CLDN11 p.Pro112=
c.336C>T · rs150789369 · VCV1675937
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.092%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.32 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.1 | GERP -3.8 |
| Overall | ||
| CADD | 0.873 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.092%
African / African-American · 69/75,030 alleles
Filtering AF
0.0745%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0682%
Overall
0.037%
597/1,614,140 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.092% | 1,087 |
| European (non-Finnish) | 0.0389% | 2,571 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,841 |
| South Asian | 0.0285% | 3,503 |
| Admixed American | 0.0267% | 3,751 |
| Middle Eastern | 0.0165% | 6,062 |
| Finnishnot grpmax-eligible | 0.00625% | 16,009 |
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
- CLDN11
- Protein
- p.Pro112=
- Coding
- c.336C>T
- MANE Select
- NM_005602
- dbSNP
- rs150789369
- Type
- single nucleotide variant
- Location
- chr3:170423272 (GRCh38)
- Gene constraint
- LOEUF 0.348 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 85.60
Similar variants
- CLDN11 p.Ter208Gln Pathogenic ★ same type
- CLDN11 p.Ala194Val Uncertain significance ★ ⚠ same type
- CLDN11 p.Arg107Gly Uncertain significance ★ ⚠ same type
- CLDN11 p.Asn188Ser Uncertain significance ★ ⚠ same type
- CLDN11 p.Gly92Ser Uncertain significance ★ ⚠ same type
- CLDN11 p.His201Tyr Uncertain significance ★ ⚠ same type
- CLDN11 p.His64Tyr Uncertain significance ★ same type
- CLDN11 p.Met1Ile 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/cldn11-p-pro112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown