This gene encodes a membrane-bound protein that is involved in signal transduction and protein interactions. The encoded product is an E3 ubiquitin-protein ligase, which mediates ubiquitination and subsequent proteasomal degradation of proteins containing phosphotyrosine binding (PTB) domains. This protein may play an important role in tumorogenesis. Alternatively spliced trans... See more...

Aliases for LNX1 Gene

Aliases for LNX1 Gene

  • Ligand Of Numb-Protein X 1 2 3 4 5
  • PDZRN2 2 3 4
  • Ligand Of Numb-Protein X 1, E3 Ubiquitin Protein Ligase 2 3
  • RING-Type E3 Ubiquitin Transferase LNX 3 4
  • E3 Ubiquitin-Protein Ligase LNX 3 4
  • Numb-Binding Protein 1 3 4
  • MPDZ 2 3
  • LNX 3 4
  • Multi-PDZ-Domain-Containing Protein, E3 Ubiquitin-Protein Ligase LNX 3
  • PDZ Domain-Containing Ring Finger Protein 2 3
  • PDZ Domain-Containing RING Finger Protein 2 4
  • Ligand Of Numb-Protein X 2
  • EC 2.3.2.27 4
  • LNX1 5

External Ids for LNX1 Gene

Previous HGNC Symbols for LNX1 Gene

  • LNX

Previous GeneCards Identifiers for LNX1 Gene

  • GC04M054167
  • GC04M054020
  • GC04M054325
  • GC04M050271

Summaries for LNX1 Gene

Entrez Gene Summary for LNX1 Gene

  • This gene encodes a membrane-bound protein that is involved in signal transduction and protein interactions. The encoded product is an E3 ubiquitin-protein ligase, which mediates ubiquitination and subsequent proteasomal degradation of proteins containing phosphotyrosine binding (PTB) domains. This protein may play an important role in tumorogenesis. Alternatively spliced transcript variants encoding distinct isoforms have been described. A pseudogene, which is located on chromosome 17, has been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for LNX1 Gene

LNX1 (Ligand Of Numb-Protein X 1) is a Protein Coding gene. Diseases associated with LNX1 include Usher Syndrome and Q Fever. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. Gene Ontology (GO) annotations related to this gene include ligase activity and PDZ domain binding. An important paralog of this gene is LNX2.

UniProtKB/Swiss-Prot Summary for LNX1 Gene

  • E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of NUMB. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Mediates ubiquitination of isoform p66 and isoform p72 of NUMB, but not that of isoform p71 or isoform p65.
  • Isoform 2 provides an endocytic scaffold for IGSF5/JAM4.

Gene Wiki entry for LNX1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LNX1 Gene

Genomics for LNX1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LNX1 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
GH04J053589 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 260.7 +109.7 109713 4.8 MNT IKZF1 BHLHE40 ZEB1 ELF1 SIN3A ZNF395 REST VEZF1 ZEB2 LNX1 LNX1-AS2 LOC100506444 lnc-SCFD2-5 ENSG00000282278
GH04J053701 Enhancer 1.3 FANTOM5 ENCODE CraniofacialAtlas 250.7 -1.4 -1408 2.2 SP1 MXD4 BCL11A FEZF1 CTCF ZIC2 ZNF610 SIN3A FOXA2 TRIM22 LNX1 CHIC2 lnc-FIP1L1-9 LOC100506444 ENSG00000282278
GH04J053557 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 250.1 +143.2 143237 1.9 EBF1 FOSL1 SPI1 JUND PKNOX1 FOSL2 ZNF24 FOS POLR2A ZNF600 piR-38004 LNX1 piR-43105-491 ENSG00000282278
GH04J053699 Enhancer 0.5 Ensembl 250.7 +1.8 1804 0.4 GABPA HNF4A IKZF1 ZNF687 ZNF766 IKZF2 LNX1 HSALNG0034441 LOC100506444 ENSG00000282278
GH04J054217 Promoter/Enhancer 1.5 ENCODE CraniofacialAtlas dbSUPER 10.3 -516.5 -516534 1.2 CTCF REST TRIM22 KLF7 RXRA SMC3 RAD21 HNF4A ZNF189 ZSCAN29 GSX2 LNX1 LOC100506444 HSALNG0034467 RPL22P13 PDGFRA ENSG00000282278
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LNX1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LNX1

Top Transcription factor binding sites by QIAGEN in the LNX1 gene promoter:
  • ARP-1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Lmo2
  • RFX1
  • Roaz

Genomic Locations for LNX1 Gene

Latest Assembly
chr4:53,458,264-53,701,405
(GRCh38/hg38)
Size:
243,142 bases
Orientation:
Minus strand

Previous Assembly
chr4:54,325,468-54,457,653
(GRCh37/hg19 by Entrez Gene)
Size:
132,186 bases
Orientation:
Minus strand

chr4:54,325,468-54,567,572
(GRCh37/hg19 by Ensembl)
Size:
242,105 bases
Orientation:
Minus strand

Genomic View for LNX1 Gene

Genes around LNX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LNX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LNX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LNX1 Gene

Proteins for LNX1 Gene

  • Protein details for LNX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TBB1-LNX1_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase LNX
    Protein Accession:
    Q8TBB1
    Secondary Accessions:
    • Q4W5K7
    • Q8N4C2
    • Q96MJ7
    • Q9BY20

    Protein attributes for LNX1 Gene

    Size:
    728 amino acids
    Molecular mass:
    80629 Da
    Quaternary structure:
    • Interacts with the phosphotyrosine interaction domain of all isoforms of NUMB (By similarity). Interacts with MAGEB18 and MAGEF1. Interacts with the Coxsackievirus and adenovirus receptor CXADR. Interacts with endogenous retrovirus K protein Np9. IGSF5/JAM4 interacts with isoform 2 through the second PDZ domain, other isoforms may also interact with IGSF5/JAM4 (By similarity).

    Three dimensional structures from OCA and Proteopedia for LNX1 Gene

    Alternative splice isoforms for LNX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LNX1 Gene

Post-translational modifications for LNX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LNX1 Gene

Domains & Families for LNX1 Gene

Gene Families for LNX1 Gene

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

Protein Domains for LNX1 Gene

InterPro:
Blocks:
  • Zn-finger, RING
  • PDZ/DHR/GLGF domain
ProtoNet:

Suggested Antigen Peptide Sequences for LNX1 Gene

GenScript: Design optimal peptide antigens:
  • Numb-binding protein 1 (LNX1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TBB1

UniProtKB/Swiss-Prot:

LNX1_HUMAN :
  • The NPXY motif is required for the interaction with the PID domain of NUMB. It is however not sufficient.
Domain:
  • The NPXY motif is required for the interaction with the PID domain of NUMB. It is however not sufficient.
  • The PDZ 1 domain participates in the interaction with the PID domain of NUMB, and participates in the isoform-specific ubiquitination of NUMB. The PDZ 2 domain of isoform 2 participates in the interaction with IGSF5/JAM4, other isoforms containing this domain may also interact with IGSF5/JAM4 (By similarity).
genes like me logo Genes that share domains with LNX1: view

Function for LNX1 Gene

Molecular function for LNX1 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of NUMB. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Mediates ubiquitination of isoform p66 and isoform p72 of NUMB, but not that of isoform p71 or isoform p65.
UniProtKB/Swiss-Prot Function:
Isoform 2 provides an endocytic scaffold for IGSF5/JAM4.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27;.

Enzyme Numbers (IUBMB) for LNX1 Gene

Phenotypes From GWAS Catalog for LNX1 Gene

Gene Ontology (GO) - Molecular Function for LNX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IEA --
GO:0005515 protein binding IPI 16002321
GO:0016740 transferase activity IEA --
GO:0030165 PDZ domain binding IEA --
GO:0042802 identical protein binding IEA --
genes like me logo Genes that share ontologies with LNX1: view
genes like me logo Genes that share phenotypes with LNX1: view

Animal Models for LNX1 Gene

MGI Knock Outs for LNX1:

Animal Models for research

  • Taconic Biosciences Mouse Models for LNX1

miRNA for LNX1 Gene

miRTarBase miRNAs that target LNX1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LNX1

Clone products for research

  • Addgene plasmids for LNX1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LNX1 Gene

Localization for LNX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LNX1 Gene

Cytoplasm.

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 LNX1 gene
Compartment Confidence
nucleus 4
plasma membrane 2
cytoskeleton 2
cytosol 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (3)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LNX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with LNX1: view

Pathways & Interactions for LNX1 Gene

genes like me logo Genes that share pathways with LNX1: view

UniProtKB/Swiss-Prot Q8TBB1-LNX1_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

SIGNOR curated interactions for LNX1 Gene

Inactivates:

Gene Ontology (GO) - Biological Process for LNX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with LNX1: view

Drugs & Compounds for LNX1 Gene

(5) Drugs for LNX1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine monophosphate Approved, Investigational Nutra 0
Phosphate Experimental Pharma 0
ATP Investigational Nutra 0

(5) Additional Compounds for LNX1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • [(HO)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • Pyrophosphoric acid
14000-31-8
genes like me logo Genes that share compounds with LNX1: view

Transcripts for LNX1 Gene

mRNA/cDNA for LNX1 Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
9 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 LNX1

Clone products for research

  • Addgene plasmids for LNX1

Alternative Splicing Database (ASD) splice patterns (SP) for LNX1 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1:
SP2: -
SP3:
SP4:
SP5: -
SP6:

Relevant External Links for LNX1 Gene

GeneLoc Exon Structure for
LNX1

Expression for LNX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LNX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LNX1 Gene

This gene is overexpressed in Esophagus - Mucosa (x4.1).

