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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

LCA5 Gene

protein-coding   GIFtS: 49
GCID: GC06M080252

Leber congenital amaurosis 5

(Previous name: chromosome 6 open reading frame 152 )
(Previous symbol: C6orf152)
 Explore 11 diseases affiliated with
LCA5 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for LCA5    

Aliases
for LCA5 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Leber Congenital Amaurosis 51 2
C6orf1521 2 3 5
Leber Congenital Amaurosis 5 Protein2 3
Chromosome 6 Open Reading Frame 1521
Lebercilin2

External Ids:    HGNC: 319231   Entrez Gene: 1676912   Ensembl: ENSG000001353387   OMIM: 6114085   UniProtKB: Q86VQ03   

Export aliases for LCA5 gene to outside databases

Previous GC identifers: GC06U990222 GC06M077415


Summaries
for LCA5 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for LCA5:
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)

UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0
Function: Might be involved in minus end-directed microtubule transport

Gene Wiki entry for LCA5


Genomic Views
for LCA5 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NT_007299.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LCA5 gene promoter:
         MEF-2A   CBF-B   CBF-A   CP1C   aMEF-2   Evi-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: LCA5 promoter sequence
   Search SABiosciences Chromatin IP Primers for LCA5

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LCA5


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q14.1   Ensembl cytogenetic band:  6q14.1   HGNC cytogenetic band: 6q14

LCA5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LCA5 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M080252:  view genomic region     (about GC identifiers)

Start:
 80,194,708 bp from pter      End:
 80,247,175 bp from pter
Size:
 52,468 bases      Orientation:
 minus strand

Proteins
for LCA5 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0 (See protein sequence)
Recommended Name: Lebercilin  
Size: 697 amino acids; 80554 Da
Subunit: Interacts with NINL. Interacts with OFD1. Interacts with FAM161A
Subcellular location: Cytoplasm, cytoskeleton. Cytoplasm, cytoskeleton, cilium axoneme. Cytoplasm, cytoskeleton, cilium
basal body. Cytoplasm, cytoskeleton, centrosome. Note=In non-ciliated cells, localizes to the centrosome and its
associated microtubule array
Secondary accessions: E1P542 Q9BWX7

Explore the universe of human proteins at neXtProt for LCA5: NX_Q86VQ0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q86VQ0

    • LCA5 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001116241.1  NP_859065.2  

    ENSEMBL proteins: 
     ENSP00000358861   ENSP00000376686  

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    Uscn Proteins for LCA5

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005929cilium IDA--
    GO:0005932microtubule basal body IEA--
    GO:0035085cilium axoneme IEA--


    LCA5 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for LCA5

    Protein Domains /
    Families
    for LCA5 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    LCA5 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR026684 Lebercilin
     IPR026188 Lebercilin-like

    Graphical View of Domain Structure for InterPro Entry Q86VQ0

    ProtoNet protein and cluster: Q86VQ0

    UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0
    Similarity: Belongs to the LCA5 family


    Function
    for LCA5 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0
    Function: Might be involved in minus end-directed microtubule transport

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat LCA5
    8/26 QIAGEN miScript miRNA Assays for microRNAs that regulate LCA5 (see all 26):
    hsa-miR-323-3p hsa-miR-607 hsa-miR-429 hsa-miR-15a hsa-miR-503 hsa-miR-374a hsa-miR-138-2* hsa-miR-424
    SwitchGear 3'UTR luciferase reporter plasmid: LCA5 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Clone
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    Cell Line
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    Search LifeMap BioReagents cell lines for LCA5

    In Situ Assay
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
    GO:0032403protein complex binding IDA--


    LCA5 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for LCA5:
     Decreased viability of wild-ty  Downregulation of NF-kappaB pa  Increased cell number in G1, a 

    Animal Models:
         3 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Lca5):
     nervous system  pigmentation  vision/eye 

    LCA5 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for LCA5 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for LCA5

    1 Interacting protein for LCA5 (Q86VQ03) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GRIN2BQ132243I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015031protein transport IEA--


    LCA5 for ontologies           About GeneDecksing



    Drugs & Compounds
    for LCA5 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for LCA5
    Search CenterWatch for drugs/clinical trials and news about LCA5 

    Transcripts
    for LCA5 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for LCA5 gene (2 alternative transcripts): 
    NM_001122769.2  NM_181714.3  

    Unigene Cluster for LCA5:

    Leber congenital amaurosis 5
    Hs.21945  [show with all ESTs]
    Unigene Representative Sequence: BC050327
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000369846 ENST00000392959(uc003piy.3 uc003pix.3 uc011dyr.2)
    ENST00000467898

    miRNA
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    8/26 QIAGEN miScript miRNA Assays for microRNAs that regulate LCA5 (see all 26):
    hsa-miR-323-3p hsa-miR-607 hsa-miR-429 hsa-miR-15a hsa-miR-503 hsa-miR-374a hsa-miR-138-2* hsa-miR-424
    SwitchGear 3'UTR luciferase reporter plasmid: LCA5 3' UTR sequence
    Inhib. RNA
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    Clone
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    GenScript: all cDNA clones in your preferred vector: LCA5 (NM_152505)
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    Additional cDNA sequence: 

    AK299314.1 AL832214.1 BC050327.1 BX648161.1 

    2 DOTS entries:

    DT.40247242  DT.100751233 

    24/56 AceView cDNA sequences (see all 56):

    AI742190 AI287818 Z44254 CD671730 BQ226190 AI922939 BX097952 BM053085 
    CK824735 AW166971 BM263977 BQ025475 F01653 BU102073 BG720047 BM264279 
    BQ022524 BC050327 AA864885 BX648161 AL832214 AW902230 AA348619 AA490709 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for LCA5    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
    SP1:                                                                              
    SP2:                    -     -                                                   
    SP3:                    -                                                         


    ECgene alternative splicing isoforms for LCA5

    Expression
    for LCA5 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    LCA5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ACTATTTGTC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    LCA5 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Posterior foregut-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See LCA5 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LCA5

    SOURCE GeneReport for Unigene cluster: Hs.21945
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    In Situ
    Assay Products:     
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    Orthologs
    for LCA5 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for LCA5 gene from 6/15 species (see all 15)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Lca51 , 5 Leber congenital amaurosis 5 (human)1, 5 76.96(n)1
    70.71(a)1    		   9 (45.42 cM)5
    757821  NM_027448.21  NP_081724.11 
     833902935 
    chicken
    (Gallus gallus)    		 Aves LCA51 Leber congenital amaurosis 5 61.89(n)
    48.45(a)    		   421852  XM_419870.3  XP_419870.1 
    lizard
    (Anolis carolinensis)    		 Reptilia LCA56
    		 --
    		 44(a)
    		 1 ↔ 1
    		 1(199562184-199572221)
    tropical clawed frog
    (Xenopus tropicalis)    		 Amphibia Str.178092 Transcribed sequence with weak similarity to protein more 73.77(n)    AL775741.2 
    zebrafish
    (Danio rerio)    		 Actinopterygii lca51 Leber congenital amaurosis 5 49.35(n)
    42.46(a)    		   100151323  XM_001919876.1  XP_001919911.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG66526
    		 --
    		 16(a)
    		 possible ortholog
    		 3L(17013448-17015956)


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

    Paralogs
    for LCA5 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for LCA5 gene
    LCA5L2  

    LCA5 for paralogs           About GeneDecksing



    Genomic Variants
    for LCA5 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/869 NCBI SNPs in LCA5 are shown (see all 869)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 6 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1219181651,2
    		C,Fpathogenic77423965(-) AGGTAC/TAGCGA 4 Q * stg12Minor allele frequency- T:0.00NA EU 5851
    rs587175131,2
    		--77415554(+) AGAAAA/TAAAGC 2 -- ut310--------
    rs13942811,2
    		C,F,H,--77415579(+) AATGAA/C/TGTGAA 4 -- ut31 ese36NS EA NA 704
    rs1112432881,2
    		--77415653(+) GCAGAG/AAAATT 2 -- ut311Minor allele frequency- A:0.50CSA 2
    rs412693431,2
    		C,--77415803(+) GAAAAC/TTTTTT 2 -- ut314Minor allele frequency- T:0.10NA WA EA 360
    rs13942821,2
    		H--77415820(+) GTTTAG/ACACTT 2 -- ut314Minor allele frequency- A:0.00NS EA 420
    rs761041041,2
    		C,F,--77415836(+) AGATTC/TTGTTC 2 -- ut311Minor allele frequency- T:0.14WA 118
    rs773542301,2
    		C,F,--77416039(+) GCAAAT/CGCTAG 2 -- ut311Minor allele frequency- C:0.03WA 118
    rs10571741,2
    		C,F,H,--77416287(-) ACTAGA/CGTGGA 2 -- ut31 ese314Minor allele frequency- C:0.03MN NA NS EA 1288
    rs1115007791,2
    		C,--77416347(+) TAAAAC/TTAATC 2 -- ut312Minor allele frequency- T:0.03CSA WA 120

    HapMap Linkage Disequilibrium report for LCA5 (80194708 - 80247175 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for LCA5: --
    Human Gene Mutation Database (HGMD): LCA5

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing LCA5
    DNA2.0 Custom Variant and Variant Library Synthesis for LCA5

    Disorders / Diseases
    for LCA5 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    LCA5 for disorders           About GeneDecksing

    OMIM gene information: 611408   
    OMIM disorders: 604537  
    UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0
  • Defects in LCA5 are the cause of Leber congenital amaurosis type 5 (LCA5) [MIM:604537]. LCA designates a
    • clinically and genetically heterogeneous group of childhood retinal degenerations, generally inherited in an autosomal
    recessive manner. Affected infants have little or no retinal photoreceptor function as tested by electroretinography.
    LCA represents the most common genetic cause of congenital visual impairment in infants and children

    11 diseases for LCA5:    About MalaCards
    leber congenital amaurosis    leber congenital amaurosis 5    cone-rod dystrophy    fundus dystrophy
    joubert syndrome    usher syndrome    retinal degeneration    coloboma
    retinitis    cataract    blindness

    3 diseases from the University of Copenhagen DISEASES database for LCA5:
    Leber congenital amaurosis     Fundus dystrophy     Blindness
    GeneTests: LCA5
    Leber Congenital Amaurosis

    Human Genome Epidemiology (HuGE) Navigator: LCA5 (2 documents)

    Export disorders for LCA5 gene to outside databases

    Publications
    for LCA5 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for LCA5 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with LCA5)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. (PubMed id 17546029)1, 2, 3 den Hollander A.I....Roepman R. (2007)
    2. OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5- encoded lebercilin. (PubMed id 19800048)1, 2 Coene K.L.... de Brouwer A.P. (2009)
    3. Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis. (PubMed id 18334959)1, 2 Ramprasad V.L....Kumaramanickavel G. (2008)
    4. Mutations in LCA5 are an uncommon cause of Leber congenital amaurosis (LCA) type II. (PubMed id 18000884)1, 2 Gerber S....Rozet J.-M. (2007)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    6. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    7. A novel locus for Leber congenital amaurosis maps to chromosome 6q. (PubMed id 10631161)1, 3 Dharmaraj S....Maumenee I.H. (2000)
    8. FAM161A, associated with retinitis pigmentosa, is a component of the cilia-basal body complex and interacts with proteins involved in ciliopathies. (PubMed id 22940612)2 Di Gioia S.A.... Rivolta C. (2012)
    9. Genome-wide association study of hoarding traits. (PubMed id 21302353)1 Perroud N....Mataix-Cols D. (2011)
    10. Identification of a novel LCA5 mutation in a Pakistan i family with Leber congenital amaurosis and cataracts. (PubMed id 21850168)1 Ahmad A....Bolz H.J. (2011)

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    Entrez Gene: 167691 HGNC: 31923 AceView: C6orf152 Ensembl:ENSG00000135338 euGenes: HUgn167691
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