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Aliases for CLRN1 Gene

Aliases for CLRN1 Gene

  • Clarin 1 2 3 5
  • Usher Syndrome Type-3 Protein 3 4
  • USH3A 3 4
  • Usher Syndrome 3A 2
  • Clarin-1 3
  • RP61 3
  • USH3 3

External Ids for CLRN1 Gene

Previous HGNC Symbols for CLRN1 Gene

  • USH3
  • USH3A
  • RP61

Previous GeneCards Identifiers for CLRN1 Gene

  • GC03M152127
  • GC03M150643
  • GC03M148017

Summaries for CLRN1 Gene

Entrez Gene Summary for CLRN1 Gene

  • 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]

GeneCards Summary for CLRN1 Gene

CLRN1 (Clarin 1) is a Protein Coding gene. Diseases associated with CLRN1 include Usher Syndrome, Type Iiia and Retinitis Pigmentosa 61. An important paralog of this gene is CLRN2.

UniProtKB/Swiss-Prot for CLRN1 Gene

  • May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.

Gene Wiki entry for CLRN1 Gene

Additional gene information for CLRN1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLRN1 Gene

Genomics for CLRN1 Gene

GeneHancer (GH) Regulatory Elements for CLRN1 Gene

Promoters and enhancers for CLRN1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J150971 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 650.7 +0.6 643 2.5 USF1 ZNF362 NANOG JUN USF2 MIER2 REST FOSL1 CBX8 JUND CLRN1 ENSG00000260234 ENSG00000243273 CLRN1-AS1
GH03J151145 Enhancer 1.2 Ensembl ENCODE dbSUPER 10.5 -173.2 -173187 1.7 RAD21 YY1 ZNF335 SCRT2 ZNF143 RCOR1 FOS DEK ZNF654 RXRA MED12L P2RY14 ENSG00000243273 MINDY4B CLRN1 CLRN1-AS1 GC03M151148
GH03J150925 Enhancer 1.1 FANTOM5 Ensembl ENCODE 11.1 +47.2 47151 0.9 CTCF KLF1 TFAP4 ZNF654 RNF2 SIN3A REST RAD21 XRCC5 CTBP1 MINDY4B ENSG00000243273 CLRN1 CLRN1-AS1 MED12L P2RY14 ENSG00000260234
GH03J150865 Enhancer 1 Ensembl ENCODE 10.1 +107.5 107519 0.6 ZSCAN4 ZNF2 IRF4 RAD21 RFX5 ZNF143 BCLAF1 RUNX3 SMARCA5 ZNF654 ENSG00000243273 MINDY4B CLRN1 CLRN1-AS1
GH03J151002 Enhancer 0.6 ENCODE 11.2 -30.2 -30154 1.7 SOX13 GATAD2A JUND MAFF ZNF316 GLIS1 CREB1 SMAD4 BCL6 FOS MED12L CLRN1 CLRN1-AS1 MINDY4B ENSG00000243273 ENSG00000276055
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLRN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLRN1 gene promoter:
  • LCR-F1
  • Nkx2-5
  • SRY
  • ATF-2
  • FOXO3b
  • FOXO3a
  • FOXO3
  • FOXO4
  • Tal-1beta

Genomic Locations for CLRN1 Gene

Genomic Locations for CLRN1 Gene
54,110 bases
Minus strand
46,837 bases
Minus strand

Genomic View for CLRN1 Gene

Genes around CLRN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLRN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLRN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLRN1 Gene

Proteins for CLRN1 Gene

  • Protein details for CLRN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • D3DNJ3
    • E1ACU9
    • Q8N6A9

    Protein attributes for CLRN1 Gene

    232 amino acids
    Molecular mass:
    25719 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CLRN1 Gene


neXtProt entry for CLRN1 Gene

Post-translational modifications for CLRN1 Gene

  • Glycosylation at Asn48
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CLRN1 Gene

Domains & Families for CLRN1 Gene

Gene Families for CLRN1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for CLRN1 Gene


Graphical View of Domain Structure for InterPro Entry



  • Belongs to the clarin family.
  • Belongs to the clarin family.
genes like me logo Genes that share domains with CLRN1: view

Function for CLRN1 Gene

Molecular function for CLRN1 Gene

UniProtKB/Swiss-Prot Function:
May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.
genes like me logo Genes that share phenotypes with CLRN1: view

Human Phenotype Ontology for CLRN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLRN1 Gene

MGI Knock Outs for CLRN1:
  • Clrn1 Clrn1<tm1.1Kuna>
  • Clrn1 Clrn1<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLRN1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , miRNA , Transcription Factor Targets and HOMER Transcription for CLRN1 Gene

Localization for CLRN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLRN1 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLRN1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 3
golgi apparatus 2
extracellular 1

Gene Ontology (GO) - Cellular Components for CLRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA 19423712
GO:0005902 microvillus IDA 19423712
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030027 lamellipodium IDA 19423712
genes like me logo Genes that share ontologies with CLRN1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLRN1 Gene

Pathways & Interactions for CLRN1 Gene

SuperPathways for CLRN1 Gene

No Data Available

Interacting Proteins for CLRN1 Gene

Gene Ontology (GO) - Biological Process for CLRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007015 actin filament organization IDA 19423712
GO:0007601 visual perception IEA --
GO:0007605 sensory perception of sound IMP 15650299
GO:0010592 positive regulation of lamellipodium assembly IDA 19423712
GO:0045494 photoreceptor cell maintenance IMP 15521980
genes like me logo Genes that share ontologies with CLRN1: view

No data available for Pathways by source and SIGNOR curated interactions for CLRN1 Gene

Drugs & Compounds for CLRN1 Gene

No Compound Related Data Available

Transcripts for CLRN1 Gene

mRNA/cDNA for CLRN1 Gene

(5) REFSEQ mRNAs :
(13) Additional mRNA sequences :
(13) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLRN1 Gene

Clarin 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLRN1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLRN1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6
SP1: - - -
SP2: - - - -
SP4: - -
SP5: - - -

Relevant External Links for CLRN1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLRN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLRN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLRN1 Gene

This gene is overexpressed in Adrenal Gland (x37.6).

