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Aliases for CLRN3 Gene

Aliases for CLRN3 Gene

  • Clarin 3 2 3 5
  • Transmembrane Protein 12 2 3 4
  • Usher Syndrome Type-3A-Like Protein 1 3 4
  • USH3AL1 3 4
  • TMEM12 3 4
  • Clarin-3 3

External Ids for CLRN3 Gene

Previous HGNC Symbols for CLRN3 Gene

  • TMEM12

Previous GeneCards Identifiers for CLRN3 Gene

  • GC10M129568
  • GC10M129676
  • GC10M123250

Summaries for CLRN3 Gene

GeneCards Summary for CLRN3 Gene

CLRN3 (Clarin 3) is a Protein Coding gene. Diseases associated with CLRN3 include Usher Syndrome. An important paralog of this gene is CLRN2.

Additional gene information for CLRN3 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLRN3 Gene

Genomics for CLRN3 Gene

GeneHancer (GH) Regulatory Elements for CLRN3 Gene

Promoters and enhancers for CLRN3 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
GH10J127884 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.7 +3.9 3854 9.2 FOXA2 RXRA JUN MAX REST GABPA YY1 SP1 JUND ATF3 CLRN3 PTPRE BUB1P1
GH10J127986 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 11.6 -96.6 -96567 6.8 JUN FEZF1 ZFHX2 POLR2A ZNF600 ZBTB20 ZNF189 RXRA CEBPB EP300 PTPRE CLRN3 GC10P127998 GC10M127969
GH10J127917 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 11.3 -28.1 -28073 6.6 CTCF MXI1 JUN MAX GATA3 POLR2A RCOR1 FOSL2 FOS CHD2 CLRN3 PTPRE ENSG00000232259
GH10J127925 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.3 -34.4 -34404 4.7 JUN BRCA1 RFX5 GATA3 POLR2A RCOR1 FOS CHD2 EZH2 TCF7L2 PTPRE CLRN3 ENSG00000232259
GH10J127853 Enhancer 0.8 Ensembl ENCODE 11.2 +38.9 38891 0.7 CTCF ZNF654 MAX TRIM22 REST RAD21 SCRT2 ZNF143 SMC3 SPI1 CLRN3 BUB1P1 PIR59351 GC10M127798
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLRN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLRN3 gene promoter:
  • E2F
  • E2F-4
  • E2F-3a
  • E2F-2
  • E2F-1
  • E2F-5
  • Tal-1
  • E47
  • CBF-A
  • CBF-B

Genomic Locations for CLRN3 Gene

Genomic Locations for CLRN3 Gene
15,107 bases
Minus strand
15,107 bases
Minus strand

Genomic View for CLRN3 Gene

Genes around CLRN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLRN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLRN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLRN3 Gene

Proteins for CLRN3 Gene

  • Protein details for CLRN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q6MZX8

    Protein attributes for CLRN3 Gene

    226 amino acids
    Molecular mass:
    25321 Da
    Quaternary structure:
    No Data Available
    • Sequence=CAE45899.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CLRN3 Gene


neXtProt entry for CLRN3 Gene

Post-translational modifications for CLRN3 Gene

  • Glycosylation at Asn83
  • Modification sites at PhosphoSitePlus

Other Protein References for CLRN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Boster Bio Antibodies for CLRN3
  • Santa Cruz Biotechnology (SCBT) Antibodies for CLRN3

No data available for DME Specific Peptides for CLRN3 Gene

Domains & Families for CLRN3 Gene

Gene Families for CLRN3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for CLRN3 Gene


Suggested Antigen Peptide Sequences for CLRN3 Gene

GenScript: Design optimal peptide antigens:

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 CLRN3: view

Function for CLRN3 Gene

Phenotypes From GWAS Catalog for CLRN3 Gene

genes like me logo Genes that share phenotypes with CLRN3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLRN3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLRN3 Gene

Localization for CLRN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLRN3 Gene

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 CLRN3 gene
Compartment Confidence
extracellular 5
plasma membrane 3
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for CLRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with CLRN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLRN3 Gene

