CLDND2
protein-codingclaudin domain containing 2
Gene summary
Predicted to be located in membrane. Predicted to be active in 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 ~1.9 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 CLDND2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152353.3. 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 | 28 | 28 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 29 | 1 | 1 | 31 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689566.1 | 4 | MANE Select | |
| Ensembl | ENSP00000291715.1 | 4 | MANE Select | |
| Ensembl | ENSP00000471912.1 | 3 | Standard | |
| Ensembl | ENSP00000472077.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000291715
- Coding exons
- 4
- Length
- 1906
- Individuals with no LoFs
- 125604
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 130
- Defined
- 125736
- p
- 0.000525
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.408 | 87 | 98.4 | 0.884 | 0.00000463 | 1063 |
| Missense (PolyPhen) | 46 | 38.008 | 1.2103 | 369 | ||
| Synonymous | -0.466 | 46 | 42.1 | 1.09 | 0.00000198 | 339 |
| Loss of Function | -0.170 | 8 | 7.50 | 1.07 | 3.22e-7 | 76 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.00022 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00067 | 0.00065 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000092 | 0.000088 | rare |
| South Asian | 0.0036 | 0.0032 | notable |
| Other | 0.00035 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.404
- RVIS EVS
- 0.79
- RVIS percentile EVS
- 87.4
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.320
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |