CLRN1 - clarin 1 Gene

Homo sapiens

Also known as RP61; USH3; USH3A

Gene ID: 7401 | Gene type: protein coding

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	Reference	Source
enables protein binding	IPI IPI: Inferred from physical interaction	32296183	GOA

Biological Process GO Annotation	Evidence	Reference	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	Reference	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 Cross Intra	Protein Name	Protein ID	Interactor	Interactor Species	Interactor ID	Detection Method	Reference
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

Pre-clinical Phase

Bioactive Molecules (2)

Cat. No.	Product Name	Effect	Purity	Rare Diseases
HY-RS02836	CLRN1 Human Pre-designed siRNA Set A	Pre-designed Sets	/	Unkown
HY-120726	BF844		/	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

Name
Email *

	Sorry, but the email address you supplied was invalid.