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Aliases for LNX1 Gene

Aliases for LNX1 Gene

  • Ligand Of Numb-Protein X 1 2 3 4 5
  • Ligand Of Numb-Protein X 1, E3 Ubiquitin Protein Ligase 2 3
  • RING-Type E3 Ubiquitin Transferase LNX 3 4
  • Numb-Binding Protein 1 3 4
  • PDZRN2 3 4
  • 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
  • E3 Ubiquitin-Protein Ligase LNX 3
  • Ligand Of Numb-Protein X 2
  • EC 2.3.2.27 4
  • MPDZ 3

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, Type 1C and Autoimmune Enteropathy. Among its related pathways are Notch signaling pathway (KEGG) and Innate Immune System. GO annotations related to this gene include ligase activity and PDZ domain binding. An important paralog of this gene is LNX2.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for LNX1 Gene

Genomics for LNX1 Gene

Regulatory Elements for LNX1 Gene

Enhancers for LNX1 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
GH04G053676 1.6 FANTOM5 Ensembl ENCODE 18 +24.8 24767 0.8 ATF1 PKNOX1 ARNT TCF12 ZNF766 GATA2 NCOA1 MBD2 SMARCA4 MYNN LNX1 CHIC2 PDGFRA GC04M053662
GH04G053653 1.1 Ensembl ENCODE 16 +47.4 47412 1.8 TBP BMI1 RAD21 YY1 ZNF207 RELB IKZF2 TBX21 NR2F2 IKZF1 LNX1 LOC100506444 LNX1-AS2
GH04G053009 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10 +688.0 688013 7.6 CTCF PKNOX1 JUN ZBTB40 RAD21 ZNF507 ZNF316 POLR2A SMC3 FOS LOC100506444 LNX1 PIR32665 LOC101928658
GH04G053540 1 Ensembl ENCODE 14.8 +159.3 159276 4.2 PKNOX1 TEAD4 SIN3A EBF1 GATA3 CTBP1 POLR2A PRDM10 RELB FOS LNX1 LOC100506444 DANCR PIR61049 LNX1-AS1
GH04G054217 1.4 Ensembl ENCODE dbSUPER 10.3 -516.5 -516534 1.2 RB1 NFIB SIN3A KLF17 RAD21 ZNF121 GATA2 ZNF143 KLF7 ZNF263 GSX2 LNX1 LOC100506444 RPL22P13
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LNX1 on UCSC Golden Path with GeneCards custom track

Genomic Location for LNX1 Gene

Chromosome:
4
Start:
53,459,301 bp from pter
End:
53,701,405 bp from pter
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

Suggested Antigen Peptide Sequences for LNX1 Gene

GenScript: Design optimal peptide antigens:

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 CatalyticActivity:
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.
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.

Enzyme Numbers (IUBMB) 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:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0030165 PDZ domain 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 Model Products

  • Taconic Biosciences Mouse Models for LNX1

CRISPR Products

miRNA for LNX1 Gene

miRTarBase miRNAs that target LNX1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for LNX1
  • Applied Biological Materials Clones 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 3
cytosol 2
cytoskeleton 1

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 --
GO:0042787 protein ubiquitination involved in ubiquitin-dependent protein catabolic process IEA --
GO:0051260 protein homooligomerization 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
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with LNX1: view

Transcripts for LNX1 Gene

Unigene Clusters for LNX1 Gene

Ligand of numb-protein X 1, E3 ubiquitin protein ligase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for LNX1
  • Applied Biological Materials Clones 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
ECgene alternative splicing isoforms for
LNX1

Expression for LNX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for LNX1 Gene



Protein tissue co-expression partners for LNX1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LNX1 Gene:

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)
genes like me logo Genes that share expression patterns with LNX1: view

Primer Products

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 34 35
  • 99.31 (n)
dog
(Canis familiaris)
Mammalia LNX1 34 35
  • 88.51 (n)
cow
(Bos Taurus)
Mammalia LNX1 34 35
  • 88.03 (n)
rat
(Rattus norvegicus)
Mammalia Lnx1 34
  • 85.13 (n)
mouse
(Mus musculus)
Mammalia Lnx1 34 16 35
  • 84.99 (n)
oppossum
(Monodelphis domestica)
Mammalia LNX1 35
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 76 (a)
ManyToMany
-- 35
  • 14 (a)
ManyToMany
chicken
(Gallus gallus)
Aves LNX1 34 35
  • 73.47 (n)
lizard
(Anolis carolinensis)
Reptilia LNX1 35
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lnx1 34
  • 66.25 (n)
zebrafish
(Danio rerio)
Actinopterygii lnx1 34 35
  • 62.82 (n)
fruit fly
(Drosophila melanogaster)
Insecta inaD 35
  • 15 (a)
OneToMany
Species where no ortholog for LNX1 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)
  • 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 squirt (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)

Paralogs for LNX1 Gene

Paralogs for LNX1 Gene

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

Pseudogenes.org Pseudogenes for LNX1 Gene

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

Variants for LNX1 Gene

Sequence variations from dbSNP and Humsavar for LNX1 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs1000010609 -- 53,584,896(+) AACGT(A/G)TATCA intron-variant
rs1000023650 -- 53,626,087(+) GTTGC(A/G)ACATG intron-variant
rs10000315 -- 53,570,427(+) ccaaa(C/T)accgc intron-variant
rs10000457 -- 53,555,372(+) TTCCT(C/T)TAAGC intron-variant
rs1000047807 -- 53,507,149(+) CTTTC(-/T)GCCTT intron-variant

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)

Relevant External Links for LNX1 Gene

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

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

Disorders for LNX1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LNX1 Gene - From: GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type 1c
  • usher syndrome type 1c
autoimmune enteropathy
- elite association - COSMIC cancer census association via MalaCards
Search LNX1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LNX1

Genetic Association Database (GAD)
LNX1
Human Genome Epidemiology (HuGE) Navigator
LNX1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LNX1
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. (Biochem. Genet. 2001) 2 3 4 22 64
  2. 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
  3. MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases. (PMID: 20864041) Doyle J.M. … Potts P.R. (Mol. Cell 2010) 3 4 64
  4. A genome-wide association study identifies novel and functionally related susceptibility Loci for Kawasaki disease. (PMID: 19132087) Burgner D. … Hibberd M.L. (PLoS Genet. 2009) 3 46 64
  5. Mutation and copy number analysis of LNX1 and Numbl in nervous system tumors. (PMID: 18940473) Blom T. … Nupponen N.N. (Cancer Genet. Cytogenet. 2008) 3 46 64

Products for LNX1 Gene

  • Addgene plasmids for LNX1

Sources for LNX1 Gene

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