CLIC5 p.Pro33=
c.99T>A · rs367709520 · VCV2884464
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0067%, 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 0.42 | GERP -5.6, phastCons 0.96 |
| Overall | ||
| CADD | 6.752 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0067%
European (non-Finnish) · 79/1,179,888 alleles
Filtering AF
0.00546%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00506%
Overall
0.00502%
81/1,613,918 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0067% | 14,935 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,235 |
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.Pro33=
- Coding
- c.99T>A
- MANE Select
- NM_016929
- dbSNP
- rs367709520
- Type
- single nucleotide variant
- Location
- chr6:45955209 (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-pro33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown