The protein encoded by this gene is a tumor suppressor, with lowered expression levels found in gastric, renal, colorectal, lung, and breast cancer tissues. The promoter of this gene is frequently hypermethylated in these cancer tissues, although the hypermethylation does not appear to be the cause of the reduced expression of this gene. Several transcript variants encoding the... See more...

Aliases for LRRC3B Gene

Aliases for LRRC3B Gene

  • Leucine Rich Repeat Containing 3B 2 3 5
  • LRP15 2 3 4
  • Leucine-Rich Repeat-Containing Protein 3B 3 4
  • Leucine-Rich Repeat Protein 15 3 4
  • Leucine-Rich Repeat Protein LRP15 3
  • LRRC3B 5

External Ids for LRRC3B Gene

Summaries for LRRC3B Gene

Entrez Gene Summary for LRRC3B Gene

  • The protein encoded by this gene is a tumor suppressor, with lowered expression levels found in gastric, renal, colorectal, lung, and breast cancer tissues. The promoter of this gene is frequently hypermethylated in these cancer tissues, although the hypermethylation does not appear to be the cause of the reduced expression of this gene. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2015]

GeneCards Summary for LRRC3B Gene

LRRC3B (Leucine Rich Repeat Containing 3B) is a Protein Coding gene. An important paralog of this gene is LRRC3.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRRC3B Gene

Genomics for LRRC3B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRRC3B 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
GH03J026622 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.3 340 3 POLR2A SIN3A TAF1 RAD21 ZBTB20 SCRT2 LOC105377003 LRRC3B lnc-OXSM-6 NEK10
GH03J026694 Promoter 0.3 EPDnew 250.2 +71.7 71714 0.1 LRRC3B lnc-LRRC3B-1 HSALNG0024775 L13714-312 lnc-OXSM-6 NEK10
GH03J026437 Enhancer 0.5 ENCODE 7 -184.6 -184630 1.4 MAFF ZNF316 MAFK NFE2L2 ZFP37 ZNF362 ZBTB21 ZNF366 LRRC3B piR-56883-108 piR-46002-389 NGLY1
GH03J026646 Enhancer 0.2 FANTOM5 3.3 +24.0 24018 0.4 LRRC3B L13714-312 lnc-OXSM-6 NEK10
GH03J026717 Enhancer 0.2 FANTOM5 2.5 +94.6 94585 0.2 LRRC3B HSALNG0024775 lnc-LRRC3B-1 NEK10
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRRC3B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRRC3B

Top Transcription factor binding sites by QIAGEN in the LRRC3B gene promoter:
  • AP-2gamma
  • FOXJ2
  • FOXJ2 (long isoform)
  • FOXO1
  • FOXO1a
  • p300
  • Pax-4a
  • Pbx1a
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for LRRC3B Gene

Latest Assembly
chr3:26,622,772-26,717,537
(GRCh38/hg38)
Size:
94,766 bases
Orientation:
Plus strand

Previous Assembly
chr3:26,664,263-26,752,267
(GRCh37/hg19 by Entrez Gene)
Size:
88,005 bases
Orientation:
Plus strand

chr3:26,664,297-26,752,267
(GRCh37/hg19 by Ensembl)
Size:
87,971 bases
Orientation:
Plus strand

Genomic View for LRRC3B Gene

Genes around LRRC3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRC3B Gene

Proteins for LRRC3B Gene

  • Protein details for LRRC3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96PB8-LRC3B_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 3B
    Protein Accession:
    Q96PB8
    Secondary Accessions:
    • Q5M8T0

    Protein attributes for LRRC3B Gene

    Size:
    259 amino acids
    Molecular mass:
    29275 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for LRRC3B Gene

neXtProt entry for LRRC3B Gene

Post-translational modifications for LRRC3B Gene

  • Glycosylation at Asn47 and Asn94
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LRRC3B Gene

Domains & Families for LRRC3B Gene

Gene Families for LRRC3B Gene

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

Protein Domains for LRRC3B Gene

InterPro:
Blocks:
  • Cysteine-rich flanking region, N-terminal
  • Cysteine-rich flanking region, C-terminal

Suggested Antigen Peptide Sequences for LRRC3B Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat protein LRP15 (LRC3B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96PB8

UniProtKB/Swiss-Prot:

LRC3B_HUMAN :
  • Belongs to the LRRC3 family.
Family:
  • Belongs to the LRRC3 family.
genes like me logo Genes that share domains with LRRC3B: view

Function for LRRC3B Gene

Phenotypes From GWAS Catalog for LRRC3B Gene

Gene Ontology (GO) - Molecular Function for LRRC3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with LRRC3B: view
genes like me logo Genes that share phenotypes with LRRC3B: view

