CLIC5 p.Ala232=
c.696A>T · rs187897856 · VCV666618
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.403%, 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 -10 | GERP -4.4 |
| Overall | ||
| CADD | 1.137 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.403%
East Asian · 181/44,886 alleles
Filtering AF
0.355%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.337%
Overall
0.0195%
314/1,614,212 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.403% | 248 |
| South Asian | 0.0373% | 2,679 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,126 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,401 |
| Admixed American | 0.01% | 10,004 |
| European (non-Finnish) | 0.00559% | 17,879 |
| African / African-American | 0.004% | 25,020 |
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
- CLIC5
- Protein
- p.Ala232=
- Coding
- c.696A>T
- MANE Select
- NM_016929
- dbSNP
- rs187897856
- Type
- single nucleotide variant
- Location
- chr6:45903148 (GRCh38)
- Gene constraint
- LOEUF 1.233 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.06 · 3 PDB
Similar variants
- CLIC5 p.Arg203His Uncertain significance ★★ ⚠ same type
- CLIC5 p.Arg216Gln Uncertain significance ★★ ⚠ same type
- CLIC5 p.Arg224His Uncertain significance ★★ ⚠ same type
- CLIC5 p.Asn204Thr Uncertain significance ★★ ⚠ same type
- CLIC5 p.His54Arg Uncertain significance ★★ ⚠ same type
- CLIC5 p.Ile118Val Uncertain significance ★★ ⚠ same type
- CLIC5 p.Ile41Phe Uncertain significance ★★ ⚠ same type
- CLIC5 p.Leu96Phe Uncertain significance ★★ ⚠ 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/clic5-p-ala232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown