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    LSAMP limbic system associated membrane protein [ Homo sapiens (human) ]

    Gene ID: 4045, updated on 28-Oct-2024

    Summary

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    Official Symbol
    LSAMPprovided by HGNC
    Official Full Name
    limbic system associated membrane proteinprovided by HGNC
    Primary source
    HGNC:HGNC:6705
    See related
    Ensembl:ENSG00000185565 MIM:603241; AllianceGenome:HGNC:6705
    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
    LAMP; IGLON3
    Summary
    This gene encodes a member of the immunoglobulin LAMP, OBCAM and neurotrimin (IgLON) family of proteins. The encoded preproprotein is proteolytically processed to generate a neuronal surface glycoprotein. This protein may act as a selective homophilic adhesion molecule during axon guidance and neuronal growth in the developing limbic system. The encoded protein may also function as a tumor suppressor and may play a role in neuropsychiatric disorders. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]
    Expression
    Biased expression in brain (RPKM 19.9), prostate (RPKM 5.4) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LSAMP in Genome Data Viewer
    Location:
    3q13.31
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (115802374..116445487, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (118522573..119165711, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (115521221..116164334, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115376638-115377510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115377511-115378382 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115417888-115418741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:115431872-115432372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:115432373-115432873 Neighboring gene growth associated protein 43 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115502891-115503391 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:115503423-115504101 Neighboring gene uncharacterized LOC124909412 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115511955-115512480 Neighboring gene uncharacterized LOC124906269 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115512481-115513006 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:115513007-115513531 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115513693-115514194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115514334-115515272 Neighboring gene 3q13.2-q13.31 distal HERV-H recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115515273-115516210 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115517565-115518070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20285 Neighboring gene uncharacterized LOC124909413 Neighboring gene uncharacterized LOC105374053 Neighboring gene RNA, 7SL, cytoplasmic 815, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20286 Neighboring gene small nucleolar RNA, C/D box 155 Neighboring gene uncharacterized LOC107986116 Neighboring gene uncharacterized LOC124909414 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115709155-115709940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20287 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115809463-115809964 Neighboring gene uncharacterized LOC105374052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:115917016-115917516 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115975635-115976191 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:115978423-115979314 Neighboring gene MPRA-validated peak4776 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr3:116065268-116065439 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:116079173-116079763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:116110286-116110815 Neighboring gene LSAMP antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:116238426-116238927 Neighboring gene long intergenic non-protein coding RNA 903 Neighboring gene RNA, 7SL, cytoplasmic 582, pseudogene

    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. Associations between LSAMP gene polymorphisms and major depressive disorder and panic disorder. Koido K, et al. Transl Psychiatry, 2012 Aug 14. PMID 22892717, Free PMC Article
    2. cDNA cloning and structural analysis of the human limbic-system-associated membrane protein (LAMP). Pimenta AF, et al. Gene, 1996 May 8. PMID 8666243
    3. Association of limbic system-associated membrane protein (LSAMP) to male completed suicide. Must A, et al. BMC Med Genet, 2008 Apr 23. PMID 18433483, Free PMC Article
    4. LSAMP, a novel candidate tumor suppressor gene in human osteosarcomas, identified by array comparative genomic hybridization. Kresse SH, et al. Genes Chromosomes Cancer, 2009 Aug. PMID 19441093
    5. Identification of chromosomal aberrations associated with disease progression and a novel 3q13.31 deletion involving LSAMP gene in osteosarcoma. Yen CC, et al. Int J Oncol, 2009 Oct. PMID 19724913

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of recurrent 3q13.31 chromosomal rearrangement indicates LSAMP as a tumor suppressor gene in neuroblastoma.
      Title: Identification of recurrent 3q13.31 chromosomal rearrangement indicates LSAMP as a tumor suppressor gene in neuroblastoma.
    2. Limbic System Associated Membrane Protein Mutation in an Iranian Family Diagnosed with Meniere's Disease.
      Title: Limbic System Associated Membrane Protein Mutation in an Iranian Family Diagnosed with Ménière's Disease.
    3. We detected African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for ulcerative colitis.
      Title: Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease.
    4. A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men
      Title: A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men.
    5. The results showed significant allelic and haplotypic associations between LSAMP gene and schizophrenia.
      Title: Associations between polymorphisms of LSAMP gene and schizophrenia.
    6. The tumor suppressor function of LSAMP is most likely exerted by reducing the proliferation rate of the tumor cells, possibly by indirectly upregulating one or more of the genes HES1, CTAG2 or KLF10.
      Title: Reexpression of LSAMP inhibits tumor growth in a preclinical osteosarcoma model.
    7. This study presents the first evidence of a possible role of LSAMP gene in mood and anxiety disorders in humans.
      Title: Associations between LSAMP gene polymorphisms and major depressive disorder and panic disorder.
    8. 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.
    9. Identification of chromosomal aberrations associated with disease progression and a novel 3q13.31 deletion involving LSAMP gene in osteosarcoma.
      Title: Identification of chromosomal aberrations associated with disease progression and a novel 3q13.31 deletion involving LSAMP gene in osteosarcoma.
    10. results show that LSAMP is a novel candidate tumor suppressor gene in osteosarcomas
      Title: LSAMP, a novel candidate tumor suppressor gene in human osteosarcomas, identified by array comparative genomic hybridization.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    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
    Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
    EBI GWAS Catalog
    Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34254, FLJ35396, FLJ37216, FLJ54658