Animal Models for LRRC3B Gene

MGI Knock Outs for LRRC3B:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC3B

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for LRRC3B Gene

Localization for LRRC3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRC3B Gene

Membrane. Single-pass 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 LRRC3B gene
Compartment Confidence
extracellular 3
plasma membrane 2
cytoskeleton 1
golgi apparatus 1
endoplasmic reticulum 0

Gene Ontology (GO) - Cellular Components for LRRC3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031012 extracellular matrix IBA 21873635
genes like me logo Genes that share ontologies with LRRC3B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRRC3B Gene

Pathways & Interactions for LRRC3B Gene

PathCards logo

SuperPathways for LRRC3B Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRRC3B Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LRRC3B Gene

Drugs & Compounds for LRRC3B Gene

No Compound Related Data Available

Transcripts for LRRC3B Gene

mRNA/cDNA for LRRC3B Gene

5 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC3B

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC3B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b
SP1: - -
SP2:
SP3: - - - -

Relevant External Links for LRRC3B Gene

GeneLoc Exon Structure for
LRRC3B

Expression for LRRC3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRRC3B Gene

mRNA differential expression in normal tissues according to GTEx for LRRC3B Gene

This gene is overexpressed in Brain - Amygdala (x5.7), Brain - Cerebellar Hemisphere (x5.3), Brain - Nucleus accumbens (basal ganglia) (x5.0), Brain - Putamen (basal ganglia) (x4.3), Brain - Cerebellum (x4.3), and Brain - Caudate (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for LRRC3B Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRRC3B Gene



Protein tissue co-expression partners for LRRC3B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRRC3B

SOURCE GeneReport for Unigene cluster for LRRC3B Gene:

Hs.517868

Evidence on tissue expression from TISSUES for LRRC3B Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with LRRC3B: view

Primer products for research

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 LRRC3B Gene

Orthologs for LRRC3B Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRRC3B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRRC3B 29 30
  • 99.74 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LRRC3B 30
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LRRC3B 29 30
  • 95.62 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LRRC3B 30
  • 94 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lrrc3b 29
  • 91.12 (n)
Mouse
(Mus musculus)
Mammalia Lrrc3b 29 16 30
  • 90.35 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRRC3B 29 30
  • 90.09 (n)
OneToOne
Chicken
(Gallus gallus)
Aves LRRC3B 29 30
  • 87.26 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRRC3B 30
  • 94 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lrrc3b 29
  • 82.63 (n)
Zebrafish
(Danio rerio)
Actinopterygii lrrc3b 29 30
  • 63.52 (n)
OneToOne
Dr.18976 29
Species where no ortholog for LRRC3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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 LRRC3B Gene

ENSEMBL:
Gene Tree for LRRC3B (if available)
TreeFam:
Gene Tree for LRRC3B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRRC3B: view image
Alliance of Genome Resources:
Additional Orthologs for LRRC3B

Paralogs for LRRC3B Gene

(6) SIMAP similar genes for LRRC3B Gene using alignment to 3 proteins:

  • LRC3B_HUMAN
  • C9J6A1_HUMAN
  • C9JMC7_HUMAN
genes like me logo Genes that share paralogs with LRRC3B: view

Variants for LRRC3B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRRC3B Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs146526715 Benign: not provided 26,710,245(+) C/T
NM_001317808.1(LRRC3B):c.573C>T (p.Asp191=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LRRC3B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LRRC3B Gene

Variant ID Type Subtype PubMed ID
esv2660739 CNV deletion 23128226
esv2725064 CNV deletion 23290073
esv2741743 CNV deletion 23290073
esv3575557 CNV gain 25503493
esv3595648 CNV loss 21293372
esv3595649 CNV loss 21293372
nsv1007968 CNV gain 25217958
nsv526575 CNV loss 19592680
nsv834649 CNV gain 17160897

Variation tolerance for LRRC3B Gene

Residual Variation Intolerance Score: 32.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.12; 2.65% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRC3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC3B
Leiden Open Variation Database (LOVD)
LRRC3B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRC3B Gene

Disorders for LRRC3B Gene

Additional Disease Information for LRRC3B

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for LRRC3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRC3B Gene

Publications for LRRC3B Gene

  1. 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
  2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. [LRRC3B is Downregulated in Non-small Cell Lung Cancer and Connected with Cell Proliferation and Invasion]. (PMID: 27118644) Kan L … He P (Zhongguo fei ai za zhi = Chinese journal of lung cancer 2016) 3
  5. LRRC3B is downregulated in non-small-cell lung cancer and inhibits cancer cell proliferation and invasion. (PMID: 26276358) Kan L … He P (Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2016) 3

Products for LRRC3B Gene

Sources for LRRC3B Gene