This gene encodes a protein with similarity to the GS I members of the glutamine synthetase superfamily. The encoded protein is referred to as a pseudo-glutamine synthetase because it has no glutamine synthesis activity and may function as a chaperone protein. This protein is localized to the lens and may be associated with cataract disease. Alternative splicing results in mult... See more...

Aliases for LGSN Gene

Aliases for LGSN Gene

  • Lengsin, Lens Protein With Glutamine Synthetase Domain 2 3 5
  • LGS 2 3 4
  • Glutamate-Ammonia Ligase Domain-Containing Protein 1 3 4
  • Lengsin 3 4
  • GLULD1 3 4
  • Glutamate-Ammonia Ligase (Glutamine Synthetase) Domain Containing 1 2
  • Glutamate-Ammonia Ligase (Glutamine Synthase) Domain Containing 1 3
  • Lens Glutamine Synthase-Like 4
  • LGSN 5

External Ids for LGSN Gene

Previous HGNC Symbols for LGSN Gene

  • GLULD1

Previous GeneCards Identifiers for LGSN Gene

  • GC06M064048
  • GC06M061165

Summaries for LGSN Gene

Entrez Gene Summary for LGSN Gene

  • This gene encodes a protein with similarity to the GS I members of the glutamine synthetase superfamily. The encoded protein is referred to as a pseudo-glutamine synthetase because it has no glutamine synthesis activity and may function as a chaperone protein. This protein is localized to the lens and may be associated with cataract disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]

GeneCards Summary for LGSN Gene

LGSN (Lengsin, Lens Protein With Glutamine Synthetase Domain) is a Protein Coding gene. Diseases associated with LGSN include Retinitis Pigmentosa 25 and Cataract. Gene Ontology (GO) annotations related to this gene include glutamate-ammonia ligase activity. An important paralog of this gene is GLUL.

UniProtKB/Swiss-Prot Summary for LGSN Gene

  • May act as a component of the cytoskeleton or as a chaperone for the reorganization of intermediate filament proteins during terminal differentiation in the lens. Does not seem to have enzymatic activity (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LGSN Gene

Genomics for LGSN Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LGSN 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
GH06J063568 Enhancer 0.4 Ensembl dbSUPER 600.7 -0.1 -80 0.4 PRDM1 LGSN ENSG00000266680 ENSG00000285976 RF00017-5614 PTP4A1
GH06J063570 Enhancer 0.3 Ensembl 600.7 -0.8 -780 0.2 RBFOX2 LGSN ENSG00000266680 ENSG00000285976 RF00017-5614 PTP4A1
GH06J063569 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.6 -5.2 -5219 7.3 CEBPG SP1 HNRNPL CREB1 GATAD2A CTCF TEAD4 PRDM10 ZNF629 REST ENSG00000266680 ENSG00000285976 PTP4A1 PHF3 LGSN SCAT8 NONHSAG044042.2 RF00017-5614
GH06J063451 Enhancer 0.9 ENCODE 27.5 +115.2 115215 1.7 CEBPG GATAD2A ATF7 REST TFE3 SOX13 NFKBIZ RCOR2 RBFOX2 RXRB LGSN PHF3 lnc-PTP4A1-6 lnc-PTP4A1-5 PTP4A1
GH06J063456 Enhancer 1.3 FANTOM5 Ensembl ENCODE 18.7 +109.1 109119 4.8 GATAD2A ATF7 REST TFE3 SOX13 NFKBIZ RCOR2 RBFOX2 RXRB IRF2 LGSN PTP4A1 lnc-PTP4A1-6 lnc-PTP4A1-5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LGSN on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LGSN

Top Transcription factor binding sites by QIAGEN in the LGSN gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • C/EBPalpha
  • Evi-1
  • FosB
  • Fra-1
  • GATA-2
  • RSRFC4
  • TBP

Genomic Locations for LGSN Gene

Genomic Locations for LGSN Gene
chr6:63,275,951-63,567,921
(GRCh38/hg38)
Size:
291,971 bases
Orientation:
Minus strand
chr6:63,985,856-64,029,882
(GRCh37/hg19)
Size:
44,027 bases
Orientation:
Minus strand

Genomic View for LGSN Gene

Genes around LGSN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for LGSN Gene

Proteins for LGSN Gene

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

    Protein Symbol:
    Q5TDP6-LGSN_HUMAN
    Recommended name:
    Lengsin
    Protein Accession:
    Q5TDP6
    Secondary Accessions:
    • A1L421
    • Q0PVN9
    • Q0PVP0
    • Q9NYJ0

    Protein attributes for LGSN Gene

    Size:
    509 amino acids
    Molecular mass:
    57278 Da
    Quaternary structure:
    • Dodecamer. Interacts with BFSP2 AND VIM (By similarity).

    Alternative splice isoforms for LGSN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LGSN Gene

Post-translational modifications for LGSN Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LGSN Gene

Domains & Families for LGSN Gene

Gene Families for LGSN Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LGSN Gene

Suggested Antigen Peptide Sequences for LGSN Gene

GenScript: Design optimal peptide antigens:
  • Lens glutamine synthase-like (LGSN_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5TDP6

UniProtKB/Swiss-Prot:

LGSN_HUMAN :
  • Belongs to the glutamine synthetase family.
Family:
  • Belongs to the glutamine synthetase family.
genes like me logo Genes that share domains with LGSN: view

Function for LGSN Gene

Molecular function for LGSN Gene

UniProtKB/Swiss-Prot Function:
May act as a component of the cytoskeleton or as a chaperone for the reorganization of intermediate filament proteins during terminal differentiation in the lens. Does not seem to have enzymatic activity (By similarity).

Phenotypes From GWAS Catalog for LGSN Gene

Gene Ontology (GO) - Molecular Function for LGSN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004356 NOT glutamate-ammonia ligase activity IEA,IBA 21873635
genes like me logo Genes that share ontologies with LGSN: view
genes like me logo Genes that share phenotypes with LGSN: view

Animal Model Products

CRISPR Products

miRNA for LGSN Gene

miRTarBase miRNAs that target LGSN

Inhibitory RNA Products

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

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LGSN Gene

Localization for LGSN Gene

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 LGSN gene
Compartment Confidence
plasma membrane 2
nucleus 2
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LGSN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IBA 21873635
genes like me logo Genes that share ontologies with LGSN: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LGSN Gene

Pathways & Interactions for LGSN Gene

PathCards logo

SuperPathways for LGSN Gene

No Data Available

Gene Ontology (GO) - Biological Process for LGSN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006542 NOT glutamine biosynthetic process IEA,IBA 21873635
GO:0006807 nitrogen compound metabolic process IEA --
GO:0019740 NOT nitrogen utilization IBA 21873635
genes like me logo Genes that share ontologies with LGSN: view

No data available for Pathways by source and SIGNOR curated interactions for LGSN Gene

Drugs & Compounds for LGSN Gene

(1) Drugs for LGSN Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glutamic acid Approved Nutra Agonist, Full agonist 304
genes like me logo Genes that share compounds with LGSN: view

Transcripts for LGSN Gene

mRNA/cDNA for LGSN Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
4 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 LGSN

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

No ASD Table

Relevant External Links for LGSN Gene

GeneLoc Exon Structure for
LGSN

Expression for LGSN Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Eye (Sensory Organs)

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

This gene is overexpressed in Liver (x16.7) and Kidney - Cortex (x4.5).

Protein differential expression in normal tissues from HIPED for LGSN Gene

This gene is overexpressed in Vitreous humor (61.4).

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



Protein tissue co-expression partners for LGSN Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LGSN

SOURCE GeneReport for Unigene cluster for LGSN Gene:

Hs.149585

mRNA Expression by UniProt/SwissProt for LGSN Gene:

Q5TDP6-LGSN_HUMAN
Tissue specificity: Abundantly expressed in lens.

Evidence on tissue expression from TISSUES for LGSN Gene

  • Eye(4.7)
genes like me logo Genes that share expression patterns with LGSN: view

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

Orthologs for LGSN Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LGSN Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LGSN 30 31
  • 99.15 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LOC538526 30
  • 85.11 (n)
LGSN 31
  • 75 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LGSN 30 31
  • 84.78 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lgsn 30 17 31
  • 79.76 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lgsn 30
  • 78.85 (n)
Oppossum
(Monodelphis domestica)
Mammalia LGSN 31
  • 67 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LGSN 31
  • 63 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LGSN 30 31
  • 70.06 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LGSN 31
  • 64 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lgsn 30
  • 61.16 (n)
Zebrafish
(Danio rerio)
Actinopterygii lgsn 30 31
  • 58.3 (n)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU11239 30
  • 41 (n)
Species where no ortholog for LGSN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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 LGSN Gene

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

Paralogs for LGSN Gene

Paralogs for LGSN Gene

genes like me logo Genes that share paralogs with LGSN: view

Variants for LGSN Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LGSN Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
783466 Benign: not provided 63,280,226(-) T/C MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT
rs2459568 - p.Asn26Tyr
rs35691434 - p.Gly46Glu
rs6454127 - p.Asn137His

Additional dbSNP identifiers (rs#s) for LGSN Gene

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

Variant ID Type Subtype PubMed ID
dgv5995n100 CNV gain 25217958
esv2732201 CNV deletion 23290073
esv2759434 CNV gain 17122850
esv3609257 CNV gain 21293372
nsv1019831 CNV gain 25217958

Variation tolerance for LGSN Gene

Residual Variation Intolerance Score: 75.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.51; 55.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LGSN Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LGSN

SNP Genotyping and Copy Number Assay Products

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

Disorders for LGSN Gene

MalaCards: The human disease database

(3) MalaCards diseases for LGSN Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 25
  • rp25
cataract
  • cataracts
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search LGSN in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LGSN

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

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

Publications for LGSN Gene

  1. Structural and functional properties of lengsin, a pseudo-glutamine synthetase in the transparent human lens. (PMID: 17010935) Grassi F … Ottonello S (Biochemical and biophysical research communications 2006) 3 4 23
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  3. Novel spliced form of a lens protein as a novel lung cancer antigen, Lengsin splicing variant 4. (PMID: 19459848) Nakatsugawa M … Sato N (Cancer science 2009) 3 23
  4. Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. (PMID: 17161372) Wyatt K … Wistow G (Structure (London, England : 1993) 2006) 3 23
  5. Mutation screening of three candidate genes, ELOVL5, SMAP1 and GLULD1 in autosomal recessive retinitis pigmentosa. (PMID: 16273301) Barragan I … Antiñolo G (International journal of molecular medicine 2005) 3 23

Products for LGSN Gene

Sources for LGSN Gene