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Aliases for LSAMP Gene

Aliases for LSAMP Gene

  • Limbic System-Associated Membrane Protein 2 3 5
  • IgLON Family Member 3 2 3 4
  • IGLON3 3 4
  • LAMP 3 4

External Ids for LSAMP Gene

Previous GeneCards Identifiers for LSAMP Gene

  • GC03M112358
  • GC03M115111
  • GC03M116810
  • GC03M116850
  • GC03M117012
  • GC03M115528
  • GC03M112897

Summaries for LSAMP Gene

Entrez Gene Summary for LSAMP Gene

  • 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]

GeneCards Summary for LSAMP Gene

LSAMP (Limbic System-Associated Membrane Protein) is a Protein Coding gene. An important paralog of this gene is NTM.

UniProtKB/Swiss-Prot for LSAMP Gene

  • Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LSAMP Gene

Genomics for LSAMP Gene

Regulatory Elements for LSAMP Gene

Enhancers for LSAMP Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LSAMP on UCSC Golden Path with GeneCards custom track

Genomic Location for LSAMP Gene

115,802,363 bp from pter
117,139,389 bp from pter
1,337,027 bases
Minus strand

Genomic View for LSAMP Gene

Genes around LSAMP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for LSAMP Gene

Proteins for LSAMP Gene

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

    Protein Symbol:
    Recommended name:
    Limbic system-associated membrane protein
    Protein Accession:
    Secondary Accessions:
    • Q8IV49

    Protein attributes for LSAMP Gene

    338 amino acids
    Molecular mass:
    37393 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LSAMP Gene

Proteomics data for LSAMP Gene at MOPED

Post-translational modifications for LSAMP Gene

  • Glycosylation at Asn 40, Asn 66, Asn 136, Asn 148, Asn 279, Asn 287, Asn 300, and Asn 315
  • Modification sites at PhosphoSitePlus

Other Protein References for LSAMP Gene

No data available for DME Specific Peptides for LSAMP Gene

Domains & Families for LSAMP Gene

Protein Domains for LSAMP Gene

Suggested Antigen Peptide Sequences for LSAMP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 3 Ig-like C2-type (immunoglobulin-like) domains.
  • Belongs to the immunoglobulin superfamily. IgLON family.
  • Contains 3 Ig-like C2-type (immunoglobulin-like) domains.
  • Belongs to the immunoglobulin superfamily. IgLON family.
genes like me logo Genes that share domains with LSAMP: view

Function for LSAMP Gene

Molecular function for LSAMP Gene

GENATLAS Biochemistry:
limbic system-associated membrane protein,mediating selective neuronal growth and exon targetting,expressed on the surface of somata and proximal dendrites,immunoglobulin superfamily
UniProtKB/Swiss-Prot Function:
Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (By similarity).
genes like me logo Genes that share phenotypes with LSAMP: view

Animal Models for LSAMP Gene

MGI Knock Outs for LSAMP:

Animal Model Products

  • Taconic Biosciences Mouse Models for LSAMP

miRNA for LSAMP Gene

miRTarBase miRNAs that target LSAMP

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LSAMP Gene

Localization for LSAMP Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSAMP Gene

Cell membrane; Lipid-anchor, GPI-anchor.

Subcellular locations from

Jensen Localization Image for LSAMP Gene COMPARTMENTS Subcellular localization image for LSAMP gene
Compartment Confidence
plasma membrane 5
extracellular 2
lysosome 1
nucleus 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components for LSAMP Gene

Pathways & Interactions for LSAMP Gene

SuperPathways for LSAMP Gene

No Data Available

Gene Ontology (GO) - Biological Process for LSAMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
genes like me logo Genes that share ontologies with LSAMP: view

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

Drugs & Compounds for LSAMP Gene

(2) Drugs for LSAMP Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with LSAMP: view

Transcripts for LSAMP Gene

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

No ASD Table

Relevant External Links for LSAMP Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LSAMP Gene

mRNA expression in normal human tissues for LSAMP Gene

Protein differential expression in normal tissues from HIPED for LSAMP Gene

This gene is overexpressed in Frontal cortex (11.1), Serum (10.2), Cerebrospinal fluid (9.8), Nasal epithelium (8.4), and Brain (7.8).

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

SOURCE GeneReport for Unigene cluster for LSAMP Gene Hs.26409

mRNA Expression by UniProt/SwissProt for LSAMP Gene

Tissue specificity: Expressed on limbic neurons and fiber tracts as well as in single layers of the superior colliculus, spinal chord and cerebellum.
genes like me logo Genes that share expression patterns with LSAMP: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for LSAMP Gene

Orthologs for LSAMP Gene

This gene was present in the common ancestor of animals.

Orthologs for LSAMP Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia LSAMP 35
  • 94.58 (n)
  • 98.82 (a)
(Canis familiaris)
Mammalia LSAMP 35
  • 93 (n)
  • 96.75 (a)
  • 99 (a)
(Mus musculus)
Mammalia Lsamp 35
  • 94.23 (n)
  • 99.02 (a)
Lsamp 16
Lsamp 36
  • 90 (a)
(Pan troglodytes)
Mammalia LSAMP 35
  • 99.8 (n)
  • 100 (a)
  • 100 (a)
(Rattus norvegicus)
Mammalia Lsamp 35
  • 94.18 (n)
  • 98.82 (a)
(Monodelphis domestica)
Mammalia LSAMP 36
  • 89 (a)
(Ornithorhynchus anatinus)
Mammalia LSAMP 36
  • 89 (a)
(Gallus gallus)
Aves LSAMP 35
  • 85.11 (n)
  • 91.12 (a)
  • 88 (a)
(Anolis carolinensis)
Reptilia LSAMP 36
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lsamp 35
  • 76.08 (n)
  • 81.63 (a)
(Danio rerio)
Actinopterygii lsamp 35
  • 64.26 (n)
  • 62.54 (a)
  • 48 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002628 35
  • 45.8 (n)
  • 34.25 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG34353 35
  • 43.44 (n)
  • 31.1 (a)
Ama 36
  • 23 (a)
CG11320 36
  • 25 (a)
CG14010 36
  • 22 (a)
CG14521 36
  • 21 (a)
CG31646 36
  • 16 (a)
CG31708 36
  • 18 (a)
CG31814 36
  • 14 (a)
CG32791 36
  • 15 (a)
CG34353 36
  • 15 (a)
CG34391 36
  • 19 (a)
CG40378 36
  • 21 (a)
CG42343 36
  • 16 (a)
CG42368 36
  • 20 (a)
CG7166 36
  • 17 (a)
klg 36
  • 16 (a)
Lac 36
  • 24 (a)
wrapper 36
  • 16 (a)
(Caenorhabditis elegans)
Secernentea rig-5 36
  • 17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 28 (a)
Species with no ortholog for LSAMP:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • bread mold (Neurospora crassa)
  • 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)
  • 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 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)

Evolution for LSAMP Gene

Gene Tree for LSAMP (if available)
Gene Tree for LSAMP (if available)

Paralogs for LSAMP Gene

Paralogs for LSAMP Gene

(7) SIMAP similar genes for LSAMP Gene using alignment to 4 proteins:

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

Variants for LSAMP Gene

Sequence variations from dbSNP and Humsavar for LSAMP Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1898 -- 116,229,130(+) TAACT(G/T)ATCTT intron-variant
rs3054 -- 115,807,510(+) CAAGA(A/C)CTTGT utr-variant-3-prime
rs3195 -- 116,250,389(-) TTAAT(A/G)AAGGA intron-variant
rs11408 -- 115,808,425(+) ATGCA(A/G)AGAGC utr-variant-3-prime
rs17358 -- 116,193,880(-) ATGTG(-/GTG)TTTAA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv877356 CNV Gain 21882294
dgv5234n71 CNV Gain 21882294
esv2725799 CNV Deletion 23290073
esv2725800 CNV Deletion 23290073
esv2725801 CNV Deletion 23290073
esv2725802 CNV Deletion 23290073
esv274993 CNV Gain+Loss 21479260
nsv829685 CNV Gain 17160897
esv2751975 CNV Loss 17911159
esv2536613 CNV Deletion 19546169
nsv3956 CNV Insertion 18451855
nsv509847 CNV Loss 20534489
esv2751976 CNV Loss 17911159
esv2670807 CNV Deletion 23128226
nsv877360 CNV Loss 21882294
nsv3957 CNV Loss 18451855
nsv877361 CNV Gain 21882294
nsv437338 CNV Loss 16327808
dgv1487e1 CNV Complex 17122850
esv2666380 CNV Deletion 23128226
esv28824 CNV Loss 19812545
essv10707 CNV CNV 17122850
nsv516570 CNV Loss 19592680
dgv1488e1 CNV Complex 17122850

Variation tolerance for LSAMP Gene

Residual Variation Intolerance Score: 35.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.76; 16.09% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for LSAMP Gene

Disorders for LSAMP Gene

Relevant External Links for LSAMP

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for LSAMP Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LSAMP Gene

Publications for LSAMP Gene

  1. Association of limbic system-associated membrane protein (LSAMP) to male completed suicide. (PMID: 18433483) Must A. … VAoli M. (BMC Med. Genet. 2008) 3 23 48 67
  2. Assignment of the gene encoding the limbic system-associated membrane protein (LAMP) to mouse chromosome 16B5 and human chromosome 3q13.2-q21. (PMID: 9615236) Pimenta A.F. … Levitt P. (Genomics 1998) 2 3 23
  3. Proteomic analysis of membrane microdomain-associated proteins in the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder reveals alterations in LAMP, STXBP1 and BASP1 protein expression. (PMID: 18268500) Behan A.T. … Cotter D.R. (Mol. Psychiatry 2009) 3 23
  4. LSAMP, a novel candidate tumor suppressor gene in human osteosarcomas, identified by array comparative genomic hybridization. (PMID: 19441093) Kresse S.H. … Meza-Zepeda L.A. (Genes Chromosomes Cancer 2009) 3 23
  5. Identification of chromosomal aberrations associated with disease progression and a novel 3q13.31 deletion involving LSAMP gene in osteosarcoma. (PMID: 19724913) Yen C.C. … Fletcher J.A. (Int. J. Oncol. 2009) 3 23

Products for LSAMP Gene

Sources for LSAMP Gene