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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. 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

GeneHancer (GH) Regulatory Elements for LCA5 Gene

Promoters and enhancers for LCA5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J079536 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.4 -408 3.3 HDGF PKNOX1 ARID4B SIN3A ZNF2 YY1 POLR2B ZNF766 ZNF213 ZNF207 SH3BGRL2 LCA5 PHIP ENSG00000261970
GH06J079419 Enhancer 1.1 Ensembl ENCODE 32 +116.2 116233 2.6 INSM2 FEZF1 BATF ZNF2 RFX5 ZNF213 ZNF366 ZSCAN5C SCRT2 ZNF350 ENSG00000231533 LOC100506851 PHIP IRAK1BP1 LCA5 HMGN3 HMGN3-AS1 GC06P079428
GH06J079075 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.2 +459.8 459790 4.9 PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 YY1 POLR2B PHIP GC06P079077 IRAK1BP1 ENSG00000233835 LCA5 LOC100419073
GH06J079946 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 9.8 -409.8 -409839 1.8 PKNOX1 SIN3A GLI4 KLF14 ZNF2 ZNF335 GLIS2 ZNF213 ZNF366 KLF13 ELOVL4 GC06M079948 GC06M079947 LCA5 GC06M079915 GC06M079943 LINC01621
GH06J079568 Enhancer 1 Ensembl ENCODE 15.5 -32.6 -32644 2.8 NFIB NEUROD1 ZNF2 RAD21 YY1 CHAMP1 SCRT2 ZNF143 FOS RCOR1 SH3BGRL2 LCA5 ENSG00000279659 ENSG00000272137
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCA5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LCA5 gene promoter:
  • Evi-1
  • aMEF-2
  • MEF-2A
  • CBF-A
  • CBF-B
  • CP1C

Genomic Locations for LCA5 Gene

Genomic Locations for LCA5 Gene
chr6:79,484,991-79,537,458
(GRCh38/hg38)
Size:
52,468 bases
Orientation:
Minus strand
chr6:80,194,708-80,247,175
(GRCh37/hg19)
Size:
52,468 bases
Orientation:
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:
    Q86VQ0-LCA5_HUMAN
    Recommended name:
    Lebercilin
    Protein Accession:
    Q86VQ0
    Secondary Accessions:
    • E1P542
    • Q9BWX7

    Protein attributes for LCA5 Gene

    Size:
    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

Q86VQ0

UniProtKB/Swiss-Prot:

LCA5_HUMAN :
  • Belongs to the LCA5 family.
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:0044877 protein-containing 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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCA5

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

COMPARTMENTS
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: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

mRNA/cDNA for LCA5 Gene

Unigene Clusters for LCA5 Gene

Leber congenital amaurosis 5:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCA5

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
SP1:
SP2: - -
SP3: -

Relevant External Links for LCA5 Gene

GeneLoc Exon Structure for
LCA5
ECgene alternative splicing isoforms for
LCA5

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 and MOPED for LCA5 Gene



Protein tissue co-expression partners for LCA5 Gene

NURSA nuclear receptor signaling pathways regulating expression of LCA5 Gene:

LCA5

SOURCE GeneReport for Unigene cluster for LCA5 Gene:

Hs.21945

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • olfactory bulb
  • skull
Abdomen:
  • liver
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia LCA5 34 33
  • 99.47 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LCA5 34 33
  • 88.71 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LCA5 34 33
  • 83.33 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lca5 16 34 33
  • 76.62 (n)
rat
(Rattus norvegicus)
Mammalia Lca5 33
  • 75.71 (n)
oppossum
(Monodelphis domestica)
Mammalia LCA5 34
  • 44 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LCA5 34
  • 41 (a)
OneToOne
chicken
(Gallus gallus)
Aves LCA5 34 33
  • 62.76 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LCA5 34
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497171 33
  • 59.69 (n)
Str.17809 33
zebrafish
(Danio rerio)
Actinopterygii lca5 34 33
  • 49.9 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG6652 34
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 23 (a)
OneToOne
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

ENSEMBL:
Gene Tree for LCA5 (if available)
TreeFam:
Gene Tree for LCA5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LCA5: view image

Paralogs for LCA5 Gene

Paralogs for LCA5 Gene

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

  • LCA5_HUMAN
  • A7X9N5_HUMAN
  • S4R3K6_HUMAN
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 Variation AA Info Type
rs1013107942 uncertain-significance, Leber congenital amaurosis 79,513,744(-) A/T intron_variant
rs1021714733 uncertain-significance, Leber congenital amaurosis 79,537,224(-) C/T 5_prime_UTR_variant
rs1057174 uncertain-significance, Leber congenital amaurosis 79,485,960(-) T/G 3_prime_UTR_variant
rs114426854 uncertain-significance, Leber congenital amaurosis 79,513,346(-) G/A coding_sequence_variant, synonymous_variant
rs115317386 uncertain-significance, Leber congenital amaurosis 79,492,659(-) C/G/T intron_variant

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

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

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)

Additional Variant Information for LCA5 Gene

Human Gene Mutation Database (HGMD)
LCA5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCA5

SNP Genotyping and Copy Number Assay Products

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

Disorders for LCA5 Gene

MalaCards: The human disease database

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

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

UniProtKB/Swiss-Prot

LCA5_HUMAN
  • 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.

Additional Disease Information for LCA5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 58
  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 58
  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 44 58
  4. 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 58
  5. LCA5, a rare genetic cause of leber congenital amaurosis in Koreans. (PMID: 19172513) Seong MW … Park SS (Ophthalmic genetics 2009) 3 44 58

Products for LCA5 Gene

Sources for LCA5 Gene

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