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Aliases for LCA5 Gene

Aliases for LCA5 Gene

  • LCA5, Lebercilin 2 3 5
  • Leber Congenital Amaurosis 5 Protein 3 4
  • C6orf152 3 4
  • Chromosome 6 Open Reading Frame 152 2
  • Leber Congenital Amaurosis 5 2
  • Lebercilin 3

External Ids for LCA5 Gene

Previous HGNC Symbols for LCA5 Gene

  • C6orf152

Previous GeneCards Identifiers for LCA5 Gene

  • GC06U990222
  • GC06M080252
  • GC06M077415

Summaries for LCA5 Gene

Entrez Gene Summary for LCA5 Gene

  • This gene encodes a protein that is thought to be involved in centrosomal or ciliary functions. Mutations in this gene cause Leber congenital amaurosis type V. Alternatively spliced transcript variants are described. [provided by RefSeq, Oct 2009]

GeneCards Summary for LCA5 Gene

LCA5 (LCA5, Lebercilin) is a Protein Coding gene. Diseases associated with LCA5 include Leber Congenital Amaurosis 5 and Leber Congenital Amaurosis. GO annotations related to this gene include protein complex binding. An important paralog of this gene is LCA5L.

UniProtKB/Swiss-Prot for LCA5 Gene

  • Might be involved in minus end-directed microtubule transport.

Gene Wiki entry for LCA5 Gene

Additional gene information for LCA5 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCA5 Gene

Genomics for LCA5 Gene

Regulatory Elements for LCA5 Gene

Enhancers for LCA5 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
GH06H079419 1.2 Ensembl ENCODE 32 +116.2 116234 2.6 INSM2 FEZF1 BATF ZNF2 RFX5 ZNF366 ZSCAN5C SCRT2 ZNF350 ZNF143 PHIP IRAK1BP1 LCA5 HMGN3 HMGN3-AS1 ENSG00000231533 GC06P079428
GH06H079568 1.1 Ensembl ENCODE 15.5 -32.6 -32644 2.8 CTCF ESRRA NFIB ZNF2 RAD21 CHAMP1 YY1 TEAD3 CTBP1 GATA3 SH3BGRL2 LCA5 ENSG00000279659 ENSG00000272137
GH06H079869 1.2 Ensembl ENCODE 12.7 -332.4 -332418 0.6 PKNOX1 RB1 ARID4B ZNF2 RAD21 RFX5 YY1 ZNF302 ZNF143 CREM LCA5 HMGN3 ENSG00000233835 LOC100422671
GH06H079603 1 ENCODE 14 -69.9 -69870 8 FOXA2 MLX ARNT ARID4B DMAP1 TCF12 GATA2 ELK1 MXD4 NCOA1 SH3BGRL2 LCA5 ENSG00000279659
GH06H079599 1.2 Ensembl ENCODE 10.6 -63.2 -63198 2.4 PKNOX1 FOXA2 ARNT FEZF1 ZNF2 TCF12 GATA2 FOS TSHZ1 ZNF518A SH3BGRL2 PHIP LCA5 ENSG00000279659
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LCA5 on UCSC Golden Path with GeneCards custom track

Promoters for LCA5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000199193 -243 2999 HDGF PKNOX1 ARID4B SIN3A ZNF2 YY1 ZNF766 ZNF143 ZNF207 FOS

Genomic Locations for LCA5 Gene

Genomic Locations for LCA5 Gene
52,468 bases
Minus strand

Genomic View for LCA5 Gene

Genes around LCA5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCA5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCA5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCA5 Gene

Proteins for LCA5 Gene

  • Protein details for LCA5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • E1P542
    • Q9BWX7

    Protein attributes for LCA5 Gene

    697 amino acids
    Molecular mass:
    80554 Da
    Quaternary structure:
    • Interacts with NINL. Interacts with OFD1. Interacts with FAM161A.

neXtProt entry for LCA5 Gene

Post-translational modifications for LCA5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LCA5 Gene

No data available for DME Specific Peptides for LCA5 Gene

Domains & Families for LCA5 Gene

Gene Families for LCA5 Gene

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

Protein Domains for LCA5 Gene

Suggested Antigen Peptide Sequences for LCA5 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the LCA5 family.
  • Belongs to the LCA5 family.
genes like me logo Genes that share domains with LCA5: view

Function for LCA5 Gene

Molecular function for LCA5 Gene

UniProtKB/Swiss-Prot Function:
Might be involved in minus end-directed microtubule transport.

Phenotypes From GWAS Catalog for LCA5 Gene

Gene Ontology (GO) - Molecular Function for LCA5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19800048
GO:0032403 protein complex binding IDA 21606596
genes like me logo Genes that share ontologies with LCA5: view
genes like me logo Genes that share phenotypes with LCA5: view

Human Phenotype Ontology for LCA5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for LCA5 Gene

Localization for LCA5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LCA5 Gene

Cytoplasm, cytoskeleton. Cytoplasm, cytoskeleton, cilium axoneme. Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=In non- ciliated cells, localizes to the centrosome and its associated microtubule array.