Protein differential expression in normal tissues from HIPED for LNX1 Gene

This gene is overexpressed in Cervix (49.8) and Adipocyte (13.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LNX1 Gene



Protein tissue co-expression partners for LNX1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LNX1

SOURCE GeneReport for Unigene cluster for LNX1 Gene:

Hs.518760

mRNA Expression by UniProt/SwissProt for LNX1 Gene:

Q8TBB1-LNX1_HUMAN
Tissue specificity: Expressed in heart, placenta, kidney, pancreas and brain.

Evidence on tissue expression from TISSUES for LNX1 Gene

  • Nervous system(4.9)
  • Skin(2)
genes like me logo Genes that share expression patterns with LNX1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LNX1 Gene

Orthologs for LNX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LNX1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LNX1 30 31
  • 99.31 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LNX1 30 31
  • 88.51 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LNX1 30 31
  • 88.03 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lnx1 30
  • 85.13 (n)
Mouse
(Mus musculus)
Mammalia Lnx1 30 17 31
  • 84.99 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LNX1 31
  • 81 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 76 (a)
ManyToMany
-- 31
  • 14 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves LNX1 30 31
  • 73.47 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LNX1 31
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lnx1 30
  • 66.25 (n)
Zebrafish
(Danio rerio)
Actinopterygii lnx1 30 31
  • 62.82 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta inaD 31
  • 15 (a)
OneToMany
Species where no ortholog for LNX1 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)
  • 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 LNX1 Gene

ENSEMBL:
Gene Tree for LNX1 (if available)
TreeFam:
Gene Tree for LNX1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LNX1: view image

Paralogs for LNX1 Gene

Paralogs for LNX1 Gene

(10) SIMAP similar genes for LNX1 Gene using alignment to 4 proteins:

  • LNX1_HUMAN
  • D6RAH9_HUMAN
  • D6RB76_HUMAN
  • D6RE08_HUMAN

Pseudogenes.org Pseudogenes for LNX1 Gene

genes like me logo Genes that share paralogs with LNX1: view

Variants for LNX1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LNX1 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs1187998909 Likely Benign: not provided 53,459,298(-) C/T
NM_030917.4(FIP1L1):c.1638-4C>T
INTRON
rs1435218 Association Not Found: Lip and oral cavity carcinoma 53,535,732(-) C/T
NM_001126328.3(LNX1):c.381-27505G>A
INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LNX1 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 LNX1 Gene

Variant ID Type Subtype PubMed ID
esv1673226 CNV insertion 17803354
esv28169 CNV gain 19812545
esv3303852 CNV mobile element insertion 20981092
esv3307826 CNV mobile element insertion 20981092
esv3309918 CNV mobile element insertion 20981092
esv3331791 CNV duplication 20981092
esv3339869 CNV insertion 20981092
esv3379648 CNV insertion 20981092
esv3600527 CNV loss 21293372
nsv1115671 CNV duplication 24896259
nsv1146065 CNV duplication 26484159
nsv437918 CNV loss 16468122
nsv476884 CNV novel sequence insertion 20440878
nsv516916 CNV loss 19592680
nsv829936 CNV gain 17160897

Variation tolerance for LNX1 Gene

Residual Variation Intolerance Score: 49.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.27; 40.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LNX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LNX1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LNX1 Gene

Disorders for LNX1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for LNX1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
usher syndrome
  • deafness-retinitis pigmentosa syndrome
q fever
  • infection due to coxiella burnetii
autoimmune enteropathy
cystic fibrosis
  • cf
muscular dystrophy, congenital, lmna-related
  • mdcl
- elite association - COSMIC cancer census association via MalaCards
Search LNX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LNX1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with LNX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LNX1 Gene

Publications for LNX1 Gene

  1. Identification of a human LNX protein containing multiple PDZ domains. (PMID: 11521506) Xie Y … Mao Y (Biochemical genetics 2001) 2 3 4 23
  2. MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases. (PMID: 20864041) Doyle JM … Potts PR (Molecular cell 2010) 3 4
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. A genome-wide association study identifies novel and functionally related susceptibility Loci for Kawasaki disease. (PMID: 19132087) Burgner D … International Kawasaki Disease Genetics Consortium (PLoS genetics 2009) 3 41
  5. Mutation and copy number analysis of LNX1 and Numbl in nervous system tumors. (PMID: 18940473) Blom T … Nupponen NN (Cancer genetics and cytogenetics 2008) 3 41

Products for LNX1 Gene

Sources for LNX1 Gene