CLCN5 p.Arg303=
c.909G>A · rs781910933 · VCV1947156
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0109%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.50 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 0.035, phastCons 1 |
| Overall | ||
| CADD | 12.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0109%
Admixed American · 5/45,981 alleles
Filtering AF
0.00426%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0027%
Overall
0.000547%
6/1,097,094 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0109% | 9,196 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,595 |
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
- CLCN5
- Protein
- p.Arg303=
- Coding
- c.909G>A
- MANE Select
- NM_001127898
- dbSNP
- rs781910933
- Type
- single nucleotide variant
- Location
- chrX:50081823 (GRCh38)
- Structure
- AlphaFold pLDDT 80.48 · 2 PDB
Similar variants
- CLCN5 c.1014+1G>A Pathogenic/Likely pathogenic ★★ same type
- CLCN5 c.604-1G>C Likely pathogenic ★★ same type
- CLCN5 c.933+1G>A Pathogenic/Likely pathogenic ★★ same type
- CLCN5 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same type
- CLCN5 p.Arg417Ter Pathogenic ★★ same type
- CLCN5 p.Arg537Ter Pathogenic ★★ same type
- CLCN5 p.Arg586Trp Pathogenic/Likely pathogenic ★★ same type
- CLCN5 p.Arg707Ter 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-arg303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown