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    LGMN legumain [ Homo sapiens (human) ]

    Gene ID: 5641, updated on 3-Apr-2024

    Summary

    Official Symbol
    LGMNprovided by HGNC
    Official Full Name
    legumainprovided by HGNC
    Primary source
    HGNC:HGNC:9472
    See related
    Ensembl:ENSG00000100600 MIM:602620; AllianceGenome:HGNC:9472
    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
    AEP; LGMN1; PRSC1
    Summary
    This gene encodes a cysteine protease that has a strict specificity for hydrolysis of asparaginyl bonds. This enzyme may be involved in the processing of bacterial peptides and endogenous proteins for MHC class II presentation in the lysosomal/endosomal systems. Enzyme activation is triggered by acidic pH and appears to be autocatalytic. Protein expression occurs after monocytes differentiate into dendritic cells. A fully mature, active enzyme is produced following lipopolysaccharide expression in mature dendritic cells. Overexpression of this gene may be associated with the majority of solid tumor types. This gene has a pseudogene on chromosome 13. Several alternatively spliced transcript variants have been described, but the biological validity of only two has been determined. These two variants encode the same isoform. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in placenta (RPKM 135.7), spleen (RPKM 98.7) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LGMN in Genome Data Viewer
    Location:
    14q32.12
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (92703809..92748627, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (86935604..86980392, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (93170154..93214972, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:92980671-92981174 Neighboring gene uncharacterized LOC124903365 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:92990985-92991808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92994044-92994801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92994802-92995558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92997484-92997984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92997985-92998485 Neighboring gene MPRA-validated peak2237 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8931 Neighboring gene Ras and Rab interactor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8933 Neighboring gene NANOG hESC enhancer GRCh37_chr14:93039726-93040227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8938 Neighboring gene Sharpr-MPRA regulatory region 14383 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:93090702-93091901 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93122369-93122870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93128149-93128650 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:93131812-93131989 Neighboring gene uncharacterized LOC124903364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93152626-93153253 Neighboring gene Sharpr-MPRA regulatory region 13986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6038 Neighboring gene Sharpr-MPRA regulatory region 11533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93175352-93175977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93175978-93176602 Neighboring gene Sharpr-MPRA regulatory region 3328 Neighboring gene MPRA-validated peak2238 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6039 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:93260331-93260478 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93260501-93261045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93261046-93261589 Neighboring gene golgin A5 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:93312588-93313787 Neighboring gene long intergenic non-protein coding RNA 2833

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of legumain (LGMN) in peptide-treated PBMCs PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cysteine-type endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cysteine-type endopeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables cysteine-type endopeptidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables cysteine-type endopeptidase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables endopeptidase activator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables peptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables tau protein binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in activation of cysteine-type endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II TAS
    Traceable Author Statement
    more info
     
    involved_in associative learning ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in cellular response to amyloid-beta IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to calcium ion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to hepatocyte growth factor stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in dendritic spine organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in memory ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in negative regulation of ERBB signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within negative regulation of neuron apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of endothelial cell chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of long-term synaptic potentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of monocyte chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in proteolysis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in proteolysis involved in protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in proteolysis involved in protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in proteolysis involved in protein catabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in receptor catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in renal system process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to acidic pH IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to acidic pH ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in self proteolysis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in vacuolar protein processing IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in vitamin D metabolic process TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in apical part of cell IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endolysosome lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in lysosomal lumen IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    located_in lysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in lysosome TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    legumain
    Names
    asparaginyl endopeptidase
    cysteine protease 1
    protease, cysteine 1
    protease, cysteine, 1 (legumain)
    NP_001008530.1
    NP_001350625.1
    NP_001350628.1
    NP_005597.3
    XP_005267919.1
    XP_005267920.1
    XP_011535272.1
    XP_016876952.1
    XP_047287551.1
    XP_047287553.1
    XP_047287554.1
    XP_054232381.1
    XP_054232382.1
    XP_054232383.1
    XP_054232384.1
    XP_054232385.1
    XP_054232386.1
    XP_054232387.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001008530.3NP_001008530.1  legumain isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_001008530.1

      Status: REVIEWED

      Source sequence(s)
      BX161434, CD366588, DA347449
      Consensus CDS
      CCDS9904.1
      UniProtKB/Swiss-Prot
      O00123, Q86TV2, Q86TV3, Q99538, Q9BTY1
      UniProtKB/TrEMBL
      A8K669, Q53XC6, Q6I9U9
      Related
      ENSP00000376911.2, ENST00000393218.6
      Conserved Domains (1) summary
      pfam01650
      Location:29285
      Peptidase_C13; Peptidase C13 family
    2. NM_001363696.2NP_001350625.1  legumain isoform 2 precursor

      Status: REVIEWED

      Source sequence(s)
      AL132987, AL136332
      Consensus CDS
      CCDS86424.1
      UniProtKB/TrEMBL
      A8K669, Q6I9U9
      Conserved Domains (1) summary
      pfam01650
      Location:29285
      Peptidase_C13; Peptidase C13 family
    3. NM_001363699.2NP_001350628.1  legumain isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      AL132987, AL136332
      Consensus CDS
      CCDS86423.1
      Conserved Domains (1) summary
      pfam01650
      Location:29285
      Peptidase_C13; Peptidase C13 family
    4. NM_005606.7NP_005597.3  legumain isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_005597.3

      Status: REVIEWED

      Source sequence(s)
      AL132987, AL136332, BC013678, CD366588
      Consensus CDS
      CCDS9904.1
      UniProtKB/Swiss-Prot
      O00123, Q86TV2, Q86TV3, Q99538, Q9BTY1
      UniProtKB/TrEMBL
      A8K669, Q53XC6, Q6I9U9
      Related
      ENSP00000334052.4, ENST00000334869.9
      Conserved Domains (1) summary
      pfam01650
      Location:29285
      Peptidase_C13; Peptidase C13 family

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      92703809..92748627 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005267863.4XP_005267920.1  legumain isoform X4

      See identical proteins and their annotated locations for XP_005267920.1

      UniProtKB/Swiss-Prot
      Q99538
      Related
      ENSP00000451861.1, ENST00000555699.5
      Conserved Domains (1) summary
      pfam01650
      Location:29285
      Peptidase_C13; Peptidase C13 family
    2. XM_005267862.4XP_005267919.1  legumain isoform X3

      See identical proteins and their annotated locations for XP_005267919.1

      UniProtKB/TrEMBL
      A8K669, Q6I9U9
      Related
      ENSP00000452572.1, ENST00000557434.5
      Conserved Domains (1) summary
      pfam01650
      Location:29285
      Peptidase_C13; Peptidase C13 family
    3. XM_011536970.2XP_011535272.1  legumain isoform X2

      UniProtKB/TrEMBL
      A8K669, Q6I9U9
      Conserved Domains (1) summary
      pfam01650
      Location:29285
      Peptidase_C13; Peptidase C13 family
    4. XM_017021463.2XP_016876952.1  legumain isoform X1

      UniProtKB/Swiss-Prot
      O00123, Q86TV2, Q86TV3, Q99538, Q9BTY1
      UniProtKB/TrEMBL
      A8K669, Q53XC6, Q6I9U9
      Conserved Domains (1) summary
      pfam01650
      Location:29285
      Peptidase_C13; Peptidase C13 family
    5. XM_047431595.1XP_047287551.1  legumain isoform X1

      UniProtKB/Swiss-Prot
      O00123, Q86TV2, Q86TV3, Q99538, Q9BTY1
      UniProtKB/TrEMBL
      Q53XC6
    6. XM_047431598.1XP_047287554.1  legumain isoform X2

    7. XM_047431597.1XP_047287553.1  legumain isoform X1

      UniProtKB/Swiss-Prot
      O00123, Q86TV2, Q86TV3, Q99538, Q9BTY1
      UniProtKB/TrEMBL
      Q53XC6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      86935604..86980392 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376412.1XP_054232387.1  legumain isoform X4

    2. XM_054376411.1XP_054232386.1  legumain isoform X3

    3. XM_054376409.1XP_054232384.1  legumain isoform X2

    4. XM_054376407.1XP_054232382.1  legumain isoform X1

      UniProtKB/Swiss-Prot
      O00123, Q86TV2, Q86TV3, Q99538, Q9BTY1
      UniProtKB/TrEMBL
      Q53XC6
    5. XM_054376406.1XP_054232381.1  legumain isoform X1

      UniProtKB/Swiss-Prot
      O00123, Q86TV2, Q86TV3, Q99538, Q9BTY1
      UniProtKB/TrEMBL
      Q53XC6
    6. XM_054376410.1XP_054232385.1  legumain isoform X2

    7. XM_054376408.1XP_054232383.1  legumain isoform X1

      UniProtKB/Swiss-Prot
      O00123, Q86TV2, Q86TV3, Q99538, Q9BTY1
      UniProtKB/TrEMBL
      Q53XC6