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Aliases for LNX2 Gene

Aliases for LNX2 Gene

  • Ligand Of Numb-Protein X 2 2 3 5
  • PDZ Domain-Containing RING Finger Protein 1 3 4
  • PDZ Domain Containing Ring Finger 1 2 3
  • Numb-Binding Protein 2 3 4
  • PDZRN1 3 4
  • Ligand Of Numb Protein X 2 3

External Ids for LNX2 Gene

Previous HGNC Symbols for LNX2 Gene

  • PDZRN1

Previous GeneCards Identifiers for LNX2 Gene

  • GC13U990083
  • GC13M025918
  • GC13M027018
  • GC13M028120
  • GC13M008941

Summaries for LNX2 Gene

GeneCards Summary for LNX2 Gene

LNX2 (Ligand Of Numb-Protein X 2) is a Protein Coding gene. Diseases associated with LNX2 include Treacher Collins Syndrome 2 and Q Fever. Gene Ontology (GO) annotations related to this gene include PDZ domain binding. An important paralog of this gene is LNX1.

Additional gene information for LNX2 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LNX2 Gene

Genomics for LNX2 Gene

GeneHancer (GH) Regulatory Elements for LNX2 Gene

Promoters and enhancers for LNX2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J027617 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 665.3 +0.0 44 5.3 HDGF PKNOX1 CLOCK FOXA2 ZFP64 ARID4B NEUROD1 SIN3A FEZF1 DMAP1 POLR1D LNX2 CHCHD2P8 PAN3 WASF3-AS1 RNU6-63P
GH13J027599 Enhancer 1 Ensembl ENCODE 19.7 +20.4 20433 1.4 TEAD4 TAL1 JUN BMI1 ZNF7 RFX5 TEAD3 FOSL1 ZNF335 TCF12 POLR1D LNX2 RNU6-63P
GH13J027548 Enhancer 0.8 ENCODE 19.5 +70.3 70251 3 FEZF1 ZNF2 RAD21 YY1 ZNF335 ZNF366 ZFP91 RCOR1 SP3 RXRA POLR1D LNX2 RNU6-63P
GH13J027641 Enhancer 1.2 Ensembl ENCODE dbSUPER 11.9 -23.0 -23006 3.8 ELF3 FOXA2 ARID4B DMAP1 RAD21 ZNF48 RARA ZNF614 CREM MIXL1 POLR1D LNX2 RNU6-63P GC13P027624 LOC105370128
GH13J027476 Enhancer 1.2 FANTOM5 Ensembl ENCODE 10.6 +143.0 143001 1.4 FOXA2 BATF IRF4 YY1 FOS IKZF2 CREM RXRA JUNB SP1 POLR1D LNX2 MTIF3 RNU6-63P GC13P027459
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LNX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LNX2 gene promoter:
  • Pax-5
  • Pbx1a
  • Lmo2
  • AhR
  • Arnt
  • FOXI1
  • HFH-3
  • Msx-1
  • Nkx2-2

Genomic Locations for LNX2 Gene

Genomic Locations for LNX2 Gene
74,673 bases
Minus strand
74,671 bases
Minus strand

Genomic View for LNX2 Gene

Genes around LNX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LNX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LNX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LNX2 Gene

Proteins for LNX2 Gene

  • Protein details for LNX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ligand of Numb protein X 2
    Protein Accession:
    Secondary Accessions:
    • Q5W0P0
    • Q6ZMH2
    • Q96SH4

    Protein attributes for LNX2 Gene

    690 amino acids
    Molecular mass:
    76004 Da
    Quaternary structure:
    • Interacts with the phosphotyrosine interaction domain of NUMB.
    • Sequence=BAD18754.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LNX2 Gene

neXtProt entry for LNX2 Gene

Post-translational modifications for LNX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LNX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LNX2 Gene

Domains & Families for LNX2 Gene

Gene Families for LNX2 Gene

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

Protein Domains for LNX2 Gene

Suggested Antigen Peptide Sequences for LNX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The NPXY motif is required for the interaction with the PID domain of NUMB. It is however not sufficient.
  • The NPXY motif is required for the interaction with the PID domain of NUMB. It is however not sufficient.
genes like me logo Genes that share domains with LNX2: view

Function for LNX2 Gene

Phenotypes From GWAS Catalog for LNX2 Gene

Gene Ontology (GO) - Molecular Function for LNX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22458338
GO:0030165 PDZ domain binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LNX2: view
genes like me logo Genes that share phenotypes with LNX2: view