NURSA nuclear receptor signaling pathways regulating expression of CLRN1 Gene:


SOURCE GeneReport for Unigene cluster for CLRN1 Gene:


mRNA Expression by UniProt/SwissProt for CLRN1 Gene:

Tissue specificity: Widely expressed. Found in the retina.

Evidence on tissue expression from TISSUES for CLRN1 Gene

  • Eye(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLRN1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
  • penis
  • testicle
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with CLRN1: view

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for CLRN1 Gene

Orthologs for CLRN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLRN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLRN1 34 33
  • 98.78 (n)
(Bos Taurus)
Mammalia CLRN1 33
  • 90.23 (n)
(Canis familiaris)
Mammalia CLRN1 33
  • 88.51 (n)
(Rattus norvegicus)
Mammalia Clrn1 33
  • 86.21 (n)
(Mus musculus)
Mammalia Clrn1 16 33
  • 85.92 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 78 (a)
(Gallus gallus)
Aves -- 34
  • 71 (a)
CLRN1 33
  • 70.34 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clrn1 33
  • 70.83 (n)
(Danio rerio)
Actinopterygii clrn1 34 33
  • 63.79 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4175 33
Species where no ortholog for CLRN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLRN1 Gene

Gene Tree for CLRN1 (if available)
Gene Tree for CLRN1 (if available)
Evolutionary constrained regions (ECRs) for CLRN1: view image

Paralogs for CLRN1 Gene

Paralogs for CLRN1 Gene

(1) SIMAP similar genes for CLRN1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CLRN1: view

Variants for CLRN1 Gene

Sequence variations from dbSNP and Humsavar for CLRN1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1057516687 likely-pathogenic, Usher syndrome, type 3A 150,941,580(-) A/AA splice_donor_variant
rs1057517224 likely-pathogenic, Usher syndrome, type 3A 150,972,696(-) G/A/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant, stop_gained
rs1085307049 pathogenic, Usher syndrome, type 3A 150,928,174(-) AATA/A 3_prime_UTR_variant, coding_sequence_variant, inframe_indel, non_coding_transcript_variant
rs111033258 pathogenic, uncertain-significance, likely-pathogenic, Usher syndrome, type 3A, Retinitis pigmentosa-deafness syndrome, Retinitis Pigmentosa, Dominant, not provided, Retinitis pigmentosa, Usher syndrome 3A (USH3A) [MIM:276902] 150,972,565(-) A/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs111033267 pathogenic, Usher syndrome, type 3A, Retinitis pigmentosa 150,972,520(-) G/A/T coding_sequence_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, stop_gained, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for CLRN1 Gene

Variant ID Type Subtype PubMed ID
esv275573 CNV gain+loss 21479260

Variation tolerance for CLRN1 Gene

Residual Variation Intolerance Score: 26.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.68; 14.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLRN1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLRN1 Gene

Disorders for CLRN1 Gene

MalaCards: The human disease database

(9) MalaCards diseases for CLRN1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type iiia
  • ush3a
retinitis pigmentosa 61
  • rp61
retinitis pigmentosa
  • retinitis pigmentosa 1
usher syndrome
  • retinitis pigmentosa-deafness syndrome
usher syndrome type 2
  • ush2
- elite association - COSMIC cancer census association via MalaCards
Search CLRN1 in MalaCards View complete list of genes associated with diseases


  • Usher syndrome 3A (USH3A) [MIM:276902]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH3 is characterized by postlingual, progressive hearing loss, variable vestibular dysfunction, and onset of retinitis pigmentosa symptoms, including nyctalopia, constriction of the visual fields, and loss of central visual acuity, usually by the second decade of life. {ECO:0000269 PubMed:11524702, ECO:0000269 PubMed:12080385, ECO:0000269 PubMed:12145752, ECO:0000269 PubMed:15521980, ECO:0000269 PubMed:18273898, ECO:0000269 PubMed:23304067}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa 61 (RP61) [MIM:614180]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:21310491}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CLRN1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CLRN1: view

No data available for Genatlas for CLRN1 Gene

Publications for CLRN1 Gene

  1. Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability. (PMID: 15521980) Aller E … Millán JM (Clinical genetics 2004) 3 4 22 58
  2. Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations. (PMID: 12145752) Fields RR … Sumegi J (American journal of human genetics 2002) 3 4 22 58
  3. Two novel disease-causing mutations in the CLRN1 gene in patients with Usher syndrome type 3. (PMID: 23304067) García-García G … Millán JM (Molecular vision 2012) 3 4 58
  4. CLRN1 mutations cause nonsyndromic retinitis pigmentosa. (PMID: 21310491) Khan MI … den Hollander AI (Ophthalmology 2011) 3 4 58
  5. Alternative splice variants of the USH3A gene Clarin 1 (CLRN1). (PMID: 20717163) Västinsalo H … Sankila EM (European journal of human genetics : EJHG 2011) 3 4 58

Products for CLRN1 Gene

Sources for CLRN1 Gene

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