CLRN1 - clarin 1 Gene

Also Known as RP61; USH3; USH3A

Species: Homo sapiens

Gene Type: protein coding

Gene ID: 7401

About CLRN1

Cytogenetic location: 3q25.1 Genomic coordinates (GRCh38): 3:150,926,163-150,972,999 (from NCBI)

This gene has 8 transcripts (splice variants), 200 orthologues, 2 paralogues and is associated with 7 phenotypes. Biased expression in adrenal (RPKM 2.0), duodenum (RPKM 0.5) and 1 other tissue.

Summary

This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

CLRN1 Products (4)

mRNA	Protein	Name
NM_001195794.1	NP_001182723.1	clarin-1 isoform d
NM_001256819.2	NP_001243748.1	clarin-1 isoform e
NM_052995.2	NP_443721.1	clarin-1 isoform c
NM_174878.3	NP_777367.1	clarin-1 isoform a

Gene Ontology

Molecular Function
Biological Process
Cellular Component

Molecular Function GO Annotation	Evidence	References	Source
enables protein binding	IPI IPI: Inferred from physical interaction	32296183	GOA

Biological Process GO Annotation	Evidence	References	Source
acts upstream of or within actin filament organization	IDA IDA: Inferred from direct assay	19423712	GOA
acts upstream of or within cell motility	IDA IDA: Inferred from direct assay	19423712	GOA
involved in equilibrioception	IMP IMP: Inferred from mutant phenotype	15521980	GOA
involved in photoreceptor cell maintenance	IMP IMP: Inferred from mutant phenotype	15521980	GOA
acts upstream of or within positive regulation of lamellipodium assembly	IDA IDA: Inferred from direct assay	19423712	GOA
involved in sensory perception of light stimulus	IMP IMP: Inferred from mutant phenotype	15521980	GOA
involved in sensory perception of sound	IMP IMP: Inferred from mutant phenotype	15650299	GOA

Cellular Component GO Annotation	Evidence	References	Source
located in lamellipodium	IDA IDA: Inferred from direct assay	19423712	GOA
located in microvillus	IDA IDA: Inferred from direct assay	19423712	GOA
located in plasma membrane	IDA IDA: Inferred from direct assay	19423712	GOA

EXP: Inferred from Experiment IDA: Inferred from direct assay IPI: Inferred from physical interaction IMP: Inferred from mutant phenotype IGI: Inferred from genetic interaction IEP: Inferred from expression pattern

CLRN1 Protein Structure

Claudin_2

0
100
200
232 a.a.

Protein Preferred Names	Protein Names
clarin-1	Usher syndrome type-3 protein

CLRN1 Protein-protein interaction Information

Type	Protein Name	Protein ID	Interactor	Interactor Species	Interactor ID	Detection Method	References
Intra	CLRN1	P58418	NRM	Homo sapiens	Q8IXM6	Validated Y2H	32296183
Intra	CLRN1	P58418	CCL4L1	Homo sapiens	Q8NHW4	Validated Y2H	32296183
Intra	CLRN1	P58418	DRAM1	Homo sapiens	Q8N682	Validated Y2H	32296183
Intra	CLRN1	P58418	TMPRSS4	Homo sapiens	Q9NRS4	Validated Y2H	32296183
Intra	CLRN1	P58418	TMEM239	Homo sapiens	Q8WW34-2	Validated Y2H	32296183
Intra	CLRN1	P58418	TMPPE	Homo sapiens	Q6ZT21	Validated Y2H	32296183
Intra	CLRN1	P58418	CTXN3	Homo sapiens	Q4LDR2	Validated Y2H	32296183
Intra	CLRN1	P58418	BRICD5	Homo sapiens	Q6PL45-2	Validated Y2H	32296183
Intra	CLRN1	P58418	CLDN19	Homo sapiens	Q8N6F1-2	Validated Y2H	32296183
Intra	CLRN1	P58418	C2CD2L	Homo sapiens	O14523	Y2H Prey Pooling	32296183
Intra	CLRN1	P58418	ZDHHC15	Homo sapiens	Q96MV8	Validated Y2H	32296183
Intra	CLRN1	P58418	FAM24B	Homo sapiens	Q8N5W8	Validated Y2H	32296183
Intra	CLRN1	P58418	CANT1	Homo sapiens	Q8WVQ1	Validated Y2H	32296183
Intra	CLRN1	P58418	SLC34A3	Homo sapiens	Q8N130	Validated Y2H	32296183
Intra	CLRN1	P58418	TMEM86B	Homo sapiens	Q8N661	Validated Y2H	32296183
Intra	CLRN1	P58418	TMEM140	Homo sapiens	Q9NV12	Validated Y2H	32296183
Intra	CLRN1	P58418	TMEM222	Homo sapiens	Q9H0R3	Validated Y2H	32296183
Intra	CLRN1	P58418	TMEM147	Homo sapiens	Q9BVK8	Validated Y2H	32296183
Intra	CLRN1	P58418	MFSD5	Homo sapiens	Q6N075	Validated Y2H	32296183
Intra	CLRN1	P58418	ALG8	Homo sapiens	Q9BVK2	Validated Y2H	32296183
Intra	CLRN1	P58418	FUT9	Homo sapiens	Q9Y231	Validated Y2H	32296183
Intra	CLRN1	P58418	UNC50	Homo sapiens	Q53HI1	Validated Y2H	32296183

