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LCA5 lebercilin LCA5 [ Homo sapiens (human) ]

Gene ID: 167691, updated on 17-Sep-2022

Summary

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

See LCA5 in Genome Data Viewer
Location:
6q14.1
Exon count:
10
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (79484991..79538782, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (80690503..80742938, 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 Sharpr-MPRA regulatory region 1391 Neighboring gene uncharacterized LOC124901348 Neighboring gene SH3 domain binding glutamate rich protein like 2 Neighboring gene Sharpr-MPRA regulatory region 10526 Neighboring gene uncharacterized LOC124901349

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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
PubMed 
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

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_001122769.3NP_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
    Q86VQ0, Q9BWX7
    UniProtKB/TrEMBL
    A0A384MDJ7
    Related
    ENSP00000358861.4, ENST00000369846.9
    Conserved Domains (2) summary
    pfam15619
    Location:107286
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:90482
    Neuromodulin_N; Gap junction protein N-terminal region
  2. NM_181714.4NP_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
    Q86VQ0, Q9BWX7
    UniProtKB/TrEMBL
    A0A384MDJ7
    Related
    ENSP00000376686.1, ENST00000392959.5
    Conserved Domains (2) summary
    pfam15619
    Location:107286
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:90482
    Neuromodulin_N; Gap junction protein N-terminal region

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_047418251.1XP_047274207.1  lebercilin isoform X1

    UniProtKB/Swiss-Prot
    Q9BWX7
    UniProtKB/TrEMBL
    A0A384MDJ7
  2. XM_011535504.2XP_011533806.1  lebercilin isoform X1

    See identical proteins and their annotated locations for XP_011533806.1

    UniProtKB/Swiss-Prot
    Q86VQ0, Q9BWX7
    UniProtKB/TrEMBL
    A0A384MDJ7
    Conserved Domains (2) summary
    pfam15619
    Location:107286
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:90482
    Neuromodulin_N; Gap junction protein N-terminal region
  3. XM_005248665.5XP_005248722.1  lebercilin isoform X1

    See identical proteins and their annotated locations for XP_005248722.1

    UniProtKB/Swiss-Prot
    Q86VQ0, Q9BWX7
    UniProtKB/TrEMBL
    A0A384MDJ7
    Conserved Domains (2) summary
    pfam15619
    Location:107286
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:90482
    Neuromodulin_N; Gap junction protein N-terminal region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    80690503..80742938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)