OCLN

occludin, the group of MARVEL domain containing|Tetraspan junctional complex superfamily|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 5:69492292-69558104

Links

ENSG00000197822

∙ NCBI:100506658 ∙ OMIM:602876 ∙ HGNC:8104 ∙ Uniprot:Q16625 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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: CGD

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 ClinVar and linked to the OCLN gene.

Pseudo-TORCH syndrome 1 (5 variants)
not provided (3 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				10 clinvar	1 clinvar	11
missense			55 clinvar	5 clinvar	1 clinvar	61
nonsense	4 clinvar	2 clinvar				6
start loss				1 clinvar		1
frameshift	2 clinvar	3 clinvar	1 clinvar			6
inframe indel			2 clinvar			2
splice donor/acceptor (+/-2bp)	1 clinvar	2 clinvar				3
splice region	1		1	2		4
non coding				9 clinvar	6 clinvar	15
Total	7	7	58	25	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.

Position	Phenotype	Significance	ClinVar
5-69492434-G-A		Benign (Sep 17, 2019)	1276122
5-69492642-C-T		Benign (Apr 18, 2018)	378309
5-69492653-G-A	not specified	Likely benign (Jun 30, 2016)	387208
5-69492675-C-G	not specified	Likely benign (Feb 02, 2018)	515390
5-69492986-C-T		Benign (Sep 17, 2019)	1247058
5-69493132-C-T		Benign (Jun 17, 2020)	1174443
5-69504175-A-G		Uncertain significance (Sep 16, 2018)	591558
5-69504248-T-C	Pseudo-TORCH syndrome 1	Uncertain significance (Mar 04, 2013)	159461
5-69504256-G-C	Inborn genetic diseases	Uncertain significance (Dec 15, 2022)	2335739
5-69504266-AG-A		Likely pathogenic (Mar 07, 2018)	817656
5-69504278-T-TA		Pathogenic (Jan 26, 2024)	2711780
5-69504296-T-C	Pseudo-TORCH syndrome 1	Likely pathogenic (Oct 19, 2019)	1029458
5-69504312-T-C		Likely benign (Jun 13, 2022)	1654237
5-69508917-T-C		Benign (Jun 30, 2018)	1240479
5-69508998-T-C		Benign (Jun 26, 2018)	1264011
5-69509129-T-C		Likely benign (Aug 22, 2022)	1631125
5-69509133-C-A		Likely benign (Aug 15, 2022)	1674076
5-69509141-CAAACCGAATCATTATGCACCAAGCAATGACATATATGGTGGAGAGATGCATGTTCGACCAATGCTCTCTCAGCCAGCCTACTCTTTTTACCCAGAAGATGAAATTCTTCACTTCTACAAATGGACCTCTCCTCCAGGAGTGATTCGGATCCTGTCTATGCTCATTATTGTGATGTGCATTGCCATCTTTGCCTGTGTGGCCTCCACGCTTGCCTGGGACAGAGGCTATGGAACTTCCCTTTTAGGAGGTAGTGTAGGCTACCCTTATGGAGGAAGTGGCTTTGGTAGCTACGGAAGTGGCTATGGCTATGGCTATGGTTATGGCTATGGCTACGGAGGCTATACAGACCCAAGAGCAGCAAAGGGCTTCATGTTGGCCATGGCTGCCTTTTGTTTCATTGCCGCGTTGGTGATCTTTGTTACCAGTGTTATAAGATCTGAAATGTCCAGAACAAGAAGATACTACTTAAGTGTGATAATAGTGAGTGCTATCCTGGGCATCATGGTGTTTATTGCCACAATTGTCTATATAATGGGAGTGAACCCAACTGCTCAGTCTTCTGGATCTCTATATGGTTCACAAATATATGCCCTCTGCAACCAATTTTATACACCTGCAGCTACTGGACTCTACGTGGATCAGTATTTGTATCACTACTGTGTTGTGGATCCCCAGGAGGTATGAGTGGTGTTTTGGGTTTTTTCTCCATCTCCTTAGCAGAGGCCTTCAACTTGAGATATGTGATAGAATCACTCTGGAAACTCTTAAAAAATATTGATGACAAGGCTCCACTTCTAATTAAATCTGGGGGAGGGGCTGAGTCTCATTAAGATATGATTAACATACCATGTAATTTGATTACTTAAATAACAGTTCAGTGGTTTTTAATATATTCACAGAATTGTGCCACCATCACCACAATCAATTTTAGAACATTTTCACTATCCTAAAAAGAAACTTGTACCCGTTAGCGGTCACTCCTCATTTCCCTAACCATTCTTAGCCCTAGGCAACCACTAATCCTACATCTATAAATTTGTCTATTCTCTAGGTATTTCATATAAATGGAATCACACAATGTGGTCTTTGTGATGGGCTTCTTTTACGTAGCATAATGTTTTTAAGGTTTACCCATGTCATAGCTTGTGCCATTCTCTCATTCCTTTTTATTGCTAATATTCCAGTGTGTGGATAAACCACATTTTATTTATCAGTTGATAGACATTTGTGTCTACATTGGCTATTAAGAATCATGCTAGACTGGGCACGGTGGCTCATGCTTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCATGAGGTCAGGAGATTGTGACCATCCTCGCTAATAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAATTAGCTGGGCATGGTGGCAGGCACCTGTAGTCCCAGCTACTCGGGAGGCTCAGGCAGAAGAAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCTGAGATTGCGCCACTGCACTCCAGCCTGAGCGACAGAGCAAGACTCCATCTCAAAAAAAAAGAATCATGCTATAGACATTCTTGTATACGTTTTTGTGTGAACCTATGTTTTAATGATTTCTTGAGTTGGGTTATACCTAGGGGTGGAATTGCTGGGTCATATGGTGACTCTTTAATCTTTTGGGGAGCTACCAGAGTTTTTCCAAAGAGTTTGCATCATTTTACATTCACATCAGAAATGTATGAAAGTTCCAATTTCTCCACATCCTCACCAACACTTGTTATTGTCTGATTCTAGCCATGCTGATGGGTGAGAAGTGAAGTGGTGCTTTATTGTGATTTTGATTCGTATTTTCTTTATAGCTAATGTTATTAGCTATATAGTCATGTACTTATTGGCCATTTCTCTCTTATCTTTGGAGAAATGGCTGTTTAGACTTGTCCATTTTTTTTTTCTTTTTGAGACGGAGTCTTGCTCTATCGCCCAGGCTGGAGTGCAGTGGTGTGATCTTTGCTCACTGTGAGCTACGCCTCCTGGGTTCACACCATTCTCCTGCCTCAGCCTCCTGAATAGCTGGGACTACAGGCACCGGCCACCACGCCCAGCTAATTTTTTTTTTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCGTGTTAGCCACGATGGTCTCTATCTTCTGACCTCGTGATCCGCCCGCCTCGGCCTCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGTGCCCGGCCTAGACTTGCCCATGTTTTAATTGGGCTATTTTTGTTGTTGTTTTGTTTTTGAGACAGAGTCTCACTGTCACCCAGGCTGGGGTGCAGTGGTGCAGTCACAGCTCACTGCATCCTTGACCTCCTGGGCTCAAGTGACCCTCCTACCTCAGTCTCCTGAGTAGCTAGGACCACAGGGGCATGCCACCACACCCGGATAATTTTTTAAAAAATTTTTTGTAGAGACAGGGTCTCACTTTGTTGCCCGGTCTGGGCTGGAACTCCTGGGCTCAAGTGATCCTGCCTTGGCCTTCCAAACCGCTGGGATTATAGGCATCTTTTCACTTTCTTGATGGTGTCCTTTGCATAAAAGCTTTTAGTTTTGGGCCGGGCATGGTAGCTCACGCCTGTAATCCCAGCACTTTGGAAGGCCAAGGTGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACTCCATCTCTACTAAAAATAGAAAAATTACCTGGACACGGTGGCGTGCCTGTAATCCCAGCTACTCAGTAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCTGAAATTGTGCCACTGCACTCCAGCCTAGACAACAAGAGCAAAACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAATTTTTAGTTTTGATGATGTCCAGTTTATTTAATTTTTCTTCTGTTGCTTGTATTTTTGGTGTCATATCTAATGCTTTGCCTAATTCAGGGTCACAAGGATTTACTCCTATGTTTTCTATTATTTAATTTTTCTATAGTTTCATAATTTTAGCTTTTACAGTTAGGTCTGTGATTCATGTTGTGTTAATTTTGGGCATGATGGAAGCAAGGGTTCTGAAAGCTTTCGCATGTTTATATGCAGTTGTCTCAGTGTTACTTGTTGAAAGGACTGTTCCTCCACTAAGTTTTCTTCATGCCTTTGTCAAAAATGAATTGATCATAAATGTGGACATTTATTTCTGGGCTCTCAGTTCAGCTGCATTAATCATATGTCCTAATGCCAGTACCATACTGTCTTGATTACTGTAACTTTATAGTAAGTTTTGAAATTGTGGAGTGGGAGTTCTCCAACTTTGTTCTTCAAGACTGTTTTGGCTAGATTCTGGATTCCTTGCATTTCCATATGGATTTTAAGATCAGCATGTCAATTTTGGAAAAAAATGCCAGCTAGGATTTTGAAGGGTTATATTGAATCTGTAGGTCAATTTTGGATGTATTGTCATCTTTACAATTACAAGTCTTCTGATTCATGAACGTAAGATTCTTTTGATTTATGTAGGTCTTGTTAAACTTCTTTTAATAGTGTTTTATAGTTTTCAGAGTGTAAGTTAGTATGTTTAAAAGCTAAGCAAGTGATTCAAATGTGCAGGTTGGAGTTGAGAAACCTACTTTAGTAACCATGAGTCATACTGATTATATTAATATCTGAAATGTTTCTGAGTTACTGATCTTTTTTCCCTTGTTTTTCCTTTTTTCTTACACTAACTCAGGAGTTCCCATTCCTGAATGAGTCACTCCTTTGGAGTTAGACCTCTAGTATCTGTCTACCATTATTTAGAAGACTGAAGGTTTTCCCTGCAGACGTAGGTTTTCACAGTGCTCGTTGTTGCCATTTAGACATGTCCATGGTAGATAGGGACTGAGGGTTGGTACTCCTATCCTACCACACCCCTATCCCTCTTAGTTCTCTTACTACTTACTCTTTGAAAAATGATGTCACTGTCAAGACAGCTGGAAGGAGAGCCTCTTGTTCCCATTAGCAGACATCCAGGGTAGAGGCCTGATATTTCCCTCAACTTCAAGTGCCTCCCAGGCCAATATACCATTTAATATCCTATCACCACTGGGAGAACTGTTAAGAGTAGGAAGTTTCTTTGTTACAGGGCCCTTTCTAGTAGTATGCAAGACTCCTGAAACAGAGAAACCTGCCAGACCAAATCAATCATTAGTCAATTTGCTATTTATAGCTTGATTAGATCCATGTCTTCATCATTTTTGGTAAGATAGAGATCTATGGACAGAAATTTACATTCAGTGTAAAAAGGCTTGCCAAGCATATGTTTTGAACAAGATTACAAGCATGATTGGCTATTTCAAAGCTGTGAATACTTTTGAGAGTAGCATTTTTCAGGCCCTTTAGAAGTATACCAATGATTGAGTTACTTTACTGGCCATTCTCGTAGGTGCACAAAGCTTGGCCCGTAGGTGTACAAGCTTTGGAACTAGTTTTTTACAGCTCTGAAATGAGGGTGATGATTGATAGTTCCTAACATTAGGCATTTTCTGAGGATTGAGTCAAGCAGTATGTACGTGTGTGTACATTTGCTGGCCTTAGCCCAGTTAGTGTGGGTTAGGTTTTATGATATGTCTGAAATGTAACTATTTGCTTCAGTTTTCTATCAATTAAACCACATGGATTTAGTAGGGCCTTAGGGTAGATAAGGGTTTTAATAATATGTAGAGGGTGAATTGTGATTAAGCAATTAAAATCTAATTATGCCAATATTTTCCACTCCTTTTTAGGCCATTGCCATTGTACTGGGGTTCATGATTATTGTGGCTTTTGCTTTAATAATTTTCTTTGCTGTGAAAACTCGAAGAAAGATGGACAGGTATGACAAGTCCAATATTTTGTGGGACAAGGAACACATTTATGATGAGCAGCCCCCCAATGTCGAGGAGTGG-C	Pseudo-TORCH syndrome 1	Pathogenic (-)	1065616
5-69509147-G-A		Likely benign (Dec 31, 2022)	2878760
5-69509160-C-G	not specified • Pseudo-TORCH syndrome 1	Benign/Likely benign (Jul 01, 2024)	159462
5-69509196-C-T	Pseudo-TORCH syndrome 1 • OCLN-related disorder	Pathogenic (Jul 15, 2019)	1029457
5-69509211-C-G	Inborn genetic diseases	Uncertain significance (Jul 08, 2022)	1309456
5-69509224-CTT-C		Pathogenic (Apr 12, 2022)	2125619
5-69509251-A-C	Inborn genetic diseases	Uncertain significance (Feb 03, 2022)	2275724
5-69509259-AAATGGACCTCTCCTCCAGGAGTG-A	Pseudo-TORCH syndrome 1	Pathogenic (Sep 10, 2010)	6750

GnomAD

Source: gnomAD

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: dbNSFP

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