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    limbic system-associated membrane protein
    Names
    IgLON family member 3

    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_001318915.2 → NP_001305844.1  limbic system-associated membrane protein isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes two alternate in-frame exons in the 3' coding region compared to variant 1. The encoded isoform (2) is longer than isoform 1. The encoded isoform (2) may undergo proteolytic processing similar to isoform 1.
      Source sequence(s)
      AA702209, AC012598, AK091573, AK092715, AK299851, BC033803
      UniProtKB/TrEMBL
      H3BLU2
      Related
      ENSP00000328455.4, ENST00000333617.8
      Conserved Domains (2) summary
      pfam13927
      Location:219 → 294
      Ig_3; Immunoglobulin domain
      cl11960
      Location:38 → 128
      Ig; Immunoglobulin domain

    2. NM_002338.5 → NP_002329.2  limbic system-associated membrane protein isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_002329.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AA702209, AC012598, AK091573, AK092715, AK299851, BC033803
      Consensus CDS
      CCDS2982.1
      UniProtKB/Swiss-Prot
      Q13449, Q8IV49
      UniProtKB/TrEMBL
      H3BLU2
      Related
      ENSP00000419000.1, ENST00000490035.7
      Conserved Domains (3) summary
      pfam13927
      Location:218 → 294
      Ig_3; Immunoglobulin domain
      cd00096
      Location:235 → 239
      Ig; Ig strand B [structural motif]
      cl11960
      Location:38 → 128
      Ig; Immunoglobulin 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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      115802374..116445487 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017006383.3 → XP_016861872.1  limbic system-associated membrane protein isoform X1

      UniProtKB/TrEMBL
      H3BLU2
      Conserved Domains (4) summary
      smart00408
      Location:232 → 297
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:40 → 128
      IG_like; Immunoglobulin like
      pfam07679
      Location:218 → 305
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:38 → 128
      Ig; Immunoglobulin domain

    2. XM_024453520.2 → XP_024309288.1  limbic system-associated membrane protein isoform X3

      Conserved Domains (2) summary
      pfam13927
      Location:34 → 104
      Ig_3; Immunoglobulin domain
      cd00096
      Location:138 → 205
      Ig; Immunoglobulin domain

    3. XM_024453522.2 → XP_024309290.1  limbic system-associated membrane protein isoform X4

      Conserved Domains (1) summary
      cd00096
      Location:71 → 138
      Ig; Immunoglobulin domain

    4. XM_017006384.3 → XP_016861873.1  limbic system-associated membrane protein isoform X4

      Conserved Domains (1) summary
      cd00096
      Location:71 → 138
      Ig; Immunoglobulin domain

    5. XM_011512840.4 → XP_011511142.1  limbic system-associated membrane protein isoform X2

      UniProtKB/TrEMBL
      H3BLU2
      Conserved Domains (4) summary
      smart00408
      Location:232 → 297
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:40 → 128
      IG_like; Immunoglobulin like
      pfam07679
      Location:218 → 305
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:38 → 128
      Ig; Immunoglobulin domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      118522573..119165711 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346509.1 → XP_054202484.1  limbic system-associated membrane protein isoform X1

    2. XM_054346511.1 → XP_054202486.1  limbic system-associated membrane protein isoform X3

    3. XM_054346512.1 → XP_054202487.1  limbic system-associated membrane protein isoform X4

    4. XM_054346513.1 → XP_054202488.1  limbic system-associated membrane protein isoform X4

    5. XM_054346510.1 → XP_054202485.1  limbic system-associated membrane protein isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13449.2 GenPept UniProtKB/Swiss-Prot:Q13449

    Gene LinkOut

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

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