CLDN1 p.Ile22=
c.66C>T · rs562285276 · VCV797100
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0312%, 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 0.71 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 12.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0312%
East Asian · 14/44,866 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0151%
Overall
0.000929%
15/1,614,228 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0312% | 3,205 |
| European (non-Finnish) | 8.47e-05% | 1,180,057 |
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
- CLDN1
- Protein
- p.Ile22=
- Coding
- c.66C>T
- MANE Select
- NM_021101
- dbSNP
- rs562285276
- Type
- single nucleotide variant
- Location
- chr3:190322141 (GRCh38)
- Gene constraint
- LOEUF 0.837 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 84.57
Similar variants
- CLDN1 p.Cys64Ter Pathogenic/Likely pathogenic ★★ same type
- CLDN1 p.Ala14Val Uncertain significance ★★ ⚠ same type
- CLDN1 p.Arg188Gln Uncertain significance ★★ ⚠ same type
- CLDN1 p.Leu165Val Uncertain significance ★★ ⚠ same type
- CLDN1 p.Pro202Leu Uncertain significance ★★ ⚠ same type
- CLDN1 p.Pro204Thr Uncertain significance ★★ ⚠ same type
- CLDN1 p.Val100Ile Uncertain significance ★★ ⚠ same type
- CLDN1 p.Val145Ile 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/cldn1-p-ile22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown