CLIC5 p.Pro68=
c.204C>T · rs151203192 · VCV1597768
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0294%, afr)
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 -2.4 | GERP -5.6 |
| Overall | ||
| CADD | 5.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0294%
African / African-American · 22/74,862 alleles
Filtering AF
0.0199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0168%
Overall
0.0135%
218/1,613,044 alleles · ultra-rare
exomes 201/1,460,890 · genomes 17/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0294% | 3,403 |
| European (non-Finnish) | 0.0157% | 6,375 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,486 |
| East Asian | 0.00669% | 14,943 |
| Admixed American | 0.00333% | 29,985 |
| South Asian | 0.0011% | 91,016 |
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.Pro68=
- Coding
- c.204C>T
- MANE Select
- NM_016929
- dbSNP
- rs151203192
- Type
- single nucleotide variant
- Location
- chr6:45949351 (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-pro68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown