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

Gene ID: 4045, updated on 3-Apr-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
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Genomic context

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Location:
3q13.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (115802374..116445487, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (118522573..119165711, complement)
105.20220307 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
  • 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. Identification of recurrent 3q13.31 chromosomal rearrangement indicates LSAMP as a tumor suppressor gene in neuroblastoma. Martinez-Monleon A, et al. Int J Oncol, 2023 Feb. PMID 36601748, Free PMC Article
  2. Limbic System Associated Membrane Protein Mutation in an Iranian Family Diagnosed with Ménière's Disease. Mehrjoo Z, et al. Arch Iran Med, 2020 May 1. PMID 32383616
  3. A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men. Petrovics G, et al. EBioMedicine, 2015 Dec. PMID 26844274, Free PMC Article
  4. Associations between polymorphisms of LSAMP gene and schizophrenia. Koido K, et al. Psychiatry Res, 2014 Mar 30. PMID 24491686
  5. Limbic system associated membrane protein as a potential target for neuropsychiatric disorders. Innos J, et al. Front Pharmacol, 2013. PMID 23532449, Free PMC Article

See all (33) 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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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_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_2023_10

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

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