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    LGSN lengsin, lens protein with glutamine synthetase domain [ Homo sapiens (human) ]

    Gene ID: 51557, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LGSNprovided by HGNC
    Official Full Name
    lengsin, lens protein with glutamine synthetase domainprovided by HGNC
    Primary source
    HGNC:HGNC:21016
    See related
    Ensembl:ENSG00000146166 MIM:611470; AllianceGenome:HGNC:21016
    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
    LGS; GLULD1
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See LGSN in Genome Data Viewer
    Location:
    6q12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (63275951..63573607, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (64421831..64588322, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (63985856..64029888, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene putative UPF0607 protein ENSP00000383144 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17307 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:64057036-64058235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24714 Neighboring gene serine palmitoyltransferase long chain base subunit 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24715 Neighboring gene DENN domain containing 1C pseudogene Neighboring gene Sharpr-MPRA regulatory region 2763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24716 Neighboring gene HNF1 motif-containing MPRA enhancer 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24718 Neighboring gene leucine rich repeat containing 59 pseudogene Neighboring gene translation initiation factor IF-2-like Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64283581-64284316 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64282845-64283580 Neighboring gene uncharacterized LOC128125822 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64282109-64282844 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64281371-64282108 Neighboring gene Sharpr-MPRA regulatory region 1413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24721 Neighboring gene eukaryotic translation elongation factor 1 beta 2 pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chr6:64344395-64344932 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64345464-64346284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24722 Neighboring gene ribosomal protein L7a pseudogene 34 Neighboring gene protein tyrosine phosphatase 4A1 Neighboring gene ribosomal protein L9 pseudogene 18 Neighboring gene PHD finger protein 3 Neighboring gene eyes shut homolog

    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
    • 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. Novel spliced form of a lens protein as a novel lung cancer antigen, Lengsin splicing variant 4. Nakatsugawa M, et al. Cancer Sci, 2009 Aug. PMID 19459848, Free PMC Article
    2. Structural and functional properties of lengsin, a pseudo-glutamine synthetase in the transparent human lens. Grassi F, et al. Biochem Biophys Res Commun, 2006 Nov 17. PMID 17010935
    3. The NEIBank project for ocular genomics: data-mining gene expression in human and rodent eye tissues. Wistow G. Prog Retin Eye Res, 2006 Jan. PMID 16005676
    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. Wyatt K, et al. Structure, 2006 Dec. PMID 17161372, Free PMC Article
    5. Mutation screening of three candidate genes, ELOVL5, SMAP1 and GLULD1 in autosomal recessive retinitis pigmentosa. Barragan I, et al. Int J Mol Med, 2005 Dec. PMID 16273301

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. In major depressive disorder genome-wide association study, best male-specific SNP was rs9362774 within LGSN gene
      Title: Genome-wide association analysis of gender differences in major depressive disorder in the Netherlands NESDA and NTR population-based samples.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. Lengsin belongs to the predominantly prokaryotic class 1 branch of glutamine synthetases but has lost enzyme activity
      Title: Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens.
    4. Novel spliced form of a lens protein as a novel lung cancer antigen, Lengsin splicing variant 4, is reported.
      Title: Novel spliced form of a lens protein as a novel lung cancer antigen, Lengsin splicing variant 4.
    5. A potential chaperone-like role of Lengsin was investigated.
      Title: Structural and functional properties of lengsin, a pseudo-glutamine synthetase in the transparent human lens.
    6. Lengsin is major novel protein of the vertebrate eye lens.
      Title: Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants.
    Submit: New GeneRIF Correction

    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
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC163238, MGC163240

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables glutamine synthetase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    NOT involved_in glutamine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT involved_in nitrogen utilization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lengsin
    Names
    glutamate-ammonia ligase (glutamine synthase) domain containing 1
    glutamate-ammonia ligase domain-containing protein 1

    NCBI Reference Sequences (RefSeq)

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    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_001143940.2 → NP_001137412.1  lengsin isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate segment of the 3' coding region, compared to variant 1, that causes a frameshift. The resulting protein (isoform b) has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AF242388, AL121949, AL450346, AL590456, DQ682605
      Consensus CDS
      CCDS55027.1
      UniProtKB/TrEMBL
      A0A0A0MTD2
      Related
      ENSP00000359692.5, ENST00000370658.9
      Conserved Domains (1) summary
      pfam03951
      Location:86 → 171
      Gln-synt_N; Glutamine synthetase, beta-Grasp domain

    2. NM_016571.3 → NP_057655.2  lengsin isoform a

      See identical proteins and their annotated locations for NP_057655.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AF242388, AL121949, AL450346, AL590456, BC130368
      Consensus CDS
      CCDS4964.1
      UniProtKB/Swiss-Prot
      A1L421, Q0PVN9, Q0PVP0, Q5TDP6, Q9NYJ0
      Related
      ENSP00000359691.4, ENST00000370657.9
      Conserved Domains (3) summary
      COG0174
      Location:81 → 493
      GlnA; Glutamine synthetase [Amino acid transport and metabolism]
      pfam00120
      Location:183 → 507
      Gln-synt_C; Glutamine synthetase, catalytic domain
      pfam03951
      Location:86 → 171
      Gln-synt_N; Glutamine synthetase, beta-Grasp domain

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      63275951..63573607 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418866.1 → XP_047274822.1  lengsin isoform X2

    2. XM_017010930.3 → XP_016866419.1  lengsin isoform X2

      Conserved Domains (3) summary
      COG0174
      Location:162 → 574
      GlnA; Glutamine synthetase [Amino acid transport and metabolism]
      pfam00120
      Location:264 → 588
      Gln-synt_C; Glutamine synthetase, catalytic domain
      pfam03951
      Location:167 → 252
      Gln-synt_N; Glutamine synthetase, beta-Grasp domain

    3. XM_011535892.4 → XP_011534194.1  lengsin isoform X1

      See identical proteins and their annotated locations for XP_011534194.1

      Conserved Domains (3) summary
      COG0174
      Location:120 → 532
      GlnA; Glutamine synthetase [Amino acid transport and metabolism]
      pfam00120
      Location:222 → 546
      Gln-synt_C; Glutamine synthetase, catalytic domain
      pfam03951
      Location:125 → 210
      Gln-synt_N; Glutamine synthetase, beta-Grasp domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      64421831..64588322 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355589.1 → XP_054211564.1  lengsin isoform X1

    2. XM_054355588.1 → XP_054211563.1  lengsin isoform X1

    3. XM_054355590.1 → XP_054211565.1  lengsin isoform X1

    4. XM_054355591.1 → XP_054211566.1  lengsin isoform X1

    5. XM_054355587.1 → XP_054211562.1  lengsin isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5TDP6.1 GenPept UniProtKB/Swiss-Prot:Q5TDP6

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