CLDN1 p.Ala36=
c.108C>T · rs72466472 · VCV261402
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 7.97%, sas) — too common for a highly-penetrant pathogenic allele
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 -1.6 | GERP -4.5 |
| Overall | ||
| CADD | 6.134 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.97%
South Asian · 7,260/91,088 alleles
Filtering AF
7.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.75%
Overall
3.56%
57,434/1,614,160 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 7.97% | 13 |
| East Asian | 7.63% | 13 |
| Ashkenazi Jewishnot grpmax-eligible | 6.04% | 17 |
| Middle Eastern | 5.18% | 19 |
| Admixed American | 4.53% | 22 |
| Finnishnot grpmax-eligible | 4.01% | 25 |
| Remaining individualsnot grpmax-eligible | 3.96% | 25 |
| European (non-Finnish) | 3.09% | 32 |
| African / African-American | 0.6% | 167 |
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.Ala36=
- Coding
- c.108C>T
- MANE Select
- NM_021101
- dbSNP
- rs72466472
- Type
- single nucleotide variant
- Location
- chr3:190322099 (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-ala36 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown