CLDN1 p.Asp110=
c.330C>T · VCV3637412
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 -9.8 | GERP -4.1 |
| Overall | ||
| CADD | 0.213 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,006 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000929%
15/1,614,034 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,003 |
| African / African-American | 0.00267% | 37,456 |
| European (non-Finnish) | 0.000932% | 107,276 |
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.Asp110=
- Coding
- c.330C>T
- MANE Select
- NM_021101
- Type
- single nucleotide variant
- Location
- chr3:190312930 (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-asp110 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown