Human Gene LAMP2 (uc004est.4)
  Description: Homo sapiens lysosomal-associated membrane protein 2 (LAMP2), transcript variant A, mRNA.
RefSeq Summary (NM_002294): The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may play a role in tumor cell metastasis. It may also function in the protection, maintenance, and adhesion of the lysosome. Alternative splicing of this gene results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chrX:119,560,003-119,603,204 Size: 43,202 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chrX:119,565,178-119,603,024 Size: 37,847 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviews
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:119,560,003-119,603,204)mRNA (may differ from genome)Protein (410 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LAMP2_HUMAN
DESCRIPTION: RecName: Full=Lysosome-associated membrane glycoprotein 2; Short=LAMP-2; Short=Lysosome-associated membrane protein 2; AltName: Full=CD107 antigen-like family member B; AltName: CD_antigen=CD107b; Flags: Precursor;
FUNCTION: Implicated in tumor cell metastasis. May function in protection of the lysosomal membrane from autodigestion, maintenance of the acidic environment of the lysosome, adhesion when expressed on the cell surface (plasma membrane), and inter- and intracellular signal transduction. Protects cells from the toxic effects of methylating mutagens.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein. Endosome membrane; Single-pass type I membrane protein. Lysosome membrane; Single-pass type I membrane protein. Note=This protein shuttles between lysosomes, endosomes, and the plasma membrane.
TISSUE SPECIFICITY: Isoform LAMP-2A is highly expressed in placenta, lung and liver, less in kidney and pancreas, low in brain and skeletal muscle. Isoform LAMP-2B is highly expressed in skeletal muscle, less in brain, placenta, lung, kidney and pancreas, very low in liver.
PTM: O- and N-glycosylated; some of the 16 N-linked glycans are polylactosaminoglycans.
DISEASE: Defects in LAMP2 are the cause of Danon disease (DAND) [MIM:300257]; also known as glycogen storage disease type 2B (GSD2B). DAND is a lysosomal glycogen storage disease characterized by the clinical triad of cardiomyopathy, vacuolar myopathy and mental retardation. It is often associated with an accumulation of glycogen in muscle and lysosomes.
SIMILARITY: Belongs to the LAMP family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LAMP2";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LAMP2
CDC HuGE Published Literature: LAMP2

-  MalaCards Disease Associations
  MalaCards Gene Search: LAMP2
Diseases sorted by gene-association score: danon disease* (1711), cardiomyopathy* (150), atrial standstill, digenic* (126), glycogen storage disease ii (18), lysosomal acid phosphatase deficiency (14), salla disease (12), myopathy, x-linked, with excessive autophagy (12), fabry disease (9), cholesterol ester storage disease (6), myopathy (5), dilated cardiomyopathy (2), cardiomyopathy, familial hypertrophic (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 59.78 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 1126.55 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -69.00180-0.383 Picture PostScript Text
3' UTR -1281.995175-0.248 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018134 - LAMP_CS
IPR002000 - Lysosome-assoc_membr_glycop

Pfam Domains:
PF01299 - Lysosome-associated membrane glycoprotein (Lamp)

ModBase Predicted Comparative 3D Structure on P13473
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0019904 protein domain specific binding

Biological Process:
GO:0002576 platelet degranulation
GO:0006605 protein targeting
GO:0006914 autophagy
GO:0009267 cellular response to starvation
GO:0017038 protein import
GO:0031647 regulation of protein stability
GO:0032463 negative regulation of protein homooligomerization
GO:0043312 neutrophil degranulation
GO:0046716 muscle cell cellular homeostasis
GO:0050821 protein stabilization
GO:0061684 chaperone-mediated autophagy
GO:0061740 protein targeting to lysosome involved in chaperone-mediated autophagy
GO:0097352 autophagosome maturation
GO:1905146 lysosomal protein catabolic process

