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Aliases for LRRC4 Gene

Aliases for LRRC4 Gene

  • Leucine Rich Repeat Containing 4 2 3 5
  • Nasopharyngeal Carcinoma-Associated Gene 14 Protein 3 4
  • Brain Tumor-Associated Protein BAG 3 4
  • Netrin-G2 Ligand 3 4
  • NGL-2 3 4
  • Leucine-Rich Repeat-Containing Protein 4 3
  • Brain Tumor Associated Protein LRRC4 3
  • Leucine-Rich Repeat-Containing 4 2
  • NAG14 3
  • BAG 4

External Ids for LRRC4 Gene

Previous GeneCards Identifiers for LRRC4 Gene

  • GC00U991013
  • GC07M127221
  • GC07M127262
  • GC07M127454
  • GC07M127667
  • GC07M122028

Summaries for LRRC4 Gene

Entrez Gene Summary for LRRC4 Gene

  • This gene is significantly downregulated in primary brain tumors. The exact function of the protein encoded by this gene is unknown. [provided by RefSeq, Jul 2008]

GeneCards Summary for LRRC4 Gene

LRRC4 (Leucine Rich Repeat Containing 4) is a Protein Coding gene. Diseases associated with LRRC4 include Nasopharyngitis and Nasopharyngeal Disease. Among its related pathways are Cell adhesion molecules (CAMs) and Axon guidance. An important paralog of this gene is LRRC4B.

UniProtKB/Swiss-Prot for LRRC4 Gene

  • Synaptic adhesion protein. Regulates the formation of exitatory synapses through the recruitment of pre-and-postsynaptic proteins. Organize the lamina/pathway-specific differentiation of dendrites. Plays a important role for auditory synaptic responses. Involved in the suppression of glioma (By similarity).

Gene Wiki entry for LRRC4 Gene

Additional gene information for LRRC4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRC4 Gene

Genomics for LRRC4 Gene

GeneHancer (GH) Regulatory Elements for LRRC4 Gene

Promoters and enhancers for LRRC4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J128029 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 655.2 +0.6 643 3 GTF2F1 CTCF MXI1 SUZ12 SIN3A ZIC2 ZNF335 E2F1 ZFHX2 CTBP1 LRRC4 GC07M128031 GC07P128029 PIR44536 SND1 LEP
GH07J128236 Enhancer 1.4 FANTOM5 Ensembl ENCODE 21.2 -205.0 -204970 1.6 PKNOX1 ATF1 FOXA2 ZNF766 FOS ATF7 CAVIN1 REST ZNF592 MEF2D LOC105375494 LRRC4 IMPDH1 RBM28 LEP ENSG00000224138 ENSG00000242588 ZNF800 ENSG00000243230 SND1
GH07J128403 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 11.7 -375.1 -375090 7.3 HDGF ARNT ZFP64 SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 E2F8 IMPDH1 PIR61424 ENSG00000273270 ENSG00000271553 ENSG00000242588 PRRT4 ENSG00000230715 LRRC4 RBM28 ENSG00000240758
GH07J127883 Enhancer 1.3 Ensembl ENCODE dbSUPER 16.5 +146.8 146809 2.8 HDAC1 PKNOX1 ATF1 ARNT RAD21 TCF12 GATA2 FOS ATF7 CREM GC07M127883 LRRC4 SND1 GC07P127895
GH07J128020 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 15.9 +9.9 9889 2.9 MZF1 ZNF664 CTBP1 ZNF316 GATA3 PRDM10 FOSL2 NFE2 FOS CHD2 GC07P128023 LRRC4 SND1 IMPDH1 GCC1 PIR35743
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRRC4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRRC4 gene promoter:
  • AP-1
  • STAT3
  • p53
  • c-Jun
  • ATF-2
  • Nkx6-1
  • Nkx2-5

Genomic Locations for LRRC4 Gene

Genomic Locations for LRRC4 Gene
chr7:128,027,071-128,032,107
(GRCh38/hg38)
Size:
5,037 bases
Orientation:
Minus strand
chr7:127,667,124-127,672,160
(GRCh37/hg19)
Size:
5,037 bases
Orientation:
Minus strand

Genomic View for LRRC4 Gene

Genes around LRRC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRC4 Gene

Proteins for LRRC4 Gene

  • Protein details for LRRC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBW1-LRRC4_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 4
    Protein Accession:
    Q9HBW1
    Secondary Accessions:
    • A4D0Y9
    • Q14DU9
    • Q6ZMI8
    • Q96A85

    Protein attributes for LRRC4 Gene

    Size:
    653 amino acids
    Molecular mass:
    72717 Da
    Quaternary structure:
    • Interacts with DLG4 (By similarity). Interacts (via LRR repeats) with NTNG2. Forms a complex with DLG4 and with NMDA receptors.

    Three dimensional structures from OCA and Proteopedia for LRRC4 Gene

neXtProt entry for LRRC4 Gene

Post-translational modifications for LRRC4 Gene

  • N-glycosylated.
  • Glycosylation at isoforms=450, isoforms=447, posLast=440440, posLast=434434, posLast=410410, isoforms=388, isoforms=363, isoforms=322, and posLast=277277
  • Modification sites at PhosphoSitePlus

Other Protein References for LRRC4 Gene

No data available for DME Specific Peptides for LRRC4 Gene

Domains & Families for LRRC4 Gene

Gene Families for LRRC4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for LRRC4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HBW1

UniProtKB/Swiss-Prot:

LRRC4_HUMAN :
  • The last 4 C-terminal residues bind to the first 2 PDZ domains of DLG4.
Domain:
  • The last 4 C-terminal residues bind to the first 2 PDZ domains of DLG4.
genes like me logo Genes that share domains with LRRC4: view

Function for LRRC4 Gene

Molecular function for LRRC4 Gene

UniProtKB/Swiss-Prot Function:
Synaptic adhesion protein. Regulates the formation of exitatory synapses through the recruitment of pre-and-postsynaptic proteins. Organize the lamina/pathway-specific differentiation of dendrites. Plays a important role for auditory synaptic responses. Involved in the suppression of glioma (By similarity).

Phenotypes From GWAS Catalog for LRRC4 Gene

Gene Ontology (GO) - Molecular Function for LRRC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004860 protein kinase inhibitor activity IBA --
GO:0005515 protein binding IEA,IPI 21946559
genes like me logo Genes that share ontologies with LRRC4: view
genes like me logo Genes that share phenotypes with LRRC4: view

Animal Models for LRRC4 Gene

MGI Knock Outs for LRRC4:

Animal Model Products

  • Taconic Biosciences Mouse Models for LRRC4

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC4

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRRC4 Gene

Localization for LRRC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRC4 Gene

Membrane; Single-pass type I membrane protein. Cell junction, synapse, postsynaptic cell membrane. Note=LRRC4 and DLG4 are interdependent for synaptic localization. {ECO:0000250}.

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 LRRC4 gene
Compartment Confidence
plasma membrane 5
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRRC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with LRRC4: view

Pathways & Interactions for LRRC4 Gene

genes like me logo Genes that share pathways with LRRC4: view

Pathways by source for LRRC4 Gene

2 KEGG pathways for LRRC4 Gene

Gene Ontology (GO) - Biological Process for LRRC4 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:0050807 regulation of synapse organization IEA --
GO:0050808 synapse organization IEA --
genes like me logo Genes that share ontologies with LRRC4: view

No data available for SIGNOR curated interactions for LRRC4 Gene

Drugs & Compounds for LRRC4 Gene

No Compound Related Data Available

Transcripts for LRRC4 Gene

mRNA/cDNA for LRRC4 Gene

Unigene Clusters for LRRC4 Gene

Leucine rich repeat containing 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC4

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC4 Gene

No ASD Table

Relevant External Links for LRRC4 Gene

GeneLoc Exon Structure for
LRRC4
ECgene alternative splicing isoforms for
LRRC4

Expression for LRRC4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRRC4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRRC4 Gene

This gene is overexpressed in Brain - Cortex (x6.4), Brain - Frontal Cortex (BA9) (x5.5), Whole Blood (x4.9), and Brain - Anterior cingulate cortex (BA24) (x4.5).