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 LCA5 gene
Compartment Confidence
cytoskeleton 4
nucleus 3
cytosol 2
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for LCA5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005815 microtubule organizing center IEA --
GO:0005856 cytoskeleton IEA --
GO:0005929 cilium IDA 21606596
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with LCA5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LCA5 Gene

Pathways & Interactions for LCA5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LCA5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with LCA5: view

No data available for Pathways by source and SIGNOR curated interactions for LCA5 Gene

Drugs & Compounds for LCA5 Gene

No Compound Related Data Available

Transcripts for LCA5 Gene

Unigene Clusters for LCA5 Gene

Leber congenital amaurosis 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LCA5 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
SP2: - -
SP3: -

Relevant External Links for LCA5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LCA5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LCA5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LCA5 Gene

This gene is overexpressed in Plasma (34.8), Adrenal (25.5), and Pancreatic juice (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LCA5 Gene

Protein tissue co-expression partners for LCA5 Gene

NURSA nuclear receptor signaling pathways regulating expression of LCA5 Gene:


SOURCE GeneReport for Unigene cluster for LCA5 Gene:


Phenotype-based relationships between genes and organs from Gene ORGANizer for LCA5 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 LCA5: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for LCA5 Gene

Orthologs for LCA5 Gene

This gene was present in the common ancestor of animals.

Orthologs for LCA5 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LCA5 33 34
  • 99.47 (n)
(Canis familiaris)
Mammalia LCA5 33 34
  • 88.71 (n)
(Bos Taurus)
Mammalia LCA5 33 34
  • 83.33 (n)
(Mus musculus)
Mammalia Lca5 33 16 34
  • 76.62 (n)
(Rattus norvegicus)
Mammalia Lca5 33
  • 75.71 (n)
(Monodelphis domestica)
Mammalia LCA5 34
  • 44 (a)
(Ornithorhynchus anatinus)
Mammalia LCA5 34
  • 41 (a)
(Gallus gallus)
Aves LCA5 33 34
  • 62.76 (n)
(Anolis carolinensis)
Reptilia LCA5 34
  • 44 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497171 33
  • 59.69 (n)
Str.17809 33
(Danio rerio)
Actinopterygii lca5 33 34
  • 49.9 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6652 34
  • 17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 23 (a)
Species where no ortholog for LCA5 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)
  • 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 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 LCA5 Gene

Gene Tree for LCA5 (if available)
Gene Tree for LCA5 (if available)

Paralogs for LCA5 Gene

Paralogs for LCA5 Gene

(1) SIMAP similar genes for LCA5 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with LCA5: view

Variants for LCA5 Gene

Sequence variations from dbSNP and Humsavar for LCA5 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs121918165 Pathogenic 79,493,636(-) AGGTA(C/T)AGCGA reference, stop-gained
rs183261547 Pathogenic 79,491,624(+) TTTTC(A/C/G)TAACA reference, synonymous-codon
rs386834252 Pathogenic 79,489,164(-) AAACC(-/C)AATTA nc-transcript-variant, reference, frameshift-variant
rs386834253 Pathogenic 79,487,621(-) TGTTA(-/A)CCTGA intron-variant, reference, frameshift-variant
rs1057519136 Likely pathogenic 79,513,357(-) AGATA(-/A)CAGAA reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for LCA5 Gene

Variant ID Type Subtype PubMed ID
nsv830707 CNV gain 17160897
nsv604052 CNV loss 21841781
nsv463906 CNV loss 19166990
nsv1030126 CNV gain 25217958
nsv1027388 CNV gain 25217958
esv3890891 CNV gain 25118596
esv3609689 CNV gain 21293372
esv3609688 CNV gain 21293372
esv3576196 CNV gain 25503493

Variation tolerance for LCA5 Gene

Residual Variation Intolerance Score: 25.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.68; 93.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LCA5 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCA5 Gene

Disorders for LCA5 Gene

MalaCards: The human disease database

(10) MalaCards diseases for LCA5 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LCA5 in MalaCards View complete list of genes associated with diseases


  • Leber congenital amaurosis 5 (LCA5) [MIM:604537]: 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:17546029, ECO:0000269 PubMed:18000884, ECO:0000269 PubMed:18334959}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LCA5

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 LCA5: view

No data available for Genatlas for LCA5 Gene

Publications for LCA5 Gene

  1. Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. (PMID: 17546029) den Hollander AI … Roepman R (Nature genetics 2007) 2 3 4 60
  2. FAM161A, associated with retinitis pigmentosa, is a component of the cilia-basal body complex and interacts with proteins involved in ciliopathies. (PMID: 22940612) Di Gioia SA … Rivolta C (Human molecular genetics 2012) 3 4 60
  3. Genome-wide association study of hoarding traits. (PMID: 21302353) Perroud N … Mataix-Cols D (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2011) 3 45 60
  4. LCA5, a rare genetic cause of leber congenital amaurosis in Koreans. (PMID: 19172513) Seong MW … Park SS (Ophthalmic genetics 2009) 3 45 60
  5. OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5-encoded lebercilin. (PMID: 19800048) Coene KL … de Brouwer AP (American journal of human genetics 2009) 3 4 60

Products for LCA5 Gene

Sources for LCA5 Gene

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