CGN
protein-codingcingulin
Gene summary
Enables cadherin binding activity. Predicted to be involved in microtubule cytoskeleton organization. Predicted to act upstream of or within bicellular tight junction assembly and epithelial cell morphogenesis. Located in bicellular tight junction and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CGN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020770.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 197 | 12 | 2 | 211 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 201 | 13 | 3 | 217 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065821.1 | 20 | MANE Select | |
| Ensembl | ENSP00000271636.7 | 20 | MANE Select | |
| Ensembl | ENSP00000390686.1 | 5 | Standard | |
| Ensembl | ENSP00000410836.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tight junction - Homo sapiens (human)
- Signal Transduction
- TCR
- Signaling by TGF-beta Receptor Complex
- Signaling by TGF-beta family members
Biological Process
- transforming growth factor beta receptor signaling pathway
- biological_process
Molecular Function
- motor activity
- actin binding
- protein binding
- cadherin binding
Cellular Component
- plasma membrane
- bicellular tight junction
- myosin complex
- cell junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000271636
- Coding exons
- 20
- Length
- 28183
- Individuals with no LoFs
- 125475
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 273
- Defined
- 125748
- p
- 0.00109
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.170 | 695 | 708 | 0.982 | 0.0000460 | 7704 |
| Missense (PolyPhen) | 262 | 268.16 | 0.97702 | 2851 | ||
| Synonymous | 1.50 | 243 | 275 | 0.885 | 0.0000143 | 2479 |
| Loss of Function | 1.93 | 58 | 76.2 | 0.762 | 0.00000523 | 711 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0016 | notable |
| Latino/Admixed American | 0.00055 | 0.00055 | rare |
| Ashkenazi Jewish | 0.0023 | 0.0023 | notable |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0.00097 | 0.00097 | rare |
| European (Non-Finnish) | 0.0012 | 0.0012 | notable |
| South Asian | 0.00056 | 0.00056 | rare |
| Other | 0.0016 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probably plays a role in the formation and regulation of the tight junction (TJ) paracellular permeability barrier.;
Recessive Scores
- pRec
- 0.405
Intolerance Scores
- LoFtool
- 0.782
- RVIS EVS
- 1.97
- RVIS percentile EVS
- 97.57
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.511
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |