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    LCA5 lebercilin LCA5 [ Homo sapiens (human) ]

    Gene ID: 167691, updated on 5-Mar-2024

    Summary

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    Official Symbol
    LCA5provided by HGNC
    Official Full Name
    lebercilin LCA5provided by HGNC
    Primary source
    HGNC:HGNC:31923
    See related
    Ensembl:ENSG00000135338 MIM:611408; AllianceGenome:HGNC:31923
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C6orf152
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 5.0), thyroid (RPKM 4.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6q14.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (79484991..79538782, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (80690503..80744277, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (80194708..80247147, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100506851 Neighboring gene uncharacterized LOC105377867 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:80162983-80164182 Neighboring gene Sharpr-MPRA regulatory region 1391 Neighboring gene DBI pseudogene 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:80234937-80236136 Neighboring gene uncharacterized LOC124901348 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:80247043-80247616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24769 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:80248191-80248764 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:80254355-80255117 Neighboring gene SH3 domain binding glutamate rich protein like 2 Neighboring gene Sharpr-MPRA regulatory region 10526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:80373066-80373678 Neighboring gene uncharacterized LOC124901349 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_95971 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:80516189-80517388 Neighboring gene long intergenic non-protein coding RNA 1621

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Next-generation Sequencing Extends the Phenotypic Spectrum for LCA5 Mutations: Novel LCA5 Mutations in Cone Dystrophy. Chen X, et al. Sci Rep, 2016 Apr 12. PMID 27067258, Free PMC Article
    2. Involvement of LCA5 in Leber congenital amaurosis and retinitis pigmentosa in the Spanish population. Corton M, et al. Ophthalmology, 2014 Jan. PMID 24144451
    3. Screening of a large cohort of leber congenital amaurosis and retinitis pigmentosa patients identifies novel LCA5 mutations and new genotype-phenotype correlations. Mackay DS, et al. Hum Mutat, 2013 Nov. PMID 23946133, Free PMC Article
    4. Identification of a novel LCA5 mutation in a Pakistani family with Leber congenital amaurosis and cataracts. Ahmad A, et al. Mol Vis, 2011. PMID 21850168, Free PMC Article
    5. Genome-wide association study of hoarding traits. Perroud N, et al. Am J Med Genet B Neuropsychiatr Genet, 2011 Mar. PMID 21302353

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The authors report novel biallelic LCA5 mutations, Ala212Pro and Tyr441Cys, as causing cone dystrophy.
      Title: Next-generation Sequencing Extends the Phenotypic Spectrum for LCA5 Mutations: Novel LCA5 Mutations in Cone Dystrophy.
    2. Identification of novel LCA5 mutations in patients with Leber congenital amaurosis and retinitis pigmentosa.
      Title: Screening of a large cohort of leber congenital amaurosis and retinitis pigmentosa patients identifies novel LCA5 mutations and new genotype-phenotype correlations.
    3. This work reveals a higher frequency of LCA5 mutations in a Spanish Leber congenital amaurosis cohort than in other populations.
      Title: Involvement of LCA5 in Leber congenital amaurosis and retinitis pigmentosa in the Spanish population.
    4. A novel LCA5 mutation is present in a Pakistani family with Leber congenital amaurosis and cataracts.
      Title: Identification of a novel LCA5 mutation in a Pakistani family with Leber congenital amaurosis and cataracts.
    5. Leber congenital amaurosis 2 patients with LCA5 mutation had evidence of retained photoreceptors mainly in the central retina; retinal remodeling was present in pericentral regions
      Title: Leber congenital amaurosis caused by Lebercilin (LCA5) mutation: retained photoreceptors adjacent to retinal disorganization.
    6. OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5-encoded lebercilin
      Title: OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5-encoded lebercilin.
    7. This result shows that mutation in LCA5 is likely to be a rare genetic cause in Koreans
      Title: LCA5, a rare genetic cause of leber congenital amaurosis in Koreans.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: LCA5, a rare genetic cause of leber congenital amaurosis in Koreans.
    9. This is the second report of LCA5 mutations causing Leber congenital amaurosis.
      Title: Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.
    10. Data report the identification of three novel LCA5 mutations (3/3 homozygous) in three families confirming the modest implication of this gene in this series (3/179; 1.7%).
      Title: Mutations in LCA5 are an uncommon cause of Leber congenital amaurosis (LCA) type II.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of antiphospholipid antibodies.
    EBI GWAS Catalog
    Genome-wide association study of hoarding traits.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intraciliary transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within photoreceptor cell maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axoneme IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ciliary basal body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in photoreceptor connecting cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lebercilin
    Names
    LCA5, lebercilin
    epididymis secretory sperm binding protein
    leber congenital amaurosis 5 protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016011.1 RefSeqGene

      Range
      5001..57440
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001122769.3 → NP_001116241.1  lebercilin

      See identical proteins and their annotated locations for NP_001116241.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL832214, BC050327, BE883302, BX648161
      Consensus CDS
      CCDS4990.1
      UniProtKB/Swiss-Prot
      E1P542, Q86VQ0, Q9BWX7
      UniProtKB/TrEMBL
      A0A384MDJ7
      Related
      ENSP00000358861.4, ENST00000369846.9
      Conserved Domains (2) summary
      pfam15619
      Location:107 → 286
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:90 → 482
      Neuromodulin_N; Gap junction protein N-terminal region

    2. NM_181714.4 → NP_859065.2  lebercilin

      See identical proteins and their annotated locations for NP_859065.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL832214, BC050327, BE883302, BX648161
      Consensus CDS
      CCDS4990.1
      UniProtKB/Swiss-Prot
      E1P542, Q86VQ0, Q9BWX7
      UniProtKB/TrEMBL
      A0A384MDJ7
      Related
      ENSP00000376686.1, ENST00000392959.5
      Conserved Domains (2) summary
      pfam15619
      Location:107 → 286
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:90 → 482
      Neuromodulin_N; Gap junction protein N-terminal region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      79484991..79538782 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418251.1 → XP_047274207.1  lebercilin isoform X1

      UniProtKB/Swiss-Prot
      E1P542, Q86VQ0, Q9BWX7
      UniProtKB/TrEMBL
      A0A384MDJ7

    2. XM_011535504.2 → XP_011533806.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_011533806.1

      UniProtKB/Swiss-Prot
      E1P542, Q86VQ0, Q9BWX7
      UniProtKB/TrEMBL
      A0A384MDJ7
      Conserved Domains (2) summary
      pfam15619
      Location:107 → 286
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:90 → 482
      Neuromodulin_N; Gap junction protein N-terminal region

    3. XM_005248665.5 → XP_005248722.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_005248722.1

      UniProtKB/Swiss-Prot
      E1P542, Q86VQ0, Q9BWX7
      UniProtKB/TrEMBL
      A0A384MDJ7
      Conserved Domains (2) summary
      pfam15619
      Location:107 → 286
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:90 → 482
      Neuromodulin_N; Gap junction protein N-terminal region

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      80690503..80744277 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354388.1 → XP_054210363.1  lebercilin isoform X1

    2. XM_054354387.1 → XP_054210362.1  lebercilin isoform X1

    3. XM_054354386.1 → XP_054210361.1  lebercilin isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86VQ0.2 GenPept UniProtKB/Swiss-Prot:Q86VQ0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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