Cross: Cross-species interaction Intra: Intraspecies interaction

Related Diseases

Diseases	Alias
Usher Syndrome, Type Iiia	Usher Syndrome Type 3 Ush3 Usher Syndrome Type 3a USH3A Usher Syndrome, Type Iii Usher Syndrome, Type 3 Usher Syndrome, Type 3a Usher Syndrome Type Iiia Usher Syndrome 3a Usher'S Syndrome Type 3 Usher Syndrome Iii Usher Syndrome Type Iii
Retinitis Pigmentosa 61	RP61 Retinitis Pigmentosa, Type 61
Retinitis Pigmentosa	RP Rod-Cone Dystrophy Autosomal Recessive Retinitis Pigmentosa Non-Syndromic Retinitis Pigmentosa Pericentral Pigmentary Retinopathy Pigmentary Retinopathy Tapetoretinal Degeneration Rcd Retinitis Pigmentosa Autosomal Recessive ARRP Retinitis Pigmentosa, Autosomal Recessive Retinitis Pigmentosa 1
Rare Genetic Deafness	Rare Genetic Hearing Loss
Usher Syndrome	Deafness-Retinitis Pigmentosa Syndrome Dystrophia Retinae Pigmentosa-Dysostosis Syndrome Graefe-Usher Syndrome Hallgren Syndrome Usher'S Syndrome Retinitis Pigmentosa-Deafness Syndrome Retinitis Pigmentosa-Hearing Loss Syndrome Ush Usher Syndromes
Cone-Rod Dystrophy 2	Cone-Rod Dystrophy CORD2 Cone-Rod Retinal Dystrophy Rcrd2 Cone-Rod Retinal Dystrophy 2 Crd2 Cord Crd Retinal Cone-Rod Dystrophy Cone-Rod Retinal Dystrophy-2 Retinal Cone-Rod Dystrophy 2 Tapetoretinal Degeneration Cone-Rod Degeneration Cone Rod Dystrophy Dystrophy, Cone-Rod Dystrophy, Cone-Rod, Type 2 Retinitis Pigmentosa Retinitis Pigmentosa 2 Progressive Cone-Rod Dystrophy
Fundus Dystrophy	Retinal Dystrophy Retinal Dystrophies Dystrophy, Retinal
Usher Syndrome Type 2	Ush2 Usher Syndrome Type Ii
Usher Syndrome, Type I	USH1 Usher Syndrome Type 1 Us1 Usher Syndrome, Type 1b Usher Syndrome Type 1e Retinitis Pigmentosa And Congenital Deafness Usher Syndrome, Type Ie USH1E Usher Syndrome, Type 1e Usher Syndrome, Type 1a Usher Syndrome, Type Ib Usher Syndrome Type 1b Usher Syndrome Type Ie Usher Syndrome Type I Usher 1 Usher Syndrome, Type 1 Ush1a Usher Syndrome, Type I, French Variety Usher Syndrome, Type Ia Usher Syndrome 1b USH1B Usher'S Syndrome Type 1b Usher Syndrome Type Ib Ushib
Leber Congenital Amaurosis With Early-Onset Deafness	LCAEOD
Deafness, Autosomal Recessive 31	DFNB31 Whirler, Mouse, Homolog Of Autosomal Recessive Nonsyndromic Deafness 31 Autosomal Recessive Deafness 31 Deafness, Autosomal Recessive, 31 Non-Syndromic Neurosensory Deafness Autosomal Recessive Type 31 Non-Syndromic Sensorineural Deafness Autosomal Recessive Type 31 Deafness, Autosomal Recessive, Type 31
Usher Syndrome, Type Ic	USH1C Usher Syndrome Type 1c Usher Syndrome, Type 1c Usher Syndrome Type I Acadian Variety Usher Syndrome Type Ic Usher Syndrome, Type I, Acadian Variety Usher Syndrome 1c Acadian Usher Syndrome Usher'S Syndrome Type 1c
Deafness, Autosomal Recessive 23	DFNB23 Autosomal Recessive Nonsyndromic Deafness 23 Autosomal Recessive Deafness 23 Deafness, Autosomal Recessive, 23 Non-Syndromic Neurosensory Deafness Autosomal Recessive Type 23 Non-Syndromic Sensorineural Deafness Autosomal Recessive Type 23 Deafness, Autosomal Recessive, Type 23
Deafness, Autosomal Dominant 11	DFNA11 Autosomal Dominant Nonsyndromic Deafness 11 Autosomal Dominant Deafness 11 Deafness, Autosomal Dominant, 11 Non-Syndromic Sensorineural Deafness Autosomal Dominant Type 11 Deafness, Autosomal Dominant, Type 11
Phosphoglycerate Dehydrogenase Deficiency	Phgdh Deficiency 3-Phosphoglycerate Dehydrogenase Deficiency PHGDHD 3-Pgdh Deficiency 3-Phosphoglycerate Dehydrogenase Deficiency, Infantile/Juvenile Form Phgdh Deficiency, Infantile/Juvenile Form Deficiency, Phosphoglycerate Dehydrogenase