Protein differential expression in normal tissues from HIPED for LRRC4 Gene

This gene is overexpressed in Frontal cortex (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRRC4 Gene



Protein tissue co-expression partners for LRRC4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRRC4 Gene:

LRRC4

SOURCE GeneReport for Unigene cluster for LRRC4 Gene:

Hs.655003

mRNA Expression by UniProt/SwissProt for LRRC4 Gene:

Q9HBW1-LRRC4_HUMAN
Tissue specificity: Specifically expressed in brain.

Evidence on tissue expression from TISSUES for LRRC4 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with LRRC4: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRC4 Gene

Orthologs for LRRC4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRRC4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRRC4 34 33
  • 99.74 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LRRC4 34
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LRRC4 34 33
  • 95.13 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRRC4 34 33
  • 93.62 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lrrc4 33
  • 93.1 (n)
mouse
(Mus musculus)
Mammalia Lrrc4 16 34 33
  • 92.94 (n)
chicken
(Gallus gallus)
Aves LRRC4 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrc4 33
  • 75.99 (n)
zebrafish
(Danio rerio)
Actinopterygii lrrc4.2 34
  • 73 (a)
OneToMany
LOC566572 33
  • 70.59 (n)
lrrc4.1 34
  • 54 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
OneToMany
Species where no ortholog for LRRC4 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 LRRC4 Gene

ENSEMBL:
Gene Tree for LRRC4 (if available)
TreeFam:
Gene Tree for LRRC4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRRC4: view image

Paralogs for LRRC4 Gene

(18) SIMAP similar genes for LRRC4 Gene using alignment to 4 proteins:

  • LRRC4_HUMAN
  • C9J7K7_HUMAN
  • C9J7V8_HUMAN
  • C9JA92_HUMAN
genes like me logo Genes that share paralogs with LRRC4: view

Variants for LRRC4 Gene

Sequence variations from dbSNP and Humsavar for LRRC4 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
VAR_035519 A colorectal cancer sample p.Thr579Ala
rs1000118787 -- 128,032,502(-) G/A upstream_transcript_variant
rs1000171627 -- 128,030,788(-) G/C intron_variant
rs1000302461 -- 128,031,225(-) G/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000723428 -- 128,031,452(-) C/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LRRC4 Gene

Variant ID Type Subtype PubMed ID
nsv5944 CNV insertion 18451855
nsv1144199 CNV deletion 24896259
nsv1075996 CNV deletion 25765185
nsv1024743 CNV gain 25217958

Variation tolerance for LRRC4 Gene

Residual Variation Intolerance Score: 11.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.47; 43.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRC4 Gene

Human Gene Mutation Database (HGMD)
LRRC4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRC4 Gene

Disorders for LRRC4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LRRC4 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
nasopharyngitis
  • chronic nasopharyngitis
nasopharyngeal disease
  • nasopharyngeal diseases
- elite association - COSMIC cancer census association via MalaCards
Search LRRC4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LRRC4

genes like me logo Genes that share disorders with LRRC4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRRC4 Gene

Publications for LRRC4 Gene

  1. Structural basis for cell surface patterning through NetrinG-NGL interactions. (PMID: 21946559) Seiradake E … Jones EY (The EMBO journal 2011) 3 4 58
  2. Expression and functional characterization of LRRC4, a novel brain-specific member of the LRR superfamily. (PMID: 15967442) Zhang Q … Li G (FEBS letters 2005) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Expression of LRRC4 has the potential to decrease the growth rate and tumorigenesis of glioblastoma cell line U251. (PMID: 12969517) Wang JR … Li GY (Ai zheng = Aizheng = Chinese journal of cancer 2003) 2 3 58

Products for LRRC4 Gene

Sources for LRRC4 Gene

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