81 |
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
- CLCN5
- Protein
- p.Ser273=
- Coding
- c.819=
- MANE Select
- NM_001127898
- dbSNP
- rs34464675
- Type
- single nucleotide variant
- Location
- chrX:50081733 (GRCh38)
- Structure
- AlphaFold pLDDT 80.48 · 2 PDB
- Residue 273
- a UniProt-annotated variant site (in dent1; retained in the endoplasmic reticulum; improperly n-glycosylated and non-functional)
Disease context
Dent disease type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Dent disease (Orphanet):
- Inheritance
- X-linked recessive
- Onset
- Childhood
Similar variants
- CLCN5 c.1014+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CLCN5 c.604-1G>C Likely pathogenic ★★ same condition
- CLCN5 c.933+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CLCN5 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same condition
- CLCN5 p.Arg417Ter Pathogenic ★★ same condition
- CLCN5 p.Arg537Ter Pathogenic ★★ same condition
- CLCN5 p.Arg586Trp Pathogenic/Likely pathogenic ★★ same condition
- CLCN5 p.Arg707Ter Pathogenic ★★ 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/clcn5-p-ser273 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown