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 functio... See more...

Aliases for LSAMP Gene

Aliases for LSAMP Gene

  • Limbic System Associated Membrane Protein 2 3 5
  • Limbic System-Associated Membrane Protein 2 3 4
  • 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. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. An important paralog of this gene is NEGR1.

UniProtKB/Swiss-Prot Summary 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).

Additional gene information for LSAMP Gene

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

Genomics for LSAMP Gene

GeneHancer (GH) Regulatory Elements for LSAMP Gene

Promoters and enhancers for LSAMP 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
GH03J117995 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 760.6 -857.1 -857113 3.4 CTCF RAD21 ZSCAN21 PRDM1 TRIM22 ZNF143 ZSCAN4 POLR2A REST ATF7 LSAMP ENSG00000239268 piR-32442 lnc-LSAMP-5
GH03J116444 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 750 +695.4 695407 4.9 PKNOX1 ZSCAN4 POLR2A HDGF GATA3 SIN3A L3MBTL2 LSAMP LSAMP-AS1 piR-42806-008 lnc-ZBTB20-6
GH03J117137 Enhancer 0.2 Ensembl 750.6 +1.6 1588 0.4 LSAMP piR-43107-222
GH03J117872 Enhancer 0.7 Ensembl ENCODE 23.3 -734.7 -734671 2.7 EZH2 SP1 ZEB1 ZNF580 KLF8 RCOR1 FOSL2 ZC3H11A ZNF513 FEZF1 lnc-C3orf30-13 LSAMP ENSG00000239268 lnc-C3orf30-14
GH03J117722 Enhancer 0.5 FANTOM5 Ensembl 9.8 -583.5 -583512 5 MAFK ENSG00000240393 ENSG00000239268 LSAMP ENSG00000242816 LOC101926953 lnc-C3orf30-15 lnc-C3orf30-4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LSAMP on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LSAMP gene promoter:
  • AREB6
  • Cdc5
  • Evi-1
  • Lhx3a
  • LHX3b
  • Msx-1
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • POU6F1 (c2)

Genomic Locations for LSAMP Gene

Genomic Locations for LSAMP Gene
chr3:115,802,363-117,139,389
(GRCh38/hg38)
Size:
1,337,027 bases
Orientation:
Minus strand
chr3:115,521,210-117,716,095
(GRCh37/hg19)
Size:
2,194,886 bases
Orientation:
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:
    Q13449-LSAMP_HUMAN
    Recommended name:
    Limbic system-associated membrane protein
    Protein Accession:
    Q13449
    Secondary Accessions:
    • Q8IV49

    Protein attributes for LSAMP Gene

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

neXtProt entry for LSAMP Gene

Post-translational modifications for LSAMP Gene

  • Glycosylation at Asn40, Asn66, Asn136, Asn148, Asn279, Asn287, Asn300, and Asn315
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LSAMP Gene

Domains & Families for LSAMP Gene

Gene Families for LSAMP Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for LSAMP Gene

Suggested Antigen Peptide Sequences for LSAMP Gene

GenScript: Design optimal peptide antigens:
  • IgLON family member 3 (LSAMP_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13449

UniProtKB/Swiss-Prot:

LSAMP_HUMAN :
  • Belongs to the immunoglobulin superfamily. IgLON family.
Family:
  • 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

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).
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

Phenotypes From GWAS Catalog for LSAMP Gene

Gene Ontology (GO) - Molecular Function for LSAMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21982860
genes like me logo Genes that share ontologies with LSAMP: view
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

CRISPR Products

miRNA for LSAMP Gene

miRTarBase miRNAs that target LSAMP

Inhibitory RNA Products

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

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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

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 LSAMP gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytosol 4
nucleus 1
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LSAMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LSAMP: view

Pathways & Interactions for LSAMP Gene

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

Gene Ontology (GO) - Biological Process for LSAMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007399 nervous system development TAS 8666243
genes like me logo Genes that share ontologies with LSAMP: view

No data available for 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

mRNA/cDNA for LSAMP Gene

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

No ASD Table

Relevant External Links for LSAMP Gene

GeneLoc Exon Structure for
LSAMP
ECgene alternative splicing isoforms for
LSAMP

Expression for LSAMP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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 and MOPED for LSAMP Gene



NURSA nuclear receptor signaling pathways regulating expression of LSAMP Gene:

LSAMP

SOURCE GeneReport for Unigene cluster for LSAMP Gene:

Hs.26409

mRNA Expression by UniProt/SwissProt for LSAMP Gene:

Q13449-LSAMP_HUMAN
Tissue specificity: Expressed on limbic neurons and fiber tracts as well as in single layers of the superior colliculus, spinal chord and cerebellum.

