Human Gene LAMB2 (uc003cwe.3) Description and Page Index
  Description: Homo sapiens laminin, beta 2 (laminin S) (LAMB2), mRNA.
RefSeq Summary (NM_002292): Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins, composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively), form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. Several isoforms of each chain have been described. Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms which are designated by Arabic numerals in the order of their discovery, i.e. alpha1beta1gamma1 heterotrimer is laminin 1. The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo. This gene encodes the beta chain isoform laminin, beta 2. The beta 2 chain contains the 7 structural domains typical of beta chains of laminin, including the short alpha region. However, unlike beta 1 chain, beta 2 has a more restricted tissue distribution. It is enriched in the basement membrane of muscles at the neuromuscular junctions, kidney glomerulus and vascular smooth muscle. Transgenic mice in which the beta 2 chain gene was inactivated by homologous recombination, showed defects in the maturation of neuromuscular junctions and impairment of glomerular filtration. Alternative splicing involving a non consensus 5' splice site (gc) in the 5' UTR of this gene has been reported. It was suggested that inefficient splicing of this first intron, which does not change the protein sequence, results in a greater abundance of the unspliced form of the transcript than the spliced form. The full-length nature of the spliced transcript is not known. [provided by RefSeq, Aug 2011]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660807.197004.1, SRR1803613.286762.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000305544.9/ ENSP00000307156.4 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr3:49,158,547-49,170,599 Size: 12,053 Total Exon Count: 32 Strand: -
Coding Region
   Position: hg19 chr3:49,158,659-49,170,300 Size: 11,642 Coding Exon Count: 32 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:49,158,547-49,170,599)mRNA (may differ from genome)Protein (1798 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: LAMB2_HUMAN
DESCRIPTION: RecName: Full=Laminin subunit beta-2; AltName: Full=Laminin B1s chain; AltName: Full=Laminin-11 subunit beta; AltName: Full=Laminin-14 subunit beta; AltName: Full=Laminin-15 subunit beta; AltName: Full=Laminin-3 subunit beta; AltName: Full=Laminin-4 subunit beta; AltName: Full=Laminin-7 subunit beta; AltName: Full=Laminin-9 subunit beta; AltName: Full=S-laminin subunit beta; Short=S-LAM beta; Flags: Precursor;
FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.
SUBUNIT: Laminin is a complex glycoprotein, consisting of three different polypeptide chains (alpha, beta, gamma), which are bound to each other by disulfide bonds into a cross-shaped molecule comprising one long and three short arms with globules at each end. Beta-2 is a subunit of laminin-3 (laminin-121 or S-laminin), laminin-4 (laminin-221 or S-merosin), laminin-7 (laminin-321 or KS-laminin), laminin-9 (laminin-421), laminin-11 (laminin-521), laminin-14 (laminin-423) and laminin-15 (laminin-523).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix, basement membrane. Note=S-laminin is concentrated in the synaptic cleft of the neuromuscular junction.
DOMAIN: The alpha-helical domains I and II are thought to interact with other laminin chains to form a coiled coil structure.
DOMAIN: Domains VI and IV are globular.
DISEASE: Defects in LAMB2 are the cause of Pierson syndrome (PIERSS) [MIM:609049]; also known as microcoria-congenital nephrotic syndrome. Pierson syndrome is characterized by nephrotic syndrome with neonatal onset, diffuse mesangial sclerosis and eye abnormalities with microcoria as the leading clinical feature. Death usually occurs within the first weeks of life. Disease severity depends on the mutation type: nontruncating LAMB2 mutations may display variable phenotypes ranging from a milder variant of Pierson syndrome to isolated congenital nephrotic syndrome.
DISEASE: Defects in LAMB2 are the cause of nephrotic syndrome type 5 with or without ocular abnormalities (NPHS5) [MIM:614199]. NPHS5 is a renal disease characterized clinically by proteinuria, hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. NPHS5 is characterized by very early onset of progressive renal failure. A subset of patients may develop mild ocular anomalies, such as myopia, nystagmus, and strabismus.
SIMILARITY: Contains 13 laminin EGF-like domains.
SIMILARITY: Contains 1 laminin IV type B domain.
SIMILARITY: Contains 1 laminin N-terminal domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LAMB2";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LAMB2
CDC HuGE Published Literature: LAMB2
Positive Disease Associations: nephrotic syndrome
Related Studies:
  1. nephrotic syndrome
    Hinkes, B. G. et al. 2007, Nephrotic Syndrome in the First Year of Life, Pediatrics 2007. [PubMed 17371932]
    First, two thirds of nephrotic syndrome manifesting in the first year of life can be explained by mutations in 4 genes only (NPHS1, NPHS2, WT1, or LAMB2).

-  MalaCards Disease Associations
  MalaCards Gene Search: LAMB2
Diseases sorted by gene-association score: pierson syndrome* (1689), nephrotic syndrome, type 5, with or without ocular abnormalities* (1650), myasthenic syndrome, congenital, 5* (247), diffuse mesangial sclerosis (16), nephrotic syndrome (15), ecthyma (11), focal segmental glomerulosclerosis (10), hypoparathyroidism, sensorineural deafness, and renal dysplasia (8), cyclothymic disorder (7), walker-warburg syndrome (6), muscle eye brain disease (4), congenital myasthenic syndrome (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C573693 2-(4-((4-(6-methoxy-3-pyridinyl)-5-(4-(trifluoromethoxy)phenyl)-2-thiazolyl)methoxy)-2-methylphenoxy)acetic acid
  • C009505 4,4'-diaminodiphenylmethane
  • C547126 AZM551248
  • D000082 Acetaminophen
  • D000535 Aluminum
  • D000643 Ammonium Chloride
  • C038328 BEP protocol
  • D019256 Cadmium Chloride
          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: 118.16 RPKM in Ovary
Total median expression: 2611.88 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 -123.86299-0.414 Picture PostScript Text
3' UTR -29.90112-0.267 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
IPR013032 - EGF-like_CS
IPR002049 - EGF_laminin
IPR013015 - Laminin_IV
IPR008211 - Laminin_N

Pfam Domains:
PF00053 - Laminin EGF domain
PF00055 - Laminin N-terminal (Domain VI)

SCOP Domains:
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on P55268
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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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005178 integrin binding
GO:0005198 structural molecule activity

Biological Process:
GO:0000904 cell morphogenesis involved in differentiation
GO:0007155 cell adhesion
GO:0007411 axon guidance
GO:0007528 neuromuscular junction development
GO:0007601 visual perception
GO:0014002 astrocyte development
GO:0014044 Schwann cell development
GO:0030198 extracellular matrix organization
GO:0031175 neuron projection development
GO:0043687 post-translational protein modification
GO:0044267 cellular protein metabolic process
GO:0048677 axon extension involved in regeneration
GO:0050808 synapse organization
GO:0060041 retina development in camera-type eye
GO:0072249 metanephric glomerular visceral epithelial cell development
GO:0072274 metanephric glomerular basement membrane development