Cellular Component:
GO:0000421 autophagosome membrane
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005802 trans-Golgi network
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030670 phagocytic vesicle membrane
GO:0031088 platelet dense granule membrane
GO:0031410 cytoplasmic vesicle
GO:0031902 late endosome membrane
GO:0035577 azurophil granule membrane
GO:0043202 lysosomal lumen
GO:0044754 autolysosome
GO:0045121 membrane raft
GO:0048471 perinuclear region of cytoplasm
GO:0061742 chaperone-mediated autophagy translocation complex
GO:0070062 extracellular exosome
GO:0097637 integral component of autophagosome membrane
GO:0101003 ficolin-1-rich granule membrane
GO:1990836 lysosomal matrix
GO:0098857 membrane microdomain


-  Descriptions from all associated GenBank mRNAs
  BC040653 - Homo sapiens cDNA clone IMAGE:4797120.
LF385316 - JP 2014500723-A/192819: Polycomb-Associated Non-Coding RNAs.
AK226066 - Homo sapiens mRNA for lysosomal-associated membrane protein 2 precursor variant, clone: fj10535.
AK295038 - Homo sapiens cDNA FLJ52540 complete cds, highly similar to Lysosome-associated membrane glycoprotein 2 precursor.
AY561849 - Homo sapiens lysosomal-associated membrane protein 2C (LAMP2) mRNA, complete cds.
AB528277 - Synthetic construct DNA, clone: pF1KB9376, Homo sapiens LAMP2 gene for lysosomal-associated membrane protein 2, without stop codon, in Flexi system.
LF379868 - JP 2014500723-A/187371: Polycomb-Associated Non-Coding RNAs.
LF379869 - JP 2014500723-A/187372: Polycomb-Associated Non-Coding RNAs.
LF379870 - JP 2014500723-A/187373: Polycomb-Associated Non-Coding RNAs.
LF379871 - JP 2014500723-A/187374: Polycomb-Associated Non-Coding RNAs.
LF379872 - JP 2014500723-A/187375: Polycomb-Associated Non-Coding RNAs.
X77196 - H.sapiens mRNA for lysosome-associated membrane protein-2.
AK126232 - Homo sapiens cDNA FLJ44244 fis, clone THYMU3009006.
JD503339 - Sequence 484363 from Patent EP1572962.
AK291090 - Homo sapiens cDNA FLJ77117 complete cds, highly similar to Homo sapiens lysosomal-associated membrane protein 2 (LAMP2), transcript variant LAMP2A, mRNA.
J04183 - Homo sapiens lysosomal membrane glycoprotein-2 (LAMP2), complete cds.
LF379873 - JP 2014500723-A/187376: Polycomb-Associated Non-Coding RNAs.
S79873 - h-lamp-2=lysosome-associated membrane protein-2 {alternatively spliced} [human, liver, mRNA, 4006 nt].
U36336 - Human lysosome-associated membrane protein-2b (LAMP2) mRNA, alternatively spliced form h-lamp-2b, complete cds.
BC002965 - Homo sapiens lysosomal-associated membrane protein 2, mRNA (cDNA clone MGC:1710 IMAGE:3543019), complete cds.
AK293931 - Homo sapiens cDNA FLJ52535 complete cds, highly similar to Homo sapiens lysosomal-associated membrane protein 2 (LAMP2), transcript variant LAMP2B, mRNA.
AK304405 - Homo sapiens cDNA FLJ58780 complete cds, highly similar to Homo sapiens lysosomal-associated membrane protein 2 (LAMP2), transcript variant LAMP2B, mRNA.
KJ897118 - Synthetic construct Homo sapiens clone ccsbBroadEn_06512 LAMP2 gene, encodes complete protein.
KR709861 - Synthetic construct Homo sapiens clone CCSBHm_00006896 LAMP2 (LAMP2) mRNA, encodes complete protein.
KR709862 - Synthetic construct Homo sapiens clone CCSBHm_00006897 LAMP2 (LAMP2) mRNA, encodes complete protein.
DQ892095 - Synthetic construct clone IMAGE:100004725; FLH186841.01X; RZPDo839B0172D lysosomal-associated membrane protein 2 (LAMP2) gene, encodes complete protein.
DQ895288 - Synthetic construct Homo sapiens clone IMAGE:100009748; FLH186837.01L; RZPDo839B0162D lysosomal-associated membrane protein 2 (LAMP2) gene, encodes complete protein.
LF379882 - JP 2014500723-A/187385: Polycomb-Associated Non-Coding RNAs.
LF379883 - JP 2014500723-A/187386: Polycomb-Associated Non-Coding RNAs.
LF379887 - JP 2014500723-A/187390: Polycomb-Associated Non-Coding RNAs.
LF379888 - JP 2014500723-A/187391: Polycomb-Associated Non-Coding RNAs.
CU678318 - Synthetic construct Homo sapiens gateway clone IMAGE:100019273 5' read LAMP2 mRNA.
LF379889 - JP 2014500723-A/187392: Polycomb-Associated Non-Coding RNAs.
LF379891 - JP 2014500723-A/187394: Polycomb-Associated Non-Coding RNAs.
LF379893 - JP 2014500723-A/187396: Polycomb-Associated Non-Coding RNAs.
LF211457 - JP 2014500723-A/18960: Polycomb-Associated Non-Coding RNAs.
JD071608 - Sequence 52632 from Patent EP1572962.
MA620893 - JP 2018138019-A/192819: Polycomb-Associated Non-Coding RNAs.
MA615445 - JP 2018138019-A/187371: Polycomb-Associated Non-Coding RNAs.
MA615446 - JP 2018138019-A/187372: Polycomb-Associated Non-Coding RNAs.
MA615447 - JP 2018138019-A/187373: Polycomb-Associated Non-Coding RNAs.
MA615448 - JP 2018138019-A/187374: Polycomb-Associated Non-Coding RNAs.
MA615449 - JP 2018138019-A/187375: Polycomb-Associated Non-Coding RNAs.
MA615450 - JP 2018138019-A/187376: Polycomb-Associated Non-Coding RNAs.
MA615459 - JP 2018138019-A/187385: Polycomb-Associated Non-Coding RNAs.
MA615460 - JP 2018138019-A/187386: Polycomb-Associated Non-Coding RNAs.
MA615464 - JP 2018138019-A/187390: Polycomb-Associated Non-Coding RNAs.
MA615465 - JP 2018138019-A/187391: Polycomb-Associated Non-Coding RNAs.
MA615466 - JP 2018138019-A/187392: Polycomb-Associated Non-Coding RNAs.
MA615468 - JP 2018138019-A/187394: Polycomb-Associated Non-Coding RNAs.
MA615470 - JP 2018138019-A/187396: Polycomb-Associated Non-Coding RNAs.
MA447034 - JP 2018138019-A/18960: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04142 - Lysosome

Reactome (by CSHL, EBI, and GO)

Protein P13473 (Reactome details) participates in the following event(s):

R-HSA-481010 Surface deployment of platelet dense granule membrane components
R-HSA-6798739 Exocytosis of azurophil granule membrane proteins
R-HSA-6800426 Exocytosis of ficolin-rich granule membrane proteins
R-HSA-114608 Platelet degranulation
R-HSA-6798695 Neutrophil degranulation
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-168249 Innate Immune System
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-168256 Immune System
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: A8K4X5, D3DTF0, LAMP2_HUMAN, NM_002294, NP_002285, P13473, Q16641, Q6Q3G8, Q96J30, Q99534, Q9UD93
UCSC ID: uc004est.4
RefSeq Accession: NM_002294
Protein: P13473 (aka LAMP2_HUMAN or LMP2_HUMAN)
CCDS: CCDS14599.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LAMP2:
danon (Danon Disease)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002294.2
exon count: 9CDS single in 3' UTR: no RNA size: 6603
ORF size: 1233CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2631.50frame shift in genome: no % Coverage: 99.77
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.