LUM Gene (Protein Coding)

Lumican

GC12M091102
GIFtS:
43
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 o... See more...

Aliases for LUM Gene

Aliases for LUM Gene

  • Lumican 2 3 4 5
  • Keratan Sulfate Proteoglycan Lumican 3 4
  • Lumican Proteoglycan 2 3
  • KSPG Lumican 3 4
  • SLRR2D 3 4
  • LDC 3 4
  • Epididymis Secretory Sperm Binding Protein 3

External Ids for LUM Gene

Previous HGNC Symbols for LUM Gene

  • LDC

Previous GeneCards Identifiers for LUM Gene

  • GC12M090819
  • GC12M091944
  • GC12M091430
  • GC12M089999
  • GC12M088565

Summaries for LUM Gene

Entrez Gene Summary for LUM Gene

  • 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]

GeneCards Summary for LUM Gene

LUM (Lumican) is a Protein Coding gene. Diseases associated with LUM include Cornea Plana and Corneal Dystrophy, Posterior Amorphous. Among its related pathways are Keratan sulfate/keratin metabolism and Proteoglycans in cancer. Gene Ontology (GO) annotations related to this gene include collagen binding and extracellular matrix structural constituent. An important paralog of this gene is FMOD.

Gene Wiki entry for LUM Gene

Additional gene information for LUM Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LUM Gene

Genomics for LUM Gene

GeneHancer (GH) Regulatory Elements for LUM Gene

Promoters and enhancers for LUM Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH12J091108 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 750.6 +1.2 1237 3.9 CTCF RAD21 MAX TRIM22 SMC3 ZNF143 L3MBTL2 LUM KERA
GH12J091175 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.2 -68.1 -68094 9.7 CTCF RAD21 PRDM1 POLR2A ZNF512 ZSCAN4 CEBPB ZNF316 SMC3 NR2F2 DCN lnc-LUM-1 KERA LUM ENSG00000258100
GH12J091137 Enhancer 1.2 VISTA Ensembl ENCODE dbSUPER 11.4 -29.1 -29136 6.6 ZNF384 POLR2A CEBPB JUN EP300 FOS STAT3 RCOR1 FEZF1 LUM DCN KERA ENSG00000258100 lnc-LUM-1
GH12J091357 Enhancer 0.9 Ensembl ENCODE CraniofacialAtlas 10.4 -245.8 -245824 1.1 NFYC ELF3 SP1 PKNOX1 CTBP1 POLR2A ZNF217 GATA3 ELF1 JUND LUM DCN LOC105369898 LINC02823 ENSG00000258100
GH12J091073 Enhancer 0.7 Ensembl ENCODE dbSUPER 10.6 +37.4 37439 1.7 ZBTB10 FOXA2 LUM KERA
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LUM on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LUM gene promoter:
  • AML1a
  • CBF-B
  • Meis-1
  • Meis-1a
  • Meis-1b
  • NF-Y
  • NF-YA
  • NF-YB
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for LUM Gene

Genomic Locations for LUM Gene
chr12:91,102,629-91,111,765
(GRCh38/hg38)
Size:
9,137 bases
Orientation:
Minus strand
chr12:91,496,406-91,505,608
(GRCh37/hg19)
Size:
9,203 bases
Orientation:
Minus strand

Genomic View for LUM Gene

Genes around LUM on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for LUM Gene

Proteins for LUM Gene

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

    Protein Symbol:
    P51884-LUM_HUMAN
    Recommended name:
    Lumican
    Protein Accession:
    P51884
    Secondary Accessions:
    • B2R6R5
    • Q96QM7

    Protein attributes for LUM Gene

    Size:
    338 amino acids
    Molecular mass:
    38429 Da
    Quaternary structure:
    • Binds to laminin.

neXtProt entry for LUM Gene

Protein Expression for LUM Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LUM Gene

