LNX1 ligand of numb-protein X 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LNX1provided by HGNC
Official Full Name: ligand of numb-protein X 1provided by HGNC
Primary source: HGNC:HGNC:6657
See related: Ensembl:ENSG00000072201 MIM:609732; AllianceGenome:HGNC:6657
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LNX; MPDZ; PDZRN2
Summary: 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]
Expression: Ubiquitous expression in brain (RPKM 10.1), esophagus (RPKM 8.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q12

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (53459301..53652477, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (56946519..57139835, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (54325468..54457653, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study reveals how the LNX1 RING domain is structurally and mechanistically dependent on other motifs for its E3 ligase activity, and describes how dimeric LNX1 recruits ubiquitin (Ub)-loaded Ubc13 for Ub transfer via E3 ligase-mediated catalysis.
Title: Structure of LNX1:Ubc13~Ubiquitin Complex Reveals the Role of Additional Motifs for the E3 Ligase Activity of LNX1.
study provided the evidences that LNX1 signaling plays important roles in regulating the stemness of colon cancer cells
Title: Suppression of cancer stemness by upregulating Ligand-of-Numb protein X1 in colorectal carcinoma.
LNX was closely related to human gliomas and suggested it plays an important role in gliomas by notch signaling.
Title: [Molecular cloning and identify expression of the novel human LNX gene in gliomas].
LNX1-mediated ubiquitination and degradation of PBK inhibited cell proliferation and enhanced sensitivity to doxorubicin-induced apoptosis.
Title: Proteomics strategy to identify substrates of LNX, a PDZ domain-containing E3 ubiquitin ligase.
identify and confirm six novel LNX1 binding partners: KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2 and PBK, and suggest that LNX1 functions as a signalling scaffold.
Title: Biochemical and computational analysis of LNX1 interacting proteins.
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.
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.
Down-regulation of LNX could result in cell cycle arrest in G0/G1 phase through inhibition of beta-catenin, MAPK, NFkappaB, c-Myc-dependent pathway and activation of p53, TGF-beta-dependent pathway.
Title: A global genomic view on LNX siRNA-mediated cell cycle arrest.
LNX and RhoC might be part of a larger protein complex that would have important functions in signaling transduction about regulating the transcriptional activities of AP-1.
Title: LNX (Ligand of Numb-protein X) interacts with RhoC, both of which regulate AP-1-mediated transcriptional activation.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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
GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-67779 (e-PCR)
- UniSTS:28467

D4S2897 (e-PCR)
- UniSTS:154168

A006X48 (e-PCR)
- UniSTS:20281

STS-R85294 (e-PCR)
- UniSTS:2364

D4S2783 (e-PCR)
- UniSTS:77119

G19694 (e-PCR)
- UniSTS:17219

A001V35 (e-PCR)
- UniSTS:17220

SHGC-78604 (e-PCR)
- UniSTS:101709

SHGC-59803 (e-PCR)
- UniSTS:64864

SHGC-67415 (e-PCR)
- UniSTS:13418

RH122481 (e-PCR)
- UniSTS:135354

D4S2583E (e-PCR)
- UniSTS:150985

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 protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in synapse maturation	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in hippocampal mossy fiber to CA3 synapse	IEA Inferred from Electronic Annotation more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase LNX

Names: PDZ domain-containing ring finger protein 2; RING-type E3 ubiquitin transferase LNX; ligand of numb-protein X 1, E3 ubiquitin protein ligase; multi-PDZ-domain-containing protein, E3 ubiquitin-protein ligase LNX; numb-binding protein 1

NP_001119800.1

EC 2.3.2.27

NP_116011.2

EC 2.3.2.27

XP_005265842.1

EC 2.3.2.27

XP_024310030.1

EC 2.3.2.27

XP_047272284.1

EC 2.3.2.27

XP_054207084.1

EC 2.3.2.27

XP_054207085.1

EC 2.3.2.27

XP_054207086.1

EC 2.3.2.27

XP_054207087.1

EC 2.3.2.27

XP_054207088.1

EC 2.3.2.27

XP_054207089.1

EC 2.3.2.27

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)

NM_001126328.3 → NP_001119800.1 E3 ubiquitin-protein ligase LNX isoform a

See identical proteins and their annotated locations for NP_001119800.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a, also known as LNXp80).

Source sequence(s)

AC058822, BC022983, BC034737, DB159390

Consensus CDS

CCDS47057.1

UniProtKB/Swiss-Prot

Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20

Related

ENSP00000263925.7, ENST00000263925.8

Conserved Domains (2) summary

cd00992
Location:637 → 721

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) ...

cd16779
Location:38 → 79

mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
NM_032622.3 → NP_116011.2 E3 ubiquitin-protein ligase LNX isoform b precursor

See identical proteins and their annotated locations for NP_116011.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1. The resulting isoform (b, also known as LNXp70) contains a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

AC058822, BC034737, DA154083

Consensus CDS

CCDS3492.1

UniProtKB/TrEMBL

B4DGI5

Related

ENSP00000302879.2, ENST00000306888.6

Conserved Domains (1) summary

cd00992
Location:541 → 625

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) ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

53459301..53652477 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005265785.6 → XP_005265842.1 E3 ubiquitin-protein ligase LNX isoform X1

See identical proteins and their annotated locations for XP_005265842.1

UniProtKB/Swiss-Prot

Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20

Conserved Domains (2) summary

cd00992
Location:637 → 721

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) ...

cd16779
Location:38 → 79

mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
XM_024454262.2 → XP_024310030.1 E3 ubiquitin-protein ligase LNX isoform X1

UniProtKB/Swiss-Prot

Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20

Conserved Domains (2) summary

cd00992
Location:637 → 721

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) ...

cd16779
Location:38 → 79

mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
XM_047416328.1 → XP_047272284.1 E3 ubiquitin-protein ligase LNX isoform X2