Usher Syndrome, Type Iid	Usher Syndrome Type 2d USH2D Usher Syndrome, Type 2d Usher Syndrome Type Iid Usher Syndrome 2d Usher Syndrome, Type Ii
Deafness, Autosomal Recessive 12	DFNB12 Deafness, Autosomal Recessive 12, Modifier Of Autosomal Recessive Nonsyndromic Deafness 12 Autosomal Recessive Deafness 12 Deafness, Autosomal Recessive, 12 Congenital Neurosensory Deafness Autosomal Recessive 12 Non-Syndromic Neurosensory Deafness Autosomal Recessive Type 12 Non-Syndromic Sensorineural Deafness Autosomal Recessive Type 12 Deafness, Autosomal Recessive, Type 12
Retinitis Pigmentosa 25	RP25 Retinitis Pigmentosa-25 Retinitis Pigmentosa, Type 25
Auditory System Disease	Ear Diseases Ear And Mastoid Disease
Autosomal Dominant Nonsyndromic Deafness	Autosomal Dominant Deafness
Usher Syndrome, Type Iia	Usher Syndrome Type 2a USH2A Usher Syndrome, Type 2a Usher Syndrome Type Iia Retinal Disease In Usher Syndrome Type Iia, Modifier Of Us2 Ush2 Usher Syndrome 2a Usher'S Syndrome Type 2a Ushiia
Eye Degenerative Disease
Autosomal Recessive Nonsyndromic Deafness	Deafness, Autosomal Recessive, Nonsyndromic
Leber Plus Disease	Leber Congenital Amaurosis Lca Leber'S Amaurosis Leber'S Disease Amaurosis Congenita Of Leber Amaurosis Congenita Of Leber, Type 1 Lhon Plus Disease Congenital Absence Of The Rods And Cones Congenital Retinal Blindness Crb Congenital Amaurosis Of Retinal Origin Leber'S Congenital Amaurosis Leber Congenital Amaurosis 1 Leber'S Congenital Tapetoretinal Degeneration Leber'S Congenital Tapetoretinal Dysplasia Lca1 Leber Congenital Amaurosis Type 1 Retinal Blindness, Congenital Amaurosis, Leber Congenital Dysgenesis Neuroepithelialis Retinae Hereditary Epithelial Dysplasia Of Retina Hereditary Retinal Aplasia Heredoretinopathia Congenitalis Leber Abiotrophy Leber Congenital Tapetoretinal Degeneration Lebers Congenital Amaurosis Optic Atrophy, Hereditary, Leber
Congenital Stationary Night Blindness	Night Blindness, Congenital Stationary Congenital Essential Nyctalopia Oguchi Disease Blindness, Night, Stationary, Congenital
Sensorineural Hearing Loss	Sensory Hearing Loss Sensorineural Deafness Sensorineural Hearing Loss Disorder Hearing Loss, Sensorineural Central Hearing Loss High Frequency Deafness High Frequency Hearing Loss High-Frequency Hearing Loss Perceptive Deafness Perceptive Hearing Loss Perceptive Hearing Loss Or Deafness Hearing Loss Sensorineural Deafness Sensorineural Hearing Loss High-Frequency Hearing Loss, Central Hearing Loss, High-Frequency
Zellweger Syndrome	Cerebrohepatorenal Syndrome Zellweger Leukodystrophy Zs Congenital Iron Overload Chr Zws Severe Pbd-Zsd Severe Peroxisome Biogenesis Disorder-Zellweger Spectrum Disorder
Bardet-Biedl Syndrome	Bbs Biedl-Bardet Syndrome

Diseases	Alias
Waldenstroem'S Macroglobulinemia	Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma

Related Agents

Clinical Phase
Pre-clinical Phase

Clinical Phase

Bioactive Molecules (1)

Cat. No.	Product Name	Effect	Purity	Phase
HY-120726	BF844		/	Phase 1

Pre-clinical Phase

Bioactive Molecules (1)

Cat. No.	Product Name	Effect	Purity	Rare Diseases
HY-RS02836	CLRN1 Human Pre-designed siRNA Set A	Pre-designed Set	/	Unkown

Orthologs Information

Species	Symbol	Source	ID
Rattus norvegicus	CLRN1	RGD	RGD:628779
Bos taurus	CLRN1	VGNC	VGNC:53519
Canis familiaris	CLRN1	VGNC	VGNC:52871
Felis catus	CLRN1	VGNC	VGNC:97384
Mus musculus	CLRN1	MGD	MGI:2388124
Macaca mulatta	CLRN1	VGNC	VGNC:84200
Others	CLRN1	NCBI