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LNX2 ligand of numb-protein X 2 [ Homo sapiens (human) ]

Gene ID: 222484, updated on 3-Apr-2024

Summary

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Official Symbol
LNX2provided by HGNC
Official Full Name
ligand of numb-protein X 2provided by HGNC
Primary source
HGNC:HGNC:20421
See related
Ensembl:ENSG00000139517 MIM:609733; AllianceGenome:HGNC:20421
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PDZRN1
Summary
Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein ubiquitination. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 9.5), small intestine (RPKM 7.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
13q12.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (27545913..27621107, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (26766973..26842233, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (28120050..28194666, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:28008622-28009821 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32805 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:28023938-28024852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7507 Neighboring gene general transcription factor IIIA Neighboring gene Sharpr-MPRA regulatory region 13742 Neighboring gene mitochondrial translational initiation factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7508 Neighboring gene RNA, U6 small nuclear 63, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32806 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32807 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28107144-28107644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28107645-28108145 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32810 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:28194694-28195422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5204 Neighboring gene RNA polymerase I and III subunit D Neighboring gene nucleophosmin 1 pseudogene 4 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:28302713-28303912 Neighboring gene uncharacterized LOC105370129

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/β-catenin pathway in colorectal cancer. Camps J, et al. Cancer Res, 2013 Mar 15. PMID 23319804, Free PMC Article
  2. The ligands of Numb proteins X1 and X2 are specific markers for chronic Q fever. Mehraj V, et al. FEMS Immunol Med Microbiol, 2012 Feb. PMID 22066909
  3. E3 ubiquitin ligases LNX1 and LNX2 localize at neuronal gap junctions formed by connexin36 in rodent brain and molecularly interact with connexin36. Lynn BD, et al. Eur J Neurosci, 2018 Nov. PMID 30295974
  4. Structural basis for the indispensable role of a unique zinc finger motif in LNX2 ubiquitination. Nayak D, et al. Oncotarget, 2015 Oct 27. PMID 26451611, Free PMC Article
  5. Ligand of Numb proteins LNX1p80 and LNX2 interact with the human glycoprotein CD8α and promote its ubiquitylation and endocytosis. D'Agostino M, et al. J Cell Sci, 2011 Nov 1. PMID 22045731

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LNX2 involves in the role of ghrelin to promote the neuronal differentiation of adipose tissue-derived mesenchymal stem cells.
    Title: LNX2 involves in the role of ghrelin to promote the neuronal differentiation of adipose tissue-derived mesenchymal stem cells.
  2. FOXC2 or its associated gene expression program may provide an effective target for anti-EMT-based therapies for the treatment of claudin-low/basal B breast tumors or other EMT-/CSC-enriched tumors
    Title: Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/β-catenin pathway in colorectal cancer.
  3. The authors found a high level of LNX1 and LNX2 mRNAs in endocarditis, the principal manifestation of chronic Q fever, but not in acute Q fever.
    Title: The ligands of Numb proteins X1 and X2 are specific markers for chronic Q fever.
  4. LNX1 and LNX2 interact with CD8alpha and promote its ubiquitylation and endocytosis
    Title: Ligand of Numb proteins LNX1p80 and LNX2 interact with the human glycoprotein CD8α and promote its ubiquitylation and endocytosis.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Common variants on 14q32 and 13q12 are associated with DLBCL susceptibility.
EBI GWAS Catalog
Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of ligand of numb-protein X 2 (LNX2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ12933, FLJ23932, FLJ38000, MGC46315

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables PDZ domain binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin-protein transferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in neural precursor cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
ligand of Numb protein X 2
Names
PDZ domain containing ring finger 1
PDZ domain-containing RING finger protein 1
numb-binding protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_153371.4 → NP_699202.1  ligand of Numb protein X 2

    See identical proteins and their annotated locations for NP_699202.1

    Status: VALIDATED

    Source sequence(s)
    AK022995, BC036755, DB220129, DN990012
    Consensus CDS
    CCDS9323.1
    UniProtKB/Swiss-Prot
    Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
    UniProtKB/TrEMBL
    B2R8J5
    Related
    ENSP00000325929.3, ENST00000316334.5
    Conserved Domains (3) summary
    smart00228
    Location:230 → 316
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:599 → 683
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd16780
    Location:45 → 89
    mRING-HC-C3HC3D_LNX2; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    27545913..27621107 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020434.2 → XP_016875923.1  ligand of Numb protein X 2 isoform X1

    UniProtKB/Swiss-Prot
    Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
    UniProtKB/TrEMBL
    B2R8J5
    Conserved Domains (3) summary
    smart00228
    Location:230 → 316
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:599 → 683
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd16780
    Location:45 → 89
    mRING-HC-C3HC3D_LNX2; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2)

  2. XM_011534995.3 → XP_011533297.1  ligand of Numb protein X 2 isoform X2

    UniProtKB/TrEMBL
    B2R8J5
    Conserved Domains (3) summary
    smart00184
    Location:50 → 86
    RING; Ring finger
    smart00228
    Location:230 → 299
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:476 → 560
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  3. XM_047430148.1 → XP_047286104.1  ligand of Numb protein X 2 isoform X1

    UniProtKB/Swiss-Prot
    Q5W0P0, Q6ZMH2, Q8N448, Q96SH4

  4. XM_047430150.1 → XP_047286106.1  ligand of Numb protein X 2 isoform X1

    UniProtKB/Swiss-Prot
    Q5W0P0, Q6ZMH2, Q8N448, Q96SH4

  5. XM_047430151.1 → XP_047286107.1  ligand of Numb protein X 2 isoform X2

  6. XM_047430145.1 → XP_047286101.1  ligand of Numb protein X 2 isoform X1

    UniProtKB/Swiss-Prot
    Q5W0P0, Q6ZMH2, Q8N448, Q96SH4

  7. XM_047430147.1 → XP_047286103.1  ligand of Numb protein X 2 isoform X1

    UniProtKB/Swiss-Prot
    Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
    Related
    ENSP00000497224.1, ENST00000649248.1

  8. XM_047430149.1 → XP_047286105.1  ligand of Numb protein X 2 isoform X1

    UniProtKB/Swiss-Prot
    Q5W0P0, Q6ZMH2, Q8N448, Q96SH4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    26766973..26842233 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374213.1 → XP_054230188.1  ligand of Numb protein X 2 isoform X1

  2. XM_054374212.1 → XP_054230187.1  ligand of Numb protein X 2 isoform X1

  3. XM_054374215.1 → XP_054230190.1  ligand of Numb protein X 2 isoform X1

  4. XM_054374219.1 → XP_054230194.1  ligand of Numb protein X 2 isoform X2

  5. XM_054374218.1 → XP_054230193.1  ligand of Numb protein X 2 isoform X1

  6. XM_054374220.1 → XP_054230195.1  ligand of Numb protein X 2 isoform X2

  7. XM_054374214.1 → XP_054230189.1  ligand of Numb protein X 2 isoform X1

  8. XM_054374217.1 → XP_054230192.1  ligand of Numb protein X 2 isoform X1

  9. XM_054374216.1 → XP_054230191.1  ligand of Numb protein X 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N448.1 GenPept UniProtKB/Swiss-Prot:Q8N448

Gene LinkOut

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