CLCN5 p.Pro489=
c.1467G>A · VCV3605678
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0208%, eas)
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 -5.8 | GERP -5.6 |
| Overall | ||
| CADD | 0.323 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0208%
East Asian · 7/33,729 alleles
Filtering AF
0.00969%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00681%
Overall
0.00157%
19/1,208,852 alleles · ultra-rare
exomes 17/1,097,964 · genomes 2/110,888 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0208% | 4,818 |
| South Asian | 0.00352% | 28,373 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,564 |
| European (non-Finnish) | 0.00101% | 99,437 |
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.Pro489=
- Coding
- c.1467G>A
- MANE Select
- NM_001127898
- Type
- single nucleotide variant
- Location
- chrX:50086780 (GRCh38)
- Structure
- AlphaFold pLDDT 80.48 · 2 PDB
Similar variants
- CLCN5 p.Pro489Leu Uncertain significance ★★ ⚠ same residue
- 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
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-pro489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown