CLCN5 p.Asp91=
c.273T>C · rs932472104 · VCV1916478
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00179%, nfe)
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 -7.6 | GERP -5.2 |
| Overall | ||
| CADD | 0.663 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00179%
European (non-Finnish) · 16/894,108 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000857%
Overall
0.00141%
17/1,207,664 alleles · very rare
exomes 13/1,096,965 · genomes 4/110,699 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00179% | 55,882 |
| African / African-American | 0.00176% | 56,790 |
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.Asp91=
- Coding
- c.273T>C
- MANE Select
- NM_001127898
- dbSNP
- rs932472104
- Type
- single nucleotide variant
- Location
- chrX:50069988 (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-asp91 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown