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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
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Genomic context

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See LCA5 in Genome Data Viewer
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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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

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