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Aliases for CLRN2 Gene

Aliases for CLRN2 Gene

  • Clarin 2 2 3 5
  • Clarin-2 3

External Ids for CLRN2 Gene

Previous GeneCards Identifiers for CLRN2 Gene

  • GC04P017126
  • GC04P016871

Summaries for CLRN2 Gene

Entrez Gene Summary for CLRN2 Gene

  • This gene belongs to the clarin family of genes. The clarins appear to belong to a large superfamily of small integral membrane glycoproteins with four transmembrane domains. The exact function of this gene is unknown. [provided by RefSeq, Oct 2008]

GeneCards Summary for CLRN2 Gene

CLRN2 (Clarin 2) is a Protein Coding gene. An important paralog of this gene is CLRN1.

Additional gene information for CLRN2 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLRN2 Gene

Genomics for CLRN2 Gene

GeneHancer (GH) Regulatory Elements for CLRN2 Gene

Promoters and enhancers for CLRN2 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
GH04J017492 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 11.3 -20.9 -20886 3 INSM2 KLF17 ZEB1 GLIS2 ZNF366 FOS ATF7 CREM SP3 RXRA GC04M017492 CLRN2 SNORA75B MED28 LAP3 QDPR GC04P017443
GH04J017543 Enhancer 1.3 FANTOM5 Ensembl ENCODE 11.2 +29.4 29410 1.3 ATF1 PKNOX1 FOXA2 MLX ARID4B ETS1 ATF7 NFKBIZ SP5 ZHX2 DCAF16 MED28 CLRN2 QDPR NCAPG GC04M017552
GH04J017490 Enhancer 1.1 ENCODE dbSUPER 11.2 -24.7 -24700 0.9 PKNOX1 FOXA2 ARID4B YY1 GATA2 RXRA ZHX2 MIER2 REST KAT8 QDPR CLRN2 SNORA75B GC04M017492 GC04P017443
GH04J017481 Enhancer 0.4 FANTOM5 dbSUPER 5.5 -33.0 -33002 0.4 QDPR CLRN2 GC04M017492 GC04P017443
GH04J017978 Enhancer 0.2 FANTOM5 4.6 +463.2 463247 0.4 LCORL CLRN2 KRT18P63
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLRN2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLRN2 gene promoter:
  • FOXD3
  • AML1a
  • Ik-2
  • NF-1/L
  • NF-1
  • FOXJ2 (long isoform)
  • RFX1
  • Pax-4a
  • FOXJ2
  • Olf-1

Genomic Locations for CLRN2 Gene

Genomic Locations for CLRN2 Gene
11,940 bases
Plus strand
11,940 bases
Plus strand

Genomic View for CLRN2 Gene

Genes around CLRN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLRN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLRN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLRN2 Gene

Proteins for CLRN2 Gene

  • Protein details for CLRN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:

    Protein attributes for CLRN2 Gene

    232 amino acids
    Molecular mass:
    25446 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CLRN2 Gene

Post-translational modifications for CLRN2 Gene

Other Protein References for CLRN2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLRN2 Gene

Domains & Families for CLRN2 Gene

Gene Families for CLRN2 Gene

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

Protein Domains for CLRN2 Gene


Suggested Antigen Peptide Sequences for CLRN2 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 CLRN2: view

Function for CLRN2 Gene

Phenotypes for CLRN2 Gene

genes like me logo Genes that share phenotypes with CLRN2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLRN2

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLRN2 Gene

Localization for CLRN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLRN2 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 CLRN2 gene
Compartment Confidence
plasma membrane 3
extracellular 2

Gene Ontology (GO) - Cellular Components for CLRN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CLRN2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLRN2 Gene

Pathways & Interactions for CLRN2 Gene

SuperPathways for CLRN2 Gene

No Data Available

Interacting Proteins for CLRN2 Gene

Gene Ontology (GO) - Biological Process for CLRN2 Gene


No data available for Pathways by source and SIGNOR curated interactions for CLRN2 Gene

Drugs & Compounds for CLRN2 Gene

No Compound Related Data Available

Transcripts for CLRN2 Gene

mRNA/cDNA for CLRN2 Gene

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

Unigene Clusters for CLRN2 Gene

Clarin 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLRN2

Alternative Splicing Database (ASD) splice patterns (SP) for CLRN2 Gene

No ASD Table

Relevant External Links for CLRN2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLRN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLRN2 Gene

mRNA differential expression in normal tissues according to GTEx for CLRN2 Gene

This gene is overexpressed in Testis (x8.4), Brain - Hypothalamus (x5.9), Brain - Spinal cord (cervical c-1) (x5.7), and Brain - Hippocampus (x4.7).

Protein differential expression in normal tissues from HIPED for CLRN2 Gene

This gene is overexpressed in Rectum (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLRN2 Gene

Protein tissue co-expression partners for CLRN2 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLRN2 Gene:


SOURCE GeneReport for Unigene cluster for CLRN2 Gene:

genes like me logo Genes that share expression patterns with CLRN2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLRN2 Gene

Orthologs for CLRN2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLRN2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLRN2 34 33
  • 98.99 (n)
(Canis familiaris)
Mammalia CLRN2 34 33
  • 90.09 (n)
(Bos Taurus)
Mammalia CLRN2 34 33
  • 87.21 (n)
(Mus musculus)
Mammalia Clrn2 16 34 33
  • 85.78 (n)
(Rattus norvegicus)
Mammalia Clrn2 33
  • 85.63 (n)
(Ornithorhynchus anatinus)
Mammalia CLRN2 34
  • 78 (a)
(Monodelphis domestica)
Mammalia CLRN2 34
  • 76 (a)
(Gallus gallus)
Aves CLRN2 34 33
  • 70.83 (n)
(Anolis carolinensis)
Reptilia CLRN2 34
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clrn2 33
  • 65.95 (n)
(Danio rerio)
Actinopterygii LOC795807 33
  • 57.9 (n)
CLRN2 34
  • 49 (a)
Species where no ortholog for CLRN2 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)
  • 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 CLRN2 Gene

Gene Tree for CLRN2 (if available)
Gene Tree for CLRN2 (if available)
Evolutionary constrained regions (ECRs) for CLRN2: view image

Paralogs for CLRN2 Gene

Paralogs for CLRN2 Gene

(1) SIMAP similar genes for CLRN2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CLRN2: view

Variants for CLRN2 Gene

Sequence variations from dbSNP and Humsavar for CLRN2 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000083393 -- 17,521,540(+) C/T intron_variant
rs1000130838 -- 17,513,869(+) C/G upstream_transcript_variant
rs1000358056 -- 17,527,341(+) A/G downstream_transcript_variant
rs1000493695 -- 17,515,818(+) T/C intron_variant
rs1000784977 -- 17,521,778(+) A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLRN2 Gene

Variant ID Type Subtype PubMed ID
nsv1003127 CNV gain 25217958
nsv593781 CNV gain 21841781

Variation tolerance for CLRN2 Gene

Residual Variation Intolerance Score: 71.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.00; 74.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLRN2 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 CLRN2 Gene

Disorders for CLRN2 Gene

Additional Disease Information for CLRN2

No disorders were found for CLRN2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLRN2 Gene

Publications for CLRN2 Gene

  1. 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
  2. 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
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58

Products for CLRN2 Gene

Sources for CLRN2 Gene

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