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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, Type 3A. An important paralog of this gene is CLRN2.

No data available for Entrez Gene 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

Regulatory Elements for CLRN3 Gene

Enhancers for CLRN3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10F127986 1.4 FANTOM5 Ensembl ENCODE 11.6 -96.6 -96567 6.8 ZNF146 JUN SIN3A FEZF1 ZNF335 ZFHX2 ZNF366 POLR2A ZNF600 ZBTB20 PTPRE CLRN3 GC10P127998 GC10M127969
GH10F127918 1.3 FANTOM5 Ensembl ENCODE 11.3 -30.8 -30768 12.0 CTCF MXI1 JUN MAX SIN3A BRCA1 RAD21 RFX5 GATA3 RCOR1 CLRN3 ENSG00000232259 PTPRE
GH10F127853 0.9 Ensembl ENCODE 11.2 +38.8 38785 0.9 CTCF ZNF654 TRIM22 REST RAD21 POLR2A SMARCA4 SCRT2 ZNF143 SMC3 CLRN3 BUB1P1 PIR59351 GC10M127798
GH10F127942 0.8 Ensembl ENCODE 11.5 -50.2 -50168 2.0 CTCF GATA3 JUN MAX PTPRE CLRN3 ENSG00000232259 ENSG00000227076 GC10M127969
GH10F127967 0.8 Ensembl ENCODE 11.2 -75.7 -75687 1.9 BCL6 NR2F2 EGR2 TRIM28 PTPRE CLRN3 GC10M127969 ENSG00000227076
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLRN3 on UCSC Golden Path with GeneCards custom track

Genomic Location for CLRN3 Gene

127,877,841 bp from pter
127,892,947 bp from pter
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 Asn 83
  • Modification sites at PhosphoSitePlus

Other Protein References for CLRN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLRN3 Gene

Domains & Families for CLRN3 Gene

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

No data available for Gene Families for CLRN3 Gene

Function for CLRN3 Gene

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

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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 IDA 19056867
genes like me logo Genes that share ontologies with CLRN3: view

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

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:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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 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:

genes like me logo Genes that share expression patterns with CLRN3: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt 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 35
  • 98.97 (n)
(Canis familiaris)
Mammalia CLRN3 34 35
  • 80.53 (n)
(Bos Taurus)
Mammalia CLRN3 34 35
  • 79.06 (n)
(Rattus norvegicus)
Mammalia Clrn3 34
  • 76.84 (n)
(Mus musculus)
Mammalia Clrn3 34 16 35
  • 76.4 (n)
(Monodelphis domestica)
Mammalia CLRN3 35
  • 54 (a)
(Gallus gallus)
Aves CLRN3 34 35
  • 56.64 (n)
(Anolis carolinensis)
Reptilia CLRN3 35
  • 45 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clrn3 34
  • 52.44 (n)
(Danio rerio)
Actinopterygii LOC100000502 34
  • 45.48 (n)
CLRN3 35
  • 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)

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 Sequence Context AA Info Type
rs10741297 -- 127,888,315(+) TCCTT(A/G)GGGAG intron-variant
rs10765176 -- 127,883,220(+) GTGGA(A/C)TCTTG intron-variant
rs10765177 -- 127,883,985(+) GGATG(C/T)CAGTT intron-variant
rs10830191 -- 127,882,765(+) GTTAA(A/G)ATGCG intron-variant
rs11018382 -- 127,879,064(+) TGTTT(A/C)TGTCT 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)

Relevant External Links for CLRN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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, type 3a
  • usher syndrome type 3
- elite association - COSMIC cancer census association via MalaCards
Search CLRN3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CLRN3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  2. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A. … Goate A. (Am. J. Hum. Genet. 2006) 3 46 64
  3. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P. … Rogers J. (Nature 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses. (PMID: 12080385) Adato A. … Lancet D. (Eur. J. Hum. Genet. 2002) 2 3 64

Products for CLRN3 Gene

Sources for CLRN3 Gene

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