OCLN
occludin, the group of MARVEL domain containing|Tetraspan junctional complex superfamily|Protein phosphatase 1 regulatory subunits
Basic information
Region (hg38): 5:69492291-69558104
Links
Phenotypes
GenCC
Source:
- pseudo-TORCH syndrome 1 (Strong), mode of inheritance: AR
- pseudo-TORCH syndrome 1 (Moderate), mode of inheritance: AR
- pseudo-TORCH syndrome (Supportive), mode of inheritance: AR
- pseudo-TORCH syndrome 1 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Pseudo-TORCH syndrome 1 (Band-like calcification with simplified gyration and polymicrogyria) | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 19012351; 19530192; 20727516 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (60 variants)
- Inborn genetic diseases (26 variants)
- Pseudo-TORCH syndrome 1 (20 variants)
- not specified (13 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OCLN gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | |||||
| missense | 50 | 56 | ||||
| nonsense | 6 | |||||
| start loss | 1 | |||||
| frameshift | 5 | |||||
| inframe indel | 2 | |||||
| splice donor/acceptor (+/-2bp) | 3 | |||||
| splice region ? | 1 | 1 | 2 | 4 | ||
| non coding ? | 15 | |||||
| Total | 7 | 7 | 52 | 21 | 8 |
Highest pathogenic variant AF is 0.0000263
Variants in OCLN
This is a list of pathogenic ClinVar variants found in the OCLN region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| OCLN | protein_coding | protein_coding | ENST00000355237 | 8 | 65813 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.56e-7 | 0.923 | 125697 | 1 | 50 | 125748 | 0.000203 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.322 | 239 | 253 | 0.943 | 0.0000128 | 3405 |
| Missense in Polyphen | 80 | 87.457 | 0.91474 | 1228 | ||
| Synonymous | 2.29 | 63 | 90.7 | 0.694 | 0.00000510 | 971 |
| Loss of Function | 1.74 | 13 | 21.7 | 0.598 | 0.00000116 | 325 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000872 | 0.000872 |
| Ashkenazi Jewish | 0.000211 | 0.000198 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000217 | 0.000202 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000982 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in the formation and regulation of the tight junction (TJ) paracellular permeability barrier. It is able to induce adhesion when expressed in cells lacking tight junctions. {ECO:0000269|PubMed:19114660}.;
- Disease
- DISEASE: Pseudo-TORCH syndrome 1 (PTORCH1) [MIM:251290]: An autosomal recessive neurologic disorder with characteristic clinical and neuroradiologic features that mimic intrauterine TORCH infection in the absence of evidence of infection. Affected individuals have congenital microcephaly, intracranial calcifications, and severe developmental delay. {ECO:0000269|PubMed:20727516}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Tight junction - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Pathogenic Escherichia coli infection;VEGFA-VEGFR2 Signaling Pathway;Transcriptional regulation by RUNX1;EMT transition in Colorectal Cancer;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Apoptotic cleavage of cell adhesion proteins;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;RUNX1 regulates expression of components of tight junctions;Transcriptional regulation by RUNX1;TGF-beta receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.395
Intolerance Scores
- loftool
- rvis_EVS
- 0.48
- rvis_percentile_EVS
- 79.25
Haploinsufficiency Scores
- pHI
- 0.379
- hipred
- Y
- hipred_score
- 0.733
- ghis
- 0.508
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.932
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ocln
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; skeleton phenotype; immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; muscle phenotype;
Gene ontology
- Biological process
- cell-cell junction organization;protein-containing complex assembly;response to interleukin-18;bicellular tight junction assembly;cellular response to tumor necrosis factor;regulation of bicellular tight junction assembly
- Cellular component
- plasma membrane;cell-cell junction;bicellular tight junction;integral component of membrane;apical plasma membrane;apicolateral plasma membrane;lateral plasma membrane;cell junction;endocytic vesicle;cytoplasmic vesicle
- Molecular function
- protein binding;protein domain specific binding