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Aliases for LNX1 Gene

Aliases for LNX1 Gene

  • Ligand Of Numb-Protein X 1 2 3 4
  • Ligand Of Numb-Protein X 1, E3 Ubiquitin Protein Ligase 2 3 5
  • 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
  • Ligand Of Numb-Protein X 2
  • EC 6.3.2.- 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 Immune System and Kit Receptor Signaling Pathway. GO annotations related to this gene include ligase activity and PDZ domain binding. An important paralog of this gene is PDZD2.

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 (By similarity).

  • Isoform 2 provides an endocytic scaffold for IGSF5/JAM4.

Gene Wiki entry for LNX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LNX1 Gene

Genomics for LNX1 Gene

Regulatory Elements for LNX1 Gene

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

Proteomics data for LNX1 Gene at MOPED

Post-translational modifications for LNX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

No data available for DME Specific Peptides for LNX1 Gene

Domains & Families for LNX1 Gene

Gene Families for LNX1 Gene

Protein Domains 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.
  • Contains 1 RING-type zinc finger.
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).
  • Contains 4 PDZ (DHR) domains.
Similarity:
  • Contains 1 RING-type zinc finger.
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 (By similarity).
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:0008270 zinc ion binding IEA --
GO:0016874 ligase 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

miRNA for LNX1 Gene

miRTarBase miRNAs that target LNX1

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

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
Jensen Localization Image for LNX1 Gene COMPARTMENTS Subcellular localization image for LNX1 gene
Compartment Confidence
nucleus 3
cytosol 2
cytoskeleton 1

No data available for Gene Ontology (GO) - Cellular Components for LNX1 Gene

Pathways & Interactions for LNX1 Gene

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

Pathways by source for LNX1 Gene

1 GeneGo (Thomson Reuters) pathway for LNX1 Gene
1 Qiagen pathway for LNX1 Gene

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

None

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 Nutra 0
Adenosine triphosphate Approved Nutra 0
Diphosphate Experimental Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
7664-38-2
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:

Inhibitory RNA Products

Flow Cytometry Products

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 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



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

Protein tissue co-expression partners for LNX1 Gene

Primer Products

In Situ Assay Products

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 35
  • 99.31 (n)
  • 99.59 (a)
LNX1 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LNX1 36
  • 88 (a)
OneToOne
LNX1 35
  • 88.03 (n)
  • 88.86 (a)
dog
(Canis familiaris)
Mammalia LNX1 35
  • 88.51 (n)
  • 88.74 (a)
LNX1 36
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lnx1 16
Lnx1 36
  • 88 (a)
OneToOne
Lnx1 35
  • 84.99 (n)
  • 88.95 (a)
oppossum
(Monodelphis domestica)
Mammalia LNX1 36
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 14 (a)
ManyToMany
-- 36
  • 76 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Lnx1 35
  • 85.13 (n)
  • 88.12 (a)
chicken
(Gallus gallus)
Aves LNX1 35
  • 73.47 (n)
  • 74.93 (a)
LNX1 36
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LNX1 36
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lnx1 35
  • 66.25 (n)
  • 64.81 (a)
zebrafish
(Danio rerio)
Actinopterygii lnx1 36
  • 57 (a)
OneToOne
lnx1 35
  • 62.82 (n)
  • 62.17 (a)
fruit fly
(Drosophila melanogaster)
Insecta inaD 36
  • 15 (a)
OneToMany
Species with no ortholog for LNX1:
  • 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
rs1077966 -- 53,651,174(+) GTAAG(C/T)AAATG intron-variant
rs716251 -- 53,555,893(+) AAATT(A/T)TTAAG intron-variant
rs1347406 -- 53,586,320(+) TCAAA(A/G)GCAGT intron-variant
rs366074 -- 53,565,967(+) ttgct(A/C/G/T)gtttc intron-variant
rs750695 -- 53,637,601(+) ACTAC(A/G)GAATT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LNX1 Gene

Variant ID Type Subtype PubMed ID
nsv516916 CNV Loss 19592680
esv268131 CNV Insertion 20981092
nsv829936 CNV Gain 17160897
esv28169 CNV Gain 19812545
esv268900 CNV Insertion 20981092
esv272100 CNV Insertion 20981092
esv274190 CNV Insertion 20981092
esv1673226 CNV Insertion 17803354
nsv437918 CNV Loss 16468122
nsv879014 CNV Loss 21882294

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

HapMap Linkage Disequilibrium report
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
  • ush1c
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 23 67
  2. LNX functions as a RING type E3 ubiquitin ligase that targets the cell fate determinant Numb for ubiquitin-dependent degradation. (PMID: 11782429) Nie J. … McGlade C.J. (EMBO J. 2002) 2 3
  3. The Lnx family proteins function as molecular scaffolds for Numb family proteins. (PMID: 11922143) Rice D.S. … Kurschner C. (Mol. Cell. Neurosci. 2001) 3 23
  4. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A. … Stelzl U. (Mol. Syst. Biol. 2015) 3
  5. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. (PMID: 24722188) Corominas R. … Iakoucheva L.M. (Nat. Commun. 2014) 3

Products for LNX1 Gene

Sources for LNX1 Gene

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