  • Sulfated on tyrosine residue(s).
  • Glycosylation at Asn88, Asn127, Asn160, and Asn252
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for LUM Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LUM Gene

Domains & Families for LUM Gene

Gene Families for LUM Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted secreted proteins

Protein Domains for LUM Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LUM Gene

GenScript: Design optimal peptide antigens:
  • Keratan sulfate proteoglycan lumican (LUM_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P51884

UniProtKB/Swiss-Prot:

LUM_HUMAN :
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.
genes like me logo Genes that share domains with LUM: view

Function for LUM Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for LUM Gene

GENATLAS Biochemistry:
lumican,keratan sulfate proteoglycan one of the three major constituents of the corneal stroma,playing a role in the regulation of collagen assembly into fibrils in various connective tissues,small-leucine-rich proteoglycans family

Phenotypes From GWAS Catalog for LUM Gene

Gene Ontology (GO) - Molecular Function for LUM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent NAS 10892350
GO:0005515 protein binding IPI 25304424
GO:0005518 collagen binding IDA,IBA 10892350
GO:0030021 extracellular matrix structural constituent conferring compression resistance RCA 20551380
genes like me logo Genes that share ontologies with LUM: view
genes like me logo Genes that share phenotypes with LUM: view

Animal Models for LUM Gene

MGI Knock Outs for LUM:
  • Lum Lum<tm1Chak>
  • Lum Lum<tm1.1(KOMP)Vlcg>
  • Lum Lum<tm1Wwk>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LUM

Clone Products

Cell Line Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for LUM Gene

Localization for LUM Gene

Subcellular locations from UniProtKB/Swiss-Prot for LUM Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
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 LUM gene
Compartment Confidence
extracellular 5
lysosome 4
golgi apparatus 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for LUM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region HDA,TAS --
GO:0005583 fibrillar collagen trimer IDA 10734230
GO:0005615 extracellular space HDA 20551380
GO:0005796 Golgi lumen TAS --
GO:0031012 extracellular matrix TAS 7665616
genes like me logo Genes that share ontologies with LUM: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LUM Gene

Pathways & Interactions for LUM Gene

genes like me logo Genes that share pathways with LUM: view

Gene Ontology (GO) - Biological Process for LUM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception TAS,IEA --
GO:0014070 response to organic cyclic compound IEA --
GO:0018146 keratan sulfate biosynthetic process TAS --
GO:0030198 extracellular matrix organization TAS --
GO:0030199 collagen fibril organization NAS 10892350
genes like me logo Genes that share ontologies with LUM: view

No data available for SIGNOR curated interactions for LUM Gene

Drugs & Compounds for LUM Gene

Products:

  1. Drug

(1) Drugs for LUM Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Copper Approved, Investigational Pharma Target 227
genes like me logo Genes that share compounds with LUM: view

Transcripts for LUM Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for LUM Gene

(1) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(1083) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LUM

Clone Products

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

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b · 3c
SP1:
SP2: - -
SP3: -

Relevant External Links for LUM Gene

GeneLoc Exon Structure for
LUM
ECgene alternative splicing isoforms for
LUM

Expression for LUM Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for LUM Gene
mRNA expression by GTEx for LUM GenemRNA expression by BioGPS for LUM Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LUM Gene

This gene is overexpressed in Lung (x4.4), Heart - Atrial Appendage (x4.1), and Adipose - Visceral (Omentum) (x4.0).

Protein differential expression in normal tissues from HIPED for LUM Gene

This gene is overexpressed in Breast (6.3) and Synovial fluid (6.2).

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



Protein tissue co-expression partners for LUM Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LUM Gene:

LUM

SOURCE GeneReport for Unigene cluster for LUM Gene:

Hs.406475

mRNA Expression by UniProt/SwissProt for LUM Gene:

P51884-LUM_HUMAN
Tissue specificity: Cornea and other tissues.

Evidence on tissue expression from TISSUES for LUM Gene

  • Lung(4.9)
  • Intestine(4.8)
  • Eye(4.7)
  • Liver(4.5)
  • Heart(4.3)
  • Bone marrow(4.2)
  • Pancreas(3.7)
  • Muscle(3.2)
  • Gall bladder(3.1)
  • Stomach(3.1)
  • Bone(2.9)
  • Lymph node(2.9)
  • Kidney(2.6)
  • Adrenal gland(2.5)
  • Nervous system(2.4)
  • Skin(2.3)
  • Blood(2.2)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with LUM: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LUM Gene

Orthologs for LUM Gene

This gene was present in the common ancestor of chordates.

Orthologs for LUM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia LUM 33 32
  • 99.41 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia LUM 33 32
  • 89.64 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia LUM 33 32
  • 87.67 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Lum 17 33 32
  • 82.45 (n)
rat
(Rattus norvegicus)
 Mammalia Lum 32
  • 82.05 (n)
oppossum
(Monodelphis domestica)
 Mammalia LUM 33
  • 75 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia LUM 33
  • 74 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LUM 33 32
  • 69.94 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia LUM 33
  • 65 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia lum 32
  • 63.01 (n)
Str.15551 32
African clawed frog
(Xenopus laevis)
 Amphibia MGC64527 32
zebrafish
(Danio rerio)
 Actinopterygii lum 33 32
  • 57.35 (n)
 OneToOne
sea squirt
(Ciona savignyi)
 Ascidiacea -- 33
  • 28 (a)
 OneToMany
Species where no ortholog for LUM was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 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 LUM Gene

ENSEMBL:
Gene Tree for LUM (if available)
TreeFam:
Gene Tree for LUM (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LUM: view image

Paralogs for LUM Gene

Paralogs for LUM Gene

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

  • LUM_HUMAN
genes like me logo Genes that share paralogs with LUM: view

Variants for LUM Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for LUM Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000372689 -- 91,112,781(-) C/T upstream_transcript_variant
rs1000905803 -- 91,103,437(-) T/C 3_prime_UTR_variant
rs1001019883 -- 91,103,138(-) G/C 3_prime_UTR_variant
rs1001137864 -- 91,109,763(-) T/C intron_variant
rs1001312923 -- 91,110,173(-) G/A intron_variant

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

Variant ID Type Subtype PubMed ID
dgv210n27 CNV loss 19166990
dgv2784n54 CNV loss 21841781
nsv559751 CNV loss 21841781

Variation tolerance for LUM Gene

Residual Variation Intolerance Score: 35.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.08; 22.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LUM Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LUM Gene

MalaCards: The human disease database

(11) MalaCards diseases for LUM Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cornea plana
  • flat cornea
corneal dystrophy, posterior amorphous
  • pacd
degenerative myopia
  • degenerative progressive high myopia
macular dystrophy, corneal
  • mcd
eccrine acrospiroma
  • eccrine hidradenoma
- elite association - COSMIC cancer census association via MalaCards
Search LUM in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LUM

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

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

Publications for LUM Gene

  1. Primary structure of human lumican (keratan sulfate proteoglycan) and localization of the gene (LUM) to chromosome 12q21.3-q22. (PMID: 7558030) Chakravarti S … Hassell JR (Genomics 1995) 2 3 4 23 56
  2. Association of the lumican gene functional 3'-UTR polymorphism with high myopia. (PMID: 19643966) Lin HJ … Tsai FJ (Investigative ophthalmology & visual science 2010) 3 23 43 56
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 43 56
  4. The association between lumican gene polymorphisms and high myopia. (PMID: 20010793) Lin HJ … Tsai FJ (Eye (London, England) 2010) 3 43 56
  5. Association of breast cancer susceptibility variants with risk of pancreatic cancer. (PMID: 19843670) Couch FJ … Petersen GM (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2009) 3 43 56

ExternalLinks

View latest publications for LUM gene in Mastermind

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