Pathways & Interactions for CLRN3 Gene

SuperPathways for CLRN3 Gene

No Data Available

Interacting Proteins for CLRN3 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: ENSP00000357660 Q8NCR9-CLRN3_HUMAN for CLRN3 Gene via STRING IID

Gene Ontology (GO) - Biological Process for CLRN3 Gene


No data available for Pathways by source and SIGNOR curated interactions for CLRN3 Gene

Drugs & Compounds for CLRN3 Gene

No Compound Related Data Available

Transcripts for CLRN3 Gene

mRNA/cDNA for CLRN3 Gene

(2) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(47) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLRN3 Gene

Clarin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLRN3

Alternative Splicing Database (ASD) splice patterns (SP) for CLRN3 Gene

No ASD Table

Relevant External Links for CLRN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLRN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLRN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLRN3 Gene

This gene is overexpressed in Colon - Transverse (x20.9), Small Intestine - Terminal Ileum (x13.4), Liver (x9.4), and Kidney - Cortex (x6.5).

Protein differential expression in normal tissues from HIPED for CLRN3 Gene

This gene is overexpressed in Liver (18.8), Fetal gut (14.6), Kidney (13.1), and Urine (11.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLRN3 Gene

Protein tissue co-expression partners for CLRN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLRN3 Gene:


SOURCE GeneReport for Unigene cluster for CLRN3 Gene:


Evidence on tissue expression from TISSUES for CLRN3 Gene

  • Liver(4.4)
genes like me logo Genes that share expression patterns with CLRN3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLRN3 Gene

Orthologs for CLRN3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLRN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLRN3 34 33
  • 98.97 (n)
(Canis familiaris)
Mammalia CLRN3 34 33
  • 80.53 (n)
(Bos Taurus)
Mammalia CLRN3 34 33
  • 79.06 (n)
(Rattus norvegicus)
Mammalia Clrn3 33
  • 76.84 (n)
(Mus musculus)
Mammalia Clrn3 16 34 33
  • 76.4 (n)
(Monodelphis domestica)
Mammalia CLRN3 34
  • 54 (a)
(Gallus gallus)
Aves CLRN3 34 33
  • 56.64 (n)
(Anolis carolinensis)
Reptilia CLRN3 34
  • 45 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clrn3 33
  • 52.44 (n)
(Danio rerio)
Actinopterygii LOC100000502 33
  • 45.48 (n)
CLRN3 34
  • 30 (a)
Species where no ortholog for CLRN3 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 CLRN3 Gene

Gene Tree for CLRN3 (if available)
Gene Tree for CLRN3 (if available)
Evolutionary constrained regions (ECRs) for CLRN3: view image

Paralogs for CLRN3 Gene

Paralogs for CLRN3 Gene

genes like me logo Genes that share paralogs with CLRN3: view

Variants for CLRN3 Gene

Sequence variations from dbSNP and Humsavar for CLRN3 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs1000069840 -- 127,886,644(-) C/A/T intron_variant
rs1000123173 -- 127,886,847(-) A/G intron_variant
rs1000675344 -- 127,892,965(-) A/G upstream_transcript_variant
rs1000699834 -- 127,882,507(-) C/T intron_variant
rs1000869913 -- 127,883,325(-) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLRN3 Gene

Variant ID Type Subtype PubMed ID
nsv832020 CNV gain 17160897

Variation tolerance for CLRN3 Gene

Residual Variation Intolerance Score: 73.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.63; 65.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLRN3 Gene

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 CLRN3 Gene

Disorders for CLRN3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLRN3 Gene - From: GeneCards

Disorder Aliases PubMed IDs
usher syndrome
  • retinitis pigmentosa-deafness syndrome
- elite association - COSMIC cancer census association via MalaCards
Search CLRN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLRN3

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 CLRN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLRN3 Gene

Publications for CLRN3 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  2. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 44 58
  3. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses. (PMID: 12080385) Adato A … Lancet D (European journal of human genetics : EJHG 2002) 2 3 58

Products for CLRN3 Gene

Sources for CLRN3 Gene

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