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Aliases for RD3 Gene

Aliases for RD3 Gene

  • Retinal Degeneration 3 2 3 5
  • Retinal Degeneration Protein 3 3 4
  • C1orf36 3 4
  • Chromosome 1 Open Reading Frame 36 2
  • Protein RD3 3
  • LCA12 3

External Ids for RD3 Gene

Previous HGNC Symbols for RD3 Gene

  • C1orf36

Previous GeneCards Identifiers for RD3 Gene

  • GC01M209717
  • GC01M211649
  • GC01M182327

Summaries for RD3 Gene

Entrez Gene Summary for RD3 Gene

  • This gene encodes a retinal protein that is associated with promyelocytic leukemia-gene product (PML) bodies in the nucleus. Mutations in this gene cause Leber congenital amaurosis type 12, a disease that results in retinal degeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

GeneCards Summary for RD3 Gene

RD3 (Retinal Degeneration 3) is a Protein Coding gene. Diseases associated with RD3 include Leber Congenital Amaurosis 12 and Leber Congenital Amaurosis. An important paralog of this gene is RD3L.

Additional gene information for RD3 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 RD3 Gene

Genomics for RD3 Gene

GeneHancer (GH) Regulatory Elements for RD3 Gene

Promoters and enhancers for RD3 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
GH01I211492 Promoter 0.8 EPDnew 550.8 +0.7 742 0.1 ZFHX2 RFX1 ZSCAN4 RCOR1 CHD2 EGR2 ENSG00000223649 RD3 ARPC3P2
GH01I211344 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 18 +148.5 148514 0.5 LEF1 ZNF644 ZBTB40 FOSL1 CTBP1 ZNF766 EGR1 NFE2 ATF7 CREM RD3 TRAF5 LINC00467
GH01I211646 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -155.7 -155716 4.7 ARID4B ZNF143 FOS NFYC REST PPARG NFIL3 MAFF MIER3 GMEB1 SNORA16B SLC30A1 ENSG00000223649 RD3 LOC91548 NEK2 ENSG00000228792 LINC01693 FDPSP8
GH01I211641 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.2 -150.6 -150554 4.3 FOXA2 MLX ARID4B FEZF1 ZNF48 YY1 TCF12 SLC30A9 ZNF121 GLIS2 ENSG00000228792 SLC30A1 ENSG00000223649 RD3 LOC91548 NEK2 LINC01693 FDPSP8
GH01I211638 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.4 -146.7 -146726 2.6 MXI1 FOXA2 JUN MAX KLF17 GTF3C2 POLR2A RCOR1 FOS TCF7L2 LINC01693 SLC30A1 ENSG00000223649 RD3 LOC91548 NEK2 ENSG00000260805 ENSG00000228792 LOC105372903
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RD3 gene promoter:

Genomic Locations for RD3 Gene

Genomic Locations for RD3 Gene
16,396 bases
Minus strand

Genomic View for RD3 Gene

Genes around RD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RD3 Gene

Proteins for RD3 Gene

  • Protein details for RD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein RD3
    Protein Accession:
    Secondary Accessions:
    • A8K595

    Protein attributes for RD3 Gene

    195 amino acids
    Molecular mass:
    22704 Da
    Quaternary structure:
    No Data Available

neXtProt entry for RD3 Gene

Post-translational modifications for RD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RD3 Gene

Domains & Families for RD3 Gene

Gene Families for RD3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for RD3 Gene


Suggested Antigen Peptide Sequences for RD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RD3: view

No data available for UniProtKB/Swiss-Prot for RD3 Gene

Function for RD3 Gene

Phenotypes From GWAS Catalog for RD3 Gene

Gene Ontology (GO) - Molecular Function for RD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with RD3: view
genes like me logo Genes that share phenotypes with RD3: view

Human Phenotype Ontology for RD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for RD3 Gene

Localization for RD3 Gene

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 RD3 gene
Compartment Confidence
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
peroxisome 1
cytosol 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for RD3 Gene

Pathways & Interactions for RD3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception IEA --
GO:0050896 response to stimulus IEA --
GO:0060041 retina development in camera-type eye IEA --
genes like me logo Genes that share ontologies with RD3: view

No data available for Pathways by source and SIGNOR curated interactions for RD3 Gene

Drugs & Compounds for RD3 Gene

No Compound Related Data Available

Transcripts for RD3 Gene

Unigene Clusters for RD3 Gene

Retinal degeneration 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RD3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4
SP1: -
SP2: -

Relevant External Links for RD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RD3 Gene

This gene is overexpressed in Esophagus - Gastroesophageal Junction (x4.4).

