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Aliases for LRRC4C Gene

Aliases for LRRC4C Gene

  • Leucine Rich Repeat Containing 4C 2 3 5
  • Netrin-G1 Ligand 3 4
  • NGL-1 3 4
  • NGL1 3 4
  • Leucine-Rich Repeat-Containing Protein 4C 3
  • 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 Chief Cell Adenoma and Extragonadal Seminoma. Among its related pathways are Axon guidance and Cell adhesion molecules (CAMs). An important paralog of this gene is LRRC4B.

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

Enhancers for LRRC4C Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F041392 0.5 ENCODE 10.5 +66.5 66458 3.3 MTA2 IKZF1 TEAD4 TBX21 LRRC4C ENSG00000255132 GC11M041362
GH11F041497 0.4 ENCODE 11.1 -37.8 -37786 0.8 TEAD4 LRRC4C RPL9P23
GH11F041428 0.3 FANTOM5 11.3 +31.2 31163 0.3 LRRC4C ENSG00000255132
GH11F041521 0.2 ENCODE 11 -62.7 -62653 2.3 LRRC4C RPL9P23
GH11F041534 0.2 ENCODE 10.2 -74.6 -74610 1.4 LRRC4C RPL9P23
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LRRC4C on UCSC Golden Path with GeneCards custom track

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

Genes around LRRC4C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC4C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for LRRC4C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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:0004860 protein kinase inhibitor activity IBA --
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

  • Taconic Biosciences Mouse Models for LRRC4C

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRRC4C gene
Compartment Confidence
plasma membrane 5
extracellular 5

Gene Ontology (GO) - Cellular Components for LRRC4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 22664934
GO:0005737 cytoplasm IBA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA,IDA 14595443
GO:0016021 integral component of membrane NAS 14595443
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:0006469 negative regulation of protein kinase activity IBA --
GO:0019221 cytokine-mediated signaling pathway IBA --
GO:0046426 negative regulation of JAK-STAT cascade IBA --
GO:0050770 regulation of axonogenesis IDA 14595443
genes like me logo Genes that share ontologies with LRRC4C: view

Transcripts for LRRC4C Gene

Unigene Clusters for LRRC4C Gene

Leucine rich repeat containing 4C:
Representative Sequences:

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and SAGE 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



Protein tissue co-expression partners for LRRC4C Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRRC4C Gene:

LRRC4C

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

Primer 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
chimpanzee
(Pan troglodytes)
Mammalia LRRC4C 34 35
  • 99.69 (n)
oppossum
(Monodelphis domestica)
Mammalia LRRC4C 35
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LRRC4C 35
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LRRC4C 34 35
  • 95.1 (n)
cow
(Bos Taurus)
Mammalia LRRC4C 34 35
  • 94.9 (n)
mouse
(Mus musculus)
Mammalia Lrrc4c 34 16 35
  • 93.23 (n)
rat
(Rattus norvegicus)
Mammalia Lrrc4c 34
  • 93.12 (n)
chicken
(Gallus gallus)
Aves LRRC4C 34 35
  • 85.79 (n)
lizard
(Anolis carolinensis)
Reptilia LRRC4C 35
  • 94 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrc4c 34
  • 79.6 (n)
zebrafish
(Danio rerio)
Actinopterygii LRRC4C 35
  • 73 (a)
OneToOne
sc:d0316 34
  • 68.53 (n)
wufd12d10 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 36 (a)
OneToMany
Species where no ortholog for LRRC4C was found in the sources mined by GeneCards:
  • 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
rs1001952 -- 41,443,120(-) GCACC(C/T)ATGTT intron-variant
rs1002254 -- 40,392,877(-) ATTTC(G/T)CGAGC intron-variant
rs10128537 -- 40,297,552(+) AGATA(A/G)AAGGT intron-variant
rs10128638 -- 40,297,556(+) AAAAG(A/G)TCCTA intron-variant
rs10128639 -- 40,297,612(+) CCCCC(C/G)CCGAC intron-variant