Evidence on tissue expression from TISSUES for LSAMP Gene

  • Nervous system(4.5)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with LSAMP: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia LSAMP 33 32
  • 99.8 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LSAMP 32
  • 94.58 (n)
mouse
(Mus musculus)
Mammalia Lsamp 17 33 32
  • 94.23 (n)
rat
(Rattus norvegicus)
Mammalia Lsamp 32
  • 94.18 (n)
dog
(Canis familiaris)
Mammalia LSAMP 33 32
  • 93 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LSAMP 33
  • 89 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LSAMP 33
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves LSAMP 33 32
  • 85.11 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LSAMP 33
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsamp 32
  • 76.08 (n)
zebrafish
(Danio rerio)
Actinopterygii lsamp 32
  • 64.26 (n)
LSAMP 33
  • 48 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002628 32
  • 45.8 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG34353 33 32
  • 43.44 (n)
ManyToMany
CG11320 33
  • 25 (a)
ManyToMany
Lac 33
  • 24 (a)
ManyToMany
Ama 33
  • 23 (a)
ManyToMany
CG14010 33
  • 22 (a)
ManyToMany
CG14521 33
  • 21 (a)
ManyToMany
CG40378 33
  • 21 (a)
ManyToMany
CG42368 33
  • 20 (a)
ManyToMany
CG34391 33
  • 19 (a)
ManyToMany
CG31708 33
  • 18 (a)
ManyToMany
CG7166 33
  • 17 (a)
ManyToMany
CG42343 33
  • 16 (a)
ManyToMany
klg 33
  • 16 (a)
ManyToMany
wrapper 33
  • 16 (a)
ManyToMany
CG31646 33
  • 16 (a)
ManyToMany
CG32791 33
  • 15 (a)
ManyToMany
CG31814 33
  • 14 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea rig-5 33
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 28 (a)
OneToMany
Species where no ortholog for LSAMP was found in the sources mined by GeneCards:
  • 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

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

Paralogs for LSAMP Gene

Paralogs for LSAMP Gene

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

  • LSAMP_HUMAN
  • C9J5G3_HUMAN
  • F5H5G1_HUMAN
  • H3BLU2_HUMAN
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 Variation AA Info Type
rs1000008790 -- 115,941,653(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000010352 -- 116,359,527(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000017130 -- 116,118,246(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000020803 -- 115,825,371(-) G/C genic_downstream_transcript_variant, intron_variant
rs1000023525 -- 116,202,454(-) C/A genic_upstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
dgv4842n100 CNV loss 25217958
dgv922e214 CNV loss 21293372
dgv923e214 CNV loss 21293372
esv2536613 CNV deletion 19546169
esv2666380 CNV deletion 23128226
esv2670807 CNV deletion 23128226
esv2725799 CNV deletion 23290073
esv2725800 CNV deletion 23290073
esv2725801 CNV deletion 23290073
esv2725802 CNV deletion 23290073
esv274993 CNV gain+loss 21479260
esv2751975 CNV loss 17911159
esv2751976 CNV loss 17911159
esv2759170 CNV loss 17122850
esv2759171 CNV loss 17122850
esv2760762 CNV gain+loss 21179565
esv28824 CNV loss 19812545
esv3597483 CNV loss 21293372
esv3597484 CNV loss 21293372
esv3597489 CNV loss 21293372
esv3597490 CNV loss 21293372
esv3893770 CNV gain 25118596
nsv1001538 CNV loss 25217958
nsv1011135 CNV gain 25217958
nsv1011591 CNV loss 25217958
nsv1073672 CNV deletion 25765185
nsv1125233 CNV insertion 24896259
nsv1130920 CNV deletion 24896259
nsv1131717 CNV deletion 24896259
nsv1136765 CNV deletion 24896259
nsv1139149 CNV deletion 24896259
nsv1146109 CNV deletion 26484159
nsv3956 CNV insertion 18451855
nsv3957 CNV deletion 18451855
nsv437338 CNV loss 16327808
nsv472891 CNV novel sequence insertion 20440878
nsv473326 CNV novel sequence insertion 20440878
nsv477803 CNV novel sequence insertion 20440878
nsv509847 OTHER sequence alteration 20534489
nsv516570 CNV loss 19592680
nsv591344 CNV loss 21841781
nsv591345 CNV loss 21841781
nsv829685 CNV gain 17160897

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)

Additional Variant Information for LSAMP Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LSAMP Gene

Additional Disease Information for LSAMP

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 … Väli M (BMC medical genetics 2008) 3 23 43 56
  2. Polymorphisms of the tumor suppressor gene LSAMP are associated with left main coronary artery disease. (PMID: 18318786) Wang L … Vance JM (Annals of human genetics 2008) 3 23 43 56
  3. 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 AF … Levitt P (Genomics 1998) 2 3 23 56
  4. cDNA cloning and structural analysis of the human limbic-system-associated membrane protein (LAMP). (PMID: 8666243) Pimenta AF … Levitt P (Gene 1996) 3 4 23 56
  5. 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 43 56

Products for LSAMP Gene

Sources for LSAMP Gene