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LRRC4B Gene(Protein Coding)

Leucine Rich Repeat Containing 4B

GCID:
GC19M050516
GIFtS:
42
Genes Participants
UDN Logo

Aliases for LRRC4B Gene

Aliases for LRRC4B Gene

  • Leucine Rich Repeat Containing 4B 2 3 5
  • Netrin-G3 Ligand 2 3 4
  • Leucine-Rich Repeats And Immunoglobulin-Like Domains 4 2 3
  • LRIG4 3 4
  • NGL-3 3 4
  • Leucine-Rich Repeat-Containing Protein 4B 3
  • HSM 3

External Ids for LRRC4B Gene

Previous HGNC Symbols for LRRC4B Gene

  • LRIG4

Previous GeneCards Identifiers for LRRC4B Gene

  • GC19M055713
  • GC19M055714
  • GC19M051020
  • GC19M047356

Summaries for LRRC4B Gene

GeneCards Summary for LRRC4B Gene

LRRC4B (Leucine Rich Repeat Containing 4B) is a Protein Coding gene. Among its related pathways are Cell adhesion molecules (CAMs). Gene Ontology (GO) annotations related to this gene include receptor binding. An important paralog of this gene is LRRC4C.

UniProtKB/Swiss-Prot for LRRC4B Gene

  • Synaptic adhesion protein. Regulates the formation of excitatory synapses. The trans-synaptic adhesion between LRRC4B and PTPRF regulates the formation of excitatory synapses in a bidirectional manner (By similarity).

Additional gene information for LRRC4B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRC4B Gene

Genomics for LRRC4B Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for LRRC4B Gene

Promoters and enhancers for LRRC4B 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
GH19I050551 Promoter/Enhancer 1.1 EPDnew dbSUPER 550.4 +16.4 16383 0.1 MAZ ZNF398 ZNF148 ZFHX2 POLR2A VEZF1 PATZ1 CTBP2 KDM1A WT1 LRRC4B ASPDH JOSD2 LINC01869 C19orf48 SNORD88C ENSG00000268231
GH19I050566 Enhancer 0.9 FANTOM5 ENCODE dbSUPER 553.1 +1.9 1866 0.3 MAZ EGR1 VEZF1 NRF1 CTBP2 EZH2 LRRC4B SYT3 KLK6 KCNC3 ENSG00000268231
GH19I050567 Enhancer 0.8 ENCODE dbSUPER 550.8 +0.8 810 0.1 MXI1 MAZ SP3 RFX1 ZNF740 SIN3A BMI1 ZBTB7A VEZF1 MYNN LRRC4B ENSG00000268231
GH19I050570 Promoter 0.7 EPDnew 550.8 +0.1 102 0.1 ZNF740 VEZF1 LRRC4B ENSG00000268231
GH19I050568 Enhancer 0.6 ENCODE 550.8 -0.2 -230 0.1 ZSCAN18 MAZ SP3 SP2 POLR2A PATZ1 VEZF1 IKZF1 ZNF143 WT1 LRRC4B SNAR-F
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRRC4B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRRC4B gene promoter:

Genomic Locations for LRRC4B Gene

Genomic Locations for LRRC4B Gene
chr19:50,516,892-50,568,219
(GRCh38/hg38)
Size:
51,328 bases
Orientation:
Minus strand
chr19:51,020,149-51,071,302
(GRCh37/hg19)

Genomic View for LRRC4B Gene

Genes around LRRC4B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC4B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC4B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for LRRC4B Gene

Proteins for LRRC4B Gene

Products:

  1. Antibody
  2. Protein
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  • Protein details for LRRC4B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NT99-LRC4B_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 4B
    Protein Accession:
    Q9NT99
    Secondary Accessions:
    • Q3ZCQ4
    • Q58F20

    Protein attributes for LRRC4B Gene

    Size:
    713 amino acids
    Molecular mass:
    76434 Da
    Quaternary structure:
    • Interacts with PTPRF. Interacts with DLG4.
    SequenceCaution:
    • Sequence=AAH19687.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for LRRC4B Gene

Protein Expression for LRRC4B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LRRC4B Gene

  • N-glycosylated. O-glycosylated; contains sialic acid.
  • Glycosylation at posLast=224224, isoforms=283, isoforms=333, posLast=374374, isoforms=400, posLast=422422, isoforms=425, isoforms=444, and isoforms=452
  • Modification sites at PhosphoSitePlus

Other Protein References for LRRC4B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRRC4B Gene

Domains & Families for LRRC4B Gene

Gene Families for LRRC4B Gene

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

Protein Domains for LRRC4B Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for LRRC4B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NT99

UniProtKB/Swiss-Prot:

LRC4B_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 LRRC4B: view

Function for LRRC4B Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for LRRC4B Gene

UniProtKB/Swiss-Prot Function:
Synaptic adhesion protein. Regulates the formation of excitatory synapses. The trans-synaptic adhesion between LRRC4B and PTPRF regulates the formation of excitatory synapses in a bidirectional manner (By similarity).