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

Variant ID Type Subtype PubMed ID
esv3308596 CNV mobile element insertion 20981092
esv3336174 CNV insertion 20981092
esv3362865 CNV insertion 20981092
esv3421064 CNV insertion 20981092
esv3429881 CNV insertion 20981092
esv3431482 CNV insertion 20981092
esv3435360 CNV insertion 20981092
esv3439455 CNV insertion 20981092
esv3547631 CNV deletion 23714750
esv3547634 CNV deletion 23714750
esv3547635 CNV deletion 23714750
esv3547637 CNV deletion 23714750
esv3308528 CNV mobile element insertion 20981092
esv3308216 CNV mobile element insertion 20981092
esv3305759 CNV mobile element insertion 20981092
esv3149503 CNV deletion 24192839
esv27841 CNV loss 19812545
esv2762907 CNV gain 21179565
esv2760566 CNV loss 21179565
esv2759823 CNV loss 17122850
esv2759822 CNV loss 17122850
esv2751023 CNV loss 17911159
esv2744398 CNV deletion 23290073
esv2744396 CNV deletion 23290073
esv2744395 CNV deletion 23290073
esv2744394 CNV deletion 23290073
esv2744393 CNV deletion 23290073
esv2744392 CNV deletion 23290073
esv2744391 CNV deletion 23290073
esv2744390 CNV deletion 23290073
esv2744389 CNV deletion 23290073
esv2677712 CNV deletion 23128226
esv2677602 CNV deletion 23128226
esv2665329 CNV deletion 23128226
esv2664526 CNV deletion 23128226
esv2662552 CNV deletion 23128226
esv2661480 CNV deletion 23128226
esv2621057 CNV insertion 19546169
esv2533975 CNV deletion 19546169
esv2527036 CNV deletion 19546169
esv2488139 CNV loss 19546169
esv2420435 CNV deletion 18987734
esv2315564 CNV deletion 18987734
esv22215 CNV gain 19812545
esv21594 CNV gain 19812545
esv2119738 CNV deletion 18987734
esv2087348 CNV deletion 18987734
esv1949037 CNV deletion 18987734
esv1589619 CNV deletion 17803354
esv1344994 CNV deletion 17803354
esv1216399 CNV insertion 17803354
esv1051262 CNV deletion 17803354
esv1007997 CNV deletion 20482838
esv1000710 CNV deletion 20482838
dgv65n21 CNV gain 19592680
dgv625n106 CNV deletion 24896259
dgv624n106 CNV deletion 24896259
dgv193e214 CNV loss 21293372
dgv1106n100 CNV loss 25217958
dgv1105n100 CNV loss 25217958
nsv958624 CNV deletion 24416366
nsv8811 CNV loss 18304495
nsv8810 CNV gain 18304495
nsv832130 CNV gain 17160897
nsv832129 CNV gain 17160897
nsv832128 CNV gain+loss 17160897
nsv818814 CNV loss 17921354
nsv7747 CNV insertion 18451855
nsv7746 CNV insertion 18451855
nsv7744 CNV deletion 18451855
nsv554093 CNV loss 21841781
nsv554092 CNV loss 21841781
nsv554091 CNV loss 21841781
nsv554090 CNV loss 21841781
nsv554089 CNV loss 21841781
nsv554088 CNV loss 21841781
nsv554087 CNV loss 21841781
nsv554086 CNV loss 21841781
nsv554085 CNV loss 21841781
nsv527603 CNV loss 19592680
nsv526365 CNV loss 19592680
nsv523225 CNV gain 19592680
nsv523070 CNV loss 19592680
nsv520942 CNV loss 19592680
nsv520201 CNV loss 19592680
nsv514614 CNV gain 21397061
nsv510250 OTHER sequence alteration 20534489
nsv508625 CNV deletion 20534489
nsv507590 OTHER sequence alteration 20534489
nsv467866 CNV loss 19166990
nsv467865 CNV loss 19166990
nsv442227 CNV gain 18776908
nsv39488 CNV deletion 16902084
nsv39060 CNV deletion 16902084
nsv38933 CNV deletion 16902084
nsv1148093 CNV deletion 26484159
nsv1144554 CNV deletion 24896259
nsv1142108 CNV tandem duplication 24896259
nsv1138013 CNV deletion 24896259
nsv1138012 CNV deletion 24896259
nsv1134109 CNV deletion 24896259
nsv1110890 OTHER inversion 24896259
nsv1078065 CNV deletion 25765185
nsv1069577 CNV deletion 25765185
nsv1069576 CNV deletion 25765185
nsv1049298 CNV gain 25217958
nsv1040072 CNV loss 25217958
nsv1039904 CNV loss 25217958
nsv1039332 CNV loss 25217958
nsv1037066 CNV loss 25217958
nsv1036216 CNV loss 25217958
esv997366 CNV deletion 20482838
esv988637 CNV deletion 20482838
esv8984 CNV loss 19470904
esv5191 CNV loss 18987735
esv4634 CNV loss 18987735
esv3891968 CNV gain 25118596
esv3626085 CNV gain 21293372
esv3626084 CNV loss 21293372
esv3626083 CNV loss 21293372
esv3626080 CNV loss 21293372
esv3626078 CNV loss 21293372
esv3626077 CNV loss 21293372
esv3626074 CNV loss 21293372
esv3626073 CNV loss 21293372
esv3626072 CNV loss 21293372
esv3626071 CNV loss 21293372
esv3626069 CNV loss 21293372
esv3626068 CNV loss 21293372
esv3626067 CNV loss 21293372
esv3626066 CNV loss 21293372
esv3626064 CNV loss 21293372
esv3626063 CNV loss 21293372
esv3626062 CNV loss 21293372
esv3626061 CNV loss 21293372
esv3626060 CNV loss 21293372
esv3626059 CNV loss 21293372
esv3626058 CNV loss 21293372
esv3626057 CNV loss 21293372
esv3579486 CNV loss 25503493
esv3579485 CNV loss 25503493
esv3579484 CNV loss 25503493
esv3579482 CNV loss 25503493
esv3547639 CNV deletion 23714750

Variation tolerance for LRRC4C Gene

Residual Variation Intolerance Score: 18.6% 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

Human Gene Mutation Database (HGMD)
LRRC4C
SNPedia medical, phenotypic, and genealogical associations of SNPs 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
chief cell adenoma
  • chief cell adenoma of parathyroid gland
extragonadal seminoma
  • primary extragonadal seminoma
- elite association - COSMIC cancer census association via MalaCards

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 netrin-G1 ligand NGL-1 promotes the outgrowth of thalamocortical axons. (PMID: 14595443) Lin J.C. … Rosenthal A. (Nat. Neurosci. 2003) 2 3 4 64
  2. Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia. (PMID: 21107309) McClay J.L. … van den Oord E.J. (Neuropsychopharmacology 2011) 3 46 64
  3. Structural basis for cell surface patterning through NetrinG-NGL interactions. (PMID: 21946559) Seiradake E. … Jones E.Y. (EMBO J. 2011) 3 4 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for LRRC4C Gene

Sources for LRRC4C Gene

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