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Aliases for LRRC4C Gene

Aliases for LRRC4C Gene

  • Leucine Rich Repeat Containing 4C 2 3
  • Netrin-G1 Ligand 3 4
  • NGL-1 3 4
  • NGL1 3 4
  • KIAA1580 4

External Ids for LRRC4C Gene

Previous GeneCards Identifiers for LRRC4C Gene

  • GC11M040093
  • GC11M039843

Summaries for LRRC4C Gene

Entrez Gene Summary for LRRC4C Gene

  • NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]

GeneCards Summary for LRRC4C Gene

LRRC4C (Leucine Rich Repeat Containing 4C) is a Protein Coding gene. Diseases associated with LRRC4C include extragonadal seminoma and chief cell adenoma. Among its related pathways are Axon guidance and Cell adhesion molecules (CAMs). An important paralog of this gene is LINGO1.

UniProtKB/Swiss-Prot for LRRC4C Gene

  • May promote neurite outgrowth of developing thalamic neurons.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRC4C Gene

Genomics for LRRC4C Gene

Regulatory Elements for LRRC4C Gene

Genomic Location for LRRC4C Gene

Chromosome:
11
Start:
40,109,938 bp from pter
End:
41,460,212 bp from pter
Size:
1,350,275 bases
Orientation:
Minus strand

Genomic View for LRRC4C Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LRRC4C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRC4C Gene

Proteins for LRRC4C Gene

  • Protein details for LRRC4C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCJ2-LRC4C_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 4C
    Protein Accession:
    Q9HCJ2
    Secondary Accessions:
    • A8K0T1
    • Q7L0N3

    Protein attributes for LRRC4C Gene

    Size:
    640 amino acids
    Molecular mass:
    71950 Da
    Quaternary structure:
    • Interacts with NTNG1 and WHRN.

    Three dimensional structures from OCA and Proteopedia for LRRC4C Gene

neXtProt entry for LRRC4C Gene

Proteomics data for LRRC4C Gene at MOPED

Post-translational modifications for LRRC4C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LRRC4C Gene

Antibody Products

  • R&D Systems Antibodies for LRRC4C (NGL-1/LRRC4C)
  • Santa Cruz Biotechnology (SCBT) Antibodies for LRRC4C

No data available for DME Specific Peptides for LRRC4C Gene

Domains & Families for LRRC4C Gene

Gene Families for LRRC4C Gene

Suggested Antigen Peptide Sequences for LRRC4C Gene

Graphical View of Domain Structure for InterPro Entry

Q9HCJ2

UniProtKB/Swiss-Prot:

LRC4C_HUMAN :
  • The LRR region is both necessary and sufficient for the interaction with NTNG1
  • Contains 9 LRR (leucine-rich) repeats.
Domain:
  • The LRR region is both necessary and sufficient for the interaction with NTNG1
  • Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
  • Contains 1 LRRCT domain.
  • Contains 1 LRRNT domain.
Similarity:
  • Contains 9 LRR (leucine-rich) repeats.
genes like me logo Genes that share domains with LRRC4C: view

Function for LRRC4C Gene

Molecular function for LRRC4C Gene

UniProtKB/Swiss-Prot Function:
May promote neurite outgrowth of developing thalamic neurons.

Gene Ontology (GO) - Molecular Function for LRRC4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 14595443
genes like me logo Genes that share ontologies with LRRC4C: view

Phenotypes for LRRC4C Gene

genes like me logo Genes that share phenotypes with LRRC4C: view

Animal Models for LRRC4C Gene

MGI Knock Outs for LRRC4C:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LRRC4C

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LRRC4C Gene

Localization for LRRC4C Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRC4C Gene

Cell junction, synapse, postsynaptic cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LRRC4C Gene COMPARTMENTS Subcellular localization image for LRRC4C gene
Compartment Confidence
extracellular 5
plasma membrane 3

Gene Ontology (GO) - Cellular Components for LRRC4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 22664934
GO:0016020 membrane IDA 14595443
GO:0016021 integral component of membrane NAS 14595443
GO:0030054 cell junction IEA --
GO:0045211 postsynaptic membrane IEA --
genes like me logo Genes that share ontologies with LRRC4C: view

Pathways & Interactions for LRRC4C Gene

genes like me logo Genes that share pathways with LRRC4C: view

Pathways by source for LRRC4C Gene

2 KEGG pathways for LRRC4C Gene

SIGNOR curated interactions for LRRC4C Gene

Other effect:

Gene Ontology (GO) - Biological Process for LRRC4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0050770 regulation of axonogenesis IDA 14595443
genes like me logo Genes that share ontologies with LRRC4C: view

Drugs & Compounds for LRRC4C Gene

No Compound Related Data Available

Transcripts for LRRC4C Gene

Unigene Clusters for LRRC4C Gene

Leucine rich repeat containing 4C:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LRRC4C

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC4C Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c
SP1: - -
SP2: -
SP3:
SP4: - - -

Relevant External Links for LRRC4C Gene

GeneLoc Exon Structure for
LRRC4C
ECgene alternative splicing isoforms for
LRRC4C

Expression for LRRC4C Gene

mRNA expression in normal human tissues for LRRC4C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRRC4C Gene

This gene is overexpressed in Brain - Cortex (x5.6), Brain - Frontal Cortex (BA9) (x5.5), Brain - Anterior cingulate cortex (BA24) (x5.5), and Brain - Nucleus accumbens (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for LRRC4C Gene

This gene is overexpressed in Retina (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRRC4C Gene



SOURCE GeneReport for Unigene cluster for LRRC4C Gene Hs.745123

mRNA Expression by UniProt/SwissProt for LRRC4C Gene

Q9HCJ2-LRC4C_HUMAN
Tissue specificity: Highly expressed in the cerebral cortex, including frontal, parietal and occipital lobes. Putamen, amygdala, hippocampus and medulla oblongata show moderate expression. Caudate nucleus and thalamus express small amounts, whereas other brain regions show very weak or no expression.
genes like me logo Genes that share expression patterns with LRRC4C: view

Protein tissue co-expression partners for LRRC4C Gene

- Elite partner

Primer Products

In Situ Assay Products

Orthologs for LRRC4C Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRRC4C Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LRRC4C 35
  • 94.9 (n)
  • 99.69 (a)
LRRC4C 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LRRC4C 35
  • 95.1 (n)
  • 99.84 (a)
LRRC4C 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lrrc4c 35
  • 93.23 (n)
  • 99.69 (a)
Lrrc4c 16
Lrrc4c 36
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LRRC4C 35
  • 99.69 (n)
  • 100 (a)
LRRC4C 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lrrc4c 35
  • 93.12 (n)
  • 99.69 (a)
oppossum
(Monodelphis domestica)
Mammalia LRRC4C 36
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LRRC4C 36
  • 97 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRRC4C 35
  • 85.79 (n)
  • 95.14 (a)
LRRC4C 36
  • 95 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRRC4C 36
  • 94 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrc4c 35
  • 79.6 (n)
  • 88.58 (a)
zebrafish
(Danio rerio)
Actinopterygii sc:d0316 35
  • 68.53 (n)
  • 73.52 (a)
wufd12d10 35
LRRC4C 36
  • 73 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 36 (a)
OneToMany
Species with no ortholog for LRRC4C:
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 LRRC4C Gene

ENSEMBL:
Gene Tree for LRRC4C (if available)
TreeFam:
Gene Tree for LRRC4C (if available)

Paralogs for LRRC4C Gene

(4) SIMAP similar genes for LRRC4C Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LRRC4C: view

Variants for LRRC4C Gene

Sequence variations from dbSNP and Humsavar for LRRC4C Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs3226 -- 40,860,921(+) AGTGA(C/T)TGGAC intron-variant
rs168533 -- 40,985,009(+) cgatt(C/T)tcctg intron-variant
rs173314 -- 41,043,188(-) AAGTT(C/T)TCCCA intron-variant
rs173315 -- 41,059,024(-) cccta(A/G)tttgt intron-variant
rs187146 -- 40,984,922(+) tttga(A/G)acgca intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LRRC4C Gene

Variant ID Type Subtype PubMed ID
dgv65n21 CNV Gain 19592680
nsv527603 CNV Loss 19592680
esv2661480 CNV Deletion 23128226
nsv39488 CNV Loss 16902084
nsv7744 CNV Loss 18451855
nsv508625 CNV Loss 20534489
nsv507590 CNV Insertion 20534489
nsv467865 CNV Loss 19166990
esv2744389 CNV Deletion 23290073

Variation tolerance for LRRC4C Gene

Residual Variation Intolerance Score: 18.59% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.86; 34.90% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LRRC4C Gene

HapMap Linkage Disequilibrium report
LRRC4C
Human Gene Mutation Database (HGMD)
LRRC4C

PCR Panel Products

  • Copy Number PCR Panels: for LRRC4C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRC4C Gene

Disorders for LRRC4C Gene

MalaCards: The human disease database

(2) MalaCards diseases for LRRC4C Gene - From: DISEASES

Disorder Aliases PubMed IDs
extragonadal seminoma
  • primary extragonadal seminoma
chief cell adenoma
  • chief cell adenoma of parathyroid gland
- elite association

Relevant External Links for LRRC4C

Genetic Association Database (GAD)
LRRC4C
Human Genome Epidemiology (HuGE) Navigator
LRRC4C
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LRRC4C
genes like me logo Genes that share disorders with LRRC4C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRRC4C Gene

Publications for LRRC4C Gene

  1. The NGL family of leucine-rich repeat-containing synaptic adhesion molecules. (PMID: 19467332) Woo J. … Kim E. (Mol. Cell. Neurosci. 2009) 23 67
  2. The netrin-G1 ligand NGL-1 promotes the outgrowth of thalamocortical axons. (PMID: 14595443) Lin J.C. … Rosenthal A. (Nat. Neurosci. 2003) 2 67
  3. Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. (PMID: 23382691) Lauc G. … Rudan I. (PLoS Genet. 2013) 67
  4. Trans-induced cis interaction in the tripartite NGL-1, netrin-G1 and LAR adhesion complex promotes development of excitatory synapses. (PMID: 23986473) Song Y.S. … Kim E. (J. Cell. Sci. 2013) 67
  5. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. (PMID: 24324551) Deng X. … Seielstad M. (PLoS ONE 2013) 67

Products for LRRC4C Gene

Sources for LRRC4C Gene

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