Phenotypes From GWAS Catalog for LRRC4B Gene

Gene Ontology (GO) - Molecular Function for LRRC4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004860 protein kinase inhibitor activity IBA --
GO:0005102 receptor binding IEA --
genes like me logo Genes that share ontologies with LRRC4B: view
genes like me logo Genes that share phenotypes with LRRC4B: view

Animal Model Products

  • Taconic Biosciences Mouse Models for LRRC4B

CRISPR Products

miRNA for LRRC4B Gene

miRTarBase miRNAs that target LRRC4B

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRRC4B Gene

Localization for LRRC4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRC4B Gene

Membrane; Single-pass membrane protein. Cell junction, synapse, presynaptic cell membrane.

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 LRRC4B gene
Compartment Confidence
plasma membrane 5
extracellular 1
mitochondrion 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LRRC4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005886 plasma membrane TAS --
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 LRRC4B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRRC4B Gene

Pathways & Interactions for LRRC4B Gene

genes like me logo Genes that share pathways with LRRC4B: view

Pathways by source for LRRC4B Gene

1 KEGG pathway for LRRC4B Gene

Gene Ontology (GO) - Biological Process for LRRC4B 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:0051965 positive regulation of synapse assembly ISS --
genes like me logo Genes that share ontologies with LRRC4B: view

No data available for SIGNOR curated interactions for LRRC4B Gene

Drugs & Compounds for LRRC4B Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for LRRC4B Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for LRRC4B Gene

(5) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(49) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LRRC4B Gene

Leucine rich repeat containing 4B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC4B Gene

No ASD Table

Relevant External Links for LRRC4B Gene

GeneLoc Exon Structure for
LRRC4B
ECgene alternative splicing isoforms for
LRRC4B

Expression for LRRC4B Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRRC4B Gene

mRNA expression in normal human tissues for LRRC4B Gene
mRNA expression by GTEx for LRRC4B Gene

mRNA differential expression in normal tissues according to GTEx for LRRC4B Gene

This gene is overexpressed in Brain - Cortex (x4.6).

Protein differential expression in normal tissues from HIPED for LRRC4B Gene

This gene is overexpressed in Cerebrospinal fluid (24.4), Fetal Brain (23.1), Frontal cortex (9.8), and Vitreous humor (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LRRC4B Gene



Protein tissue co-expression partners for LRRC4B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRRC4B Gene:

LRRC4B

SOURCE GeneReport for Unigene cluster for LRRC4B Gene:

Hs.120873

Evidence on tissue expression from TISSUES for LRRC4B Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with LRRC4B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRC4B Gene

Orthologs for LRRC4B Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRRC4B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia LRRC4B 33 34
  • 99.86 (n)
oppossum
(Monodelphis domestica)
 Mammalia LRRC4B 34
  • 99 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia LRRC4B 33 34
  • 93.25 (n)
dog
(Canis familiaris)
 Mammalia LRRC4B 33 34
  • 92.33 (n)
mouse
(Mus musculus)
 Mammalia Lrrc4b 33 16 34
  • 88.15 (n)
rat
(Rattus norvegicus)
 Mammalia Lrrc4b 33
  • 87.58 (n)
lizard
(Anolis carolinensis)
 Reptilia LRRC4B 34
  • 87 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia lrrc4b 33
  • 73.4 (n)
zebrafish
(Danio rerio)
 Actinopterygii lrrc4ba 34
  • 66 (a)
 OneToMany
lrrc4bb 34
  • 63 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 39 (a)
 OneToMany
Species where no ortholog for LRRC4B 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)
  • chicken (Gallus gallus)
  • 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)
  • 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 LRRC4B Gene

ENSEMBL:
Gene Tree for LRRC4B (if available)
TreeFam:
Gene Tree for LRRC4B (if available)

Paralogs for LRRC4B Gene

Paralogs for LRRC4B Gene

(8) SIMAP similar genes for LRRC4B Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with LRRC4B: view

Variants for LRRC4B Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for LRRC4B Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000024028 -- 50,561,654(-) G/C genic_upstream_transcript_variant, intron_variant
rs1000075005 -- 50,536,620(-) C/A intron_variant
rs1000124730 -- 50,520,485(-) C/T intron_variant
rs1000131747 -- 50,556,485(-) C/G/T genic_upstream_transcript_variant, intron_variant
rs1000181976 -- 50,551,630(-) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LRRC4B Gene

Variant ID Type Subtype PubMed ID
esv3556530 CNV deletion 23714750
esv3556531 CNV deletion 23714750
esv994565 CNV deletion 20482838
nsv1072892 CNV deletion 25765185
nsv1121984 CNV deletion 24896259
nsv1133010 OTHER inversion 24896259
nsv1140251 OTHER inversion 24896259
nsv1144879 CNV deletion 24896259
nsv1152956 OTHER inversion 26484159
nsv2530 CNV deletion 18451855
nsv509750 CNV insertion 20534489
nsv953604 CNV deletion 24416366

Variation tolerance for LRRC4B Gene

Residual Variation Intolerance Score: 6.98% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.46; 71.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRC4B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC4B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRC4B Gene

Disorders for LRRC4B Gene

Additional Disease Information for LRRC4B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for LRRC4B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRC4B Gene

Publications for LRRC4B Gene

  1. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 58
  2. 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
  3. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. (PMID: 11441184) Dehal P … Stubbs L (Science (New York, N.Y.) 2001) 2 3 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. MxA interacts with and is modified by the SUMOylation machinery. (PMID: 25447205) Brantis-de-Carvalho CE … Valentini SR (Experimental cell research 2015) 3 58

Products for LRRC4B Gene

Sources for LRRC4B Gene

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