LUM lumican [Homo sapiens (human)] - Gene

Summary

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

Location:: 12q21.33

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (91102629..91111494, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (91080108..91088974, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (91496406..91505271, complement)

Chromosome 12 - NC_000012.12 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
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?

Circulating lumican as a potential biomarker for osteosarcopenia in older adults.
Title: Circulating lumican as a potential biomarker for osteosarcopenia in older adults.
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.
The versatile roles of lumican in eye diseases: A review.
Title: The versatile roles of lumican in eye diseases: A review.
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.
The Involvement of Lumican in Human Ovulatory Processes.
Title: The Involvement of Lumican in Human Ovulatory Processes.
The Downregulation of Placental Lumican Promotes the Progression of Preeclampsia.
Title: The Downregulation of Placental Lumican Promotes the Progression of Preeclampsia.
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.
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.
Lumican promotes joint fibrosis through TGF-beta signaling.
Title: Lumican promotes joint fibrosis through TGF-β signaling.
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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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
Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. 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

RH18011 (e-PCR)
- UniSTS:53058

RH48690 (e-PCR)
- UniSTS:78410

RH69649 (e-PCR)
- UniSTS:79969

RME09 (e-PCR)
- UniSTS:251491

D12S805 (e-PCR)
- UniSTS:149115

GDB:596270 (e-PCR)
- UniSTS:158081

RH44503 (e-PCR)
- UniSTS:79746

SHGC-35342 (e-PCR)
- UniSTS:74726

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 more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular matrix	TAS Traceable Author Statement more info	PubMed
located_in extracellular region	HDA more info	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 more info	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)

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