Protein differential expression in normal tissues from HIPED for RD3 Gene

This gene is overexpressed in Retina (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RD3 Gene

Protein tissue co-expression partners for RD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of RD3 Gene:


SOURCE GeneReport for Unigene cluster for RD3 Gene:


mRNA Expression by UniProt/SwissProt for RD3 Gene:

Tissue specificity: Preferentially expressed in retina.

Evidence on tissue expression from TISSUES for RD3 Gene

  • Eye(4.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RD3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • olfactory bulb
  • skull
  • liver
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with RD3: view

Orthologs for RD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RD3 33 34
  • 98.46 (n)
(Bos Taurus)
Mammalia RD3 33 34
  • 85.57 (n)
(Canis familiaris)
Mammalia RD3 33 34
  • 84.85 (n)
(Rattus norvegicus)
Mammalia Rd3 33
  • 84.79 (n)
(Mus musculus)
Mammalia Rd3 33 16 34
  • 83.25 (n)
(Monodelphis domestica)
Mammalia RD3 34
  • 74 (a)
(Ornithorhynchus anatinus)
Mammalia RD3 34
  • 66 (a)
(Gallus gallus)
Aves RD3 33 34
  • 69.26 (n)
(Anolis carolinensis)
Reptilia RD3 34
  • 66 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rd3 33
  • 64.96 (n)
(Danio rerio)
Actinopterygii rd3 33 34
  • 62.39 (n)
Species where no ortholog for RD3 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 RD3 Gene

Gene Tree for RD3 (if available)
Gene Tree for RD3 (if available)

Paralogs for RD3 Gene

Paralogs for RD3 Gene

genes like me logo Genes that share paralogs with RD3: view

Variants for RD3 Gene

Sequence variations from dbSNP and Humsavar for RD3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1003319773 uncertain-significance, Leber congenital amaurosis 211,476,955(-) G/A 3_prime_UTR_variant
rs1006577121 uncertain-significance, Leber congenital amaurosis 211,492,257(-) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1012912070 uncertain-significance, Leber congenital amaurosis 211,476,634(-) T/C 3_prime_UTR_variant
rs1044314717 uncertain-significance, Leber congenital amaurosis 211,491,781(-) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1048579109 uncertain-significance, Leber congenital amaurosis 211,492,088(-) T/C 5_prime_UTR_variant, genic_upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RD3 Gene

Variant ID Type Subtype PubMed ID
esv2675306 CNV deletion 23128226
esv29853 CNV loss 19812545
esv3588733 CNV gain 21293372
esv3588734 CNV loss 21293372
nsv832514 CNV loss 17160897

Variation tolerance for RD3 Gene

Residual Variation Intolerance Score: 85% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.63; 56.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RD3 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 RD3 Gene

Disorders for RD3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for RD3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search RD3 in MalaCards View complete list of genes associated with diseases


  • Leber congenital amaurosis 12 (LCA12) [MIM:610612]: A severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. {ECO:0000269 PubMed:17186464}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RD3

genes like me logo Genes that share disorders with RD3: view

No data available for Genatlas for RD3 Gene

Publications for RD3 Gene

  1. Identification and characterization of C1orf36, a transcript highly expressed in photoreceptor cells, and mutation analysis in retinitis pigmentosa. (PMID: 12914764) Lavorgna G … Banfi S (Biochemical and biophysical research communications 2003) 2 3 4 58
  2. Premature truncation of a novel protein, RD3, exhibiting subnuclear localization is associated with retinal degeneration. (PMID: 17186464) Friedman JS … Swaroop A (American journal of human genetics 2006) 3 4 58
  3. 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
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for RD3 Gene

Sources for RD3 Gene

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