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LNX2 Gene

Localization for LNX2 Gene

Subcellular locations from

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 LNX2 gene
Compartment Confidence
cytosol 4
nucleus 3
plasma membrane 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
  • Vesicles (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for LNX2 Gene

Pathways & Interactions for LNX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LNX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051260 protein homooligomerization IEA --
genes like me logo Genes that share ontologies with LNX2: view

No data available for Pathways by source and SIGNOR curated interactions for LNX2 Gene

Drugs & Compounds for LNX2 Gene

No Compound Related Data Available

Transcripts for LNX2 Gene

mRNA/cDNA for LNX2 Gene

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

Unigene Clusters for LNX2 Gene

Ligand of numb-protein X 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LNX2 Gene

No ASD Table

Relevant External Links for LNX2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LNX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LNX2 Gene

Protein differential expression in normal tissues from HIPED for LNX2 Gene

This gene is overexpressed in Serum (35.5), Placenta (26.4), and Fetal heart (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LNX2 Gene

Protein tissue co-expression partners for LNX2 Gene

NURSA nuclear receptor signaling pathways regulating expression of LNX2 Gene:


SOURCE GeneReport for Unigene cluster for LNX2 Gene:


Evidence on tissue expression from TISSUES for LNX2 Gene

  • Intestine(4.2)
genes like me logo Genes that share expression patterns with LNX2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LNX2 Gene

Orthologs for LNX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for LNX2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LNX2 34 33
  • 99.37 (n)
(Monodelphis domestica)
Mammalia LNX2 34
  • 88 (a)
(Canis familiaris)
Mammalia LNX2 34 33
  • 87.95 (n)
(Ornithorhynchus anatinus)
Mammalia LNX2 34
  • 86 (a)
(Bos Taurus)
Mammalia LNX2 34 33
  • 83.33 (n)
(Rattus norvegicus)
Mammalia Lnx2 33
  • 81.8 (n)
(Mus musculus)
Mammalia Lnx2 16 34 33
  • 80.9 (n)
(Gallus gallus)
Aves LNX2 34 33
  • 77 (n)
(Anolis carolinensis)
Reptilia LNX2 34
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lnx2 33
  • 73.58 (n)
Str.16970 33
(Danio rerio)
Actinopterygii lnx2a 34 33
  • 63.75 (n)
Dr.11117 33
fruit fly
(Drosophila melanogaster)
Insecta inaD 34
  • 16 (a)
Species where no ortholog for LNX2 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 LNX2 Gene

Gene Tree for LNX2 (if available)
Gene Tree for LNX2 (if available)
Evolutionary constrained regions (ECRs) for LNX2: view image

Paralogs for LNX2 Gene

Paralogs for LNX2 Gene

(1) SIMAP similar genes for LNX2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LNX2: view

Variants for LNX2 Gene

Sequence variations from dbSNP and Humsavar for LNX2 Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs2232676 likely-benign, Treacher Collins Syndrome, Dominant 27,621,835(-) C/T upstream_transcript_variant
rs2232677 likely-benign, Treacher Collins Syndrome, Dominant 27,621,874(-) C/A upstream_transcript_variant
rs2232678 likely-benign, Treacher Collins Syndrome, Dominant 27,621,877(-) C/T upstream_transcript_variant
rs2232679 likely-benign, Treacher Collins Syndrome, Dominant 27,621,896(-) G/C upstream_transcript_variant
rs2232680 likely-benign, Treacher Collins Syndrome, Dominant 27,621,963(-) G/A/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LNX2 Gene

Variant ID Type Subtype PubMed ID
esv2048214 CNV deletion 18987734
esv3580584 CNV loss 25503493
nsv1039183 CNV loss 25217958

Variation tolerance for LNX2 Gene

Residual Variation Intolerance Score: 37% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.06; 37.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LNX2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LNX2 Gene

Disorders for LNX2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LNX2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
treacher collins syndrome 2
  • tcs2
q fever
  • infection due to coxiella burnetii
- elite association - COSMIC cancer census association via MalaCards
Search LNX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LNX2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LNX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LNX2 Gene

Publications for LNX2 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A … Ross MT (Nature 2004) 3 4 58
  3. 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
  4. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. (PMID: 29117863) Choudhury NR … Michlewski G (BMC biology 2017) 3 58
  5. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. (PMID: 27107012) Yachie N … Roth FP (Molecular systems biology 2016) 3 58

Products for LNX2 Gene

Sources for LNX2 Gene

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