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LUM lumican [ Homo sapiens (human) ]

Gene ID: 4060, updated on 3-Nov-2024

Summary

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Official Symbol
LUMprovided by HGNC
Official Full Name
lumicanprovided by HGNC
Primary source
HGNC:HGNC:6724
See related
Ensembl:ENSG00000139329 MIM:600616; AllianceGenome:HGNC:6724
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
LDC; SLRR2D
Summary
This gene encodes a member of the small leucine-rich proteoglycan (SLRP) family that includes decorin, biglycan, fibromodulin, keratocan, epiphycan, and osteoglycin. In these bifunctional molecules, the protein moiety binds collagen fibrils and the highly charged hydrophilic glycosaminoglycans regulate interfibrillar spacings. Lumican is the major keratan sulfate proteoglycan of the cornea but is also distributed in interstitial collagenous matrices throughout the body. Lumican may regulate collagen fibril organization and circumferential growth, corneal transparency, and epithelial cell migration and tissue repair. [provided by RefSeq, Jul 2008]
Expression
Broad expression in gall bladder (RPKM 981.2), urinary bladder (RPKM 643.2) and 14 other tissues See more
Orthologs
mouse all
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Genomic context

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See LUM in Genome Data Viewer
Location:
12q21.33
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (91102629..91111494, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (91080108..91088974, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (91496406..91505271, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:91377884-91378418 Neighboring gene epiphycan Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:91434914-91435454 Neighboring gene keratocan Neighboring gene VISTA enhancer hs2540 Neighboring gene decorin Neighboring gene uncharacterized LOC124903075

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 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. Association analysis of polymorphisms in lumican gene and systemic lupus erythematosus in a Taiwan Chinese Han population. Chang PC, et al. J Rheumatol, 2011 Nov. PMID 21885486
  2. Downregulation of lumican enhanced mitotic defects and aneuploidy in lung cancer cells. Yang CT, et al. Cell Cycle, 2020 Jan. PMID 31760859, Free PMC Article
  3. Lumican is upregulated in osteoarthritis and contributes to TLR4-induced pro-inflammatory activation of cartilage degradation and macrophage polarization. Barreto G, et al. Osteoarthritis Cartilage, 2020 Jan. PMID 31715293
  4. [Interference of Lumican Regulates the Invasion and Migration of Liver Cancer Cells]. Mu QM, et al. Sichuan Da Xue Xue Bao Yi Xue Ban, 2018 May. PMID 30014634
  5. Expression and roles of lumican in lung adenocarcinoma and squamous cell carcinoma. Matsuda Y, et al. Int J Oncol, 2008 Dec. PMID 19020750

See all (135) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circulating lumican as a potential biomarker for osteosarcopenia in older adults.
    Title: Circulating lumican as a potential biomarker for osteosarcopenia in older adults.
  2. LUM as a novel prognostic marker and its correlation with immune infiltration in gastric cancer: a study based on immunohistochemical analysis and bioinformatics.
    Title: LUM as a novel prognostic marker and its correlation with immune infiltration in gastric cancer: a study based on immunohistochemical analysis and bioinformatics.
  3. The versatile roles of lumican in eye diseases: A review.
    Title: The versatile roles of lumican in eye diseases: A review.
  4. Lumican is elevated in the lung in human and experimental acute respiratory distress syndrome and promotes early fibrotic responses to lung injury.
    Title: Lumican is elevated in the lung in human and experimental acute respiratory distress syndrome and promotes early fibrotic responses to lung injury.
  5. The Involvement of Lumican in Human Ovulatory Processes.
    Title: The Involvement of Lumican in Human Ovulatory Processes.
  6. The Downregulation of Placental Lumican Promotes the Progression of Preeclampsia.
    Title: The Downregulation of Placental Lumican Promotes the Progression of Preeclampsia.
  7. Lumican silencing alleviates tumor necrosis factor-alpha-induced nucleus pulposus cell inflammation and senescence by inhibiting apoptosis signal regulating kinase 1/p38 signaling pathway via inactivating Fas ligand expression.
    Title: Lumican silencing alleviates tumor necrosis factor-α-induced nucleus pulposus cell inflammation and senescence by inhibiting apoptosis signal regulating kinase 1/p38 signaling pathway via inactivating Fas ligand expression.
  8. Matrix lumican endocytosed by immune cells controls receptor ligand trafficking to promote TLR4 and restrict TLR9 in sepsis.
    Title: Matrix lumican endocytosed by immune cells controls receptor ligand trafficking to promote TLR4 and restrict TLR9 in sepsis.
  9. Lumican promotes joint fibrosis through TGF-beta signaling.
    Title: Lumican promotes joint fibrosis through TGF-β signaling.
  10. Expression and role of lumican in acute aortic dissection: A human and mouse study.
    Title: Expression and role of lumican in acute aortic dissection: A human and mouse study.
Submit: New GeneRIF Correction See all GeneRIFs (90)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9.
EBI GWAS Catalog
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables collagen binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables collagen binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables extracellular matrix structural constituent NAS
Non-traceable Author Statement
more info
 PubMed 
enables extracellular matrix structural constituent conferring compression resistance ISS
Inferred from Sequence or Structural Similarity
more info
  
enables extracellular matrix structural constituent conferring compression resistance RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in collagen fibril organization NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transforming growth factor beta1 production IEA
Inferred from Electronic Annotation
more info
  
involved_in visual perception TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi lumen TAS
Traceable Author Statement
more info
  
colocalizes_with collagen-containing extracellular matrix HDA PubMed 
located_in collagen-containing extracellular matrix HDA PubMed 
colocalizes_with collagen-containing extracellular matrix ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in extracellular matrix TAS
Traceable Author Statement
more info
 PubMed 
located_in extracellular region HDA PubMed 
located_in extracellular region NAS
Non-traceable Author Statement
more info
 PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of fibrillar collagen trimer IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal lumen TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
lumican
Names
KSPG lumican
epididymis secretory sperm binding protein
keratan sulfate proteoglycan lumican
lumican proteoglycan

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_002345.4 → NP_002336.1  lumican precursor

    See identical proteins and their annotated locations for NP_002336.1

    Status: REVIEWED

    Source sequence(s)
    AA036658, AC078873, BC007038
    Consensus CDS
    CCDS9038.1
    UniProtKB/Swiss-Prot
    B2R6R5, P51884, Q96QM7
    UniProtKB/TrEMBL
    A0A384N669, Q53FV4
    Related
    ENSP00000266718.4, ENST00000266718.5
    Conserved Domains (3) summary
    smart00013
    Location:37 → 71
    LRRNT; Leucine rich repeat N-terminal domain
    sd00033
    Location:68 → 91
    LRR_RI; leucine-rich repeat [structural motif]
    NF033190
    Location:68 → 310
    inl_like_NEAT_1; NEAT domain-containing leucine-rich repeat protein

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

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    91102629..91111494 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    91080108..91088974 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51884.2 GenPept UniProtKB/Swiss-Prot:P51884

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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