Cellular Component:
GO:0005576 extracellular region
GO:0005604 basement membrane
GO:0005605 basal lamina
GO:0005608 laminin-3 complex
GO:0005788 endoplasmic reticulum lumen
GO:0031012 extracellular matrix
GO:0043083 synaptic cleft
GO:0043256 laminin complex
GO:0043260 laminin-11 complex
GO:0045202 synapse
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF208630 - JP 2014500723-A/16133: Polycomb-Associated Non-Coding RNAs.
X72760 - H.sapiens mRNA for S-laminin, partial.
X79683 - H.sapiens LAMB2 mRNA for beta2 laminin.
AK094050 - Homo sapiens cDNA FLJ36731 fis, clone UTERU2012703, highly similar to LAMININ BETA-2 CHAIN PRECURSOR.
AX748429 - Sequence 1954 from Patent EP1308459.
S77512 - Homo sapiens laminin beta 2 chain (LAMB2) mRNA, complete cds.
JD115270 - Sequence 96294 from Patent EP1572962.
JD157231 - Sequence 138255 from Patent EP1572962.
JD124068 - Sequence 105092 from Patent EP1572962.
JD535211 - Sequence 516235 from Patent EP1572962.
BC172384 - Synthetic construct Homo sapiens clone IMAGE:100069078, MGC:199089 laminin, beta 2 (laminin S) (LAMB2) mRNA, encodes complete protein.
LF378569 - JP 2014500723-A/186072: Polycomb-Associated Non-Coding RNAs.
LF378568 - JP 2014500723-A/186071: Polycomb-Associated Non-Coding RNAs.
LF378567 - JP 2014500723-A/186070: Polycomb-Associated Non-Coding RNAs.
LF378566 - JP 2014500723-A/186069: Polycomb-Associated Non-Coding RNAs.
LF378565 - JP 2014500723-A/186068: Polycomb-Associated Non-Coding RNAs.
LF378564 - JP 2014500723-A/186067: Polycomb-Associated Non-Coding RNAs.
LF378563 - JP 2014500723-A/186066: Polycomb-Associated Non-Coding RNAs.
LF378562 - JP 2014500723-A/186065: Polycomb-Associated Non-Coding RNAs.
LF378561 - JP 2014500723-A/186064: Polycomb-Associated Non-Coding RNAs.
LF378560 - JP 2014500723-A/186063: Polycomb-Associated Non-Coding RNAs.
LF378558 - JP 2014500723-A/186061: Polycomb-Associated Non-Coding RNAs.
LF378557 - JP 2014500723-A/186060: Polycomb-Associated Non-Coding RNAs.
LF378556 - JP 2014500723-A/186059: Polycomb-Associated Non-Coding RNAs.
DQ584361 - Homo sapiens piRNA piR-51473, complete sequence.
LF378555 - JP 2014500723-A/186058: Polycomb-Associated Non-Coding RNAs.
LF378554 - JP 2014500723-A/186057: Polycomb-Associated Non-Coding RNAs.
LF378553 - JP 2014500723-A/186056: Polycomb-Associated Non-Coding RNAs.
JD409735 - Sequence 390759 from Patent EP1572962.
JD474452 - Sequence 455476 from Patent EP1572962.
JD439380 - Sequence 420404 from Patent EP1572962.
MA444207 - JP 2018138019-A/16133: Polycomb-Associated Non-Coding RNAs.
MA614146 - JP 2018138019-A/186072: Polycomb-Associated Non-Coding RNAs.
MA614145 - JP 2018138019-A/186071: Polycomb-Associated Non-Coding RNAs.
MA614144 - JP 2018138019-A/186070: Polycomb-Associated Non-Coding RNAs.
MA614143 - JP 2018138019-A/186069: Polycomb-Associated Non-Coding RNAs.
MA614142 - JP 2018138019-A/186068: Polycomb-Associated Non-Coding RNAs.
MA614141 - JP 2018138019-A/186067: Polycomb-Associated Non-Coding RNAs.
MA614140 - JP 2018138019-A/186066: Polycomb-Associated Non-Coding RNAs.
MA614139 - JP 2018138019-A/186065: Polycomb-Associated Non-Coding RNAs.
MA614138 - JP 2018138019-A/186064: Polycomb-Associated Non-Coding RNAs.
MA614137 - JP 2018138019-A/186063: Polycomb-Associated Non-Coding RNAs.
MA614135 - JP 2018138019-A/186061: Polycomb-Associated Non-Coding RNAs.
MA614134 - JP 2018138019-A/186060: Polycomb-Associated Non-Coding RNAs.
MA614133 - JP 2018138019-A/186059: Polycomb-Associated Non-Coding RNAs.
MA614132 - JP 2018138019-A/186058: Polycomb-Associated Non-Coding RNAs.
MA614131 - JP 2018138019-A/186057: Polycomb-Associated Non-Coding RNAs.
MA614130 - JP 2018138019-A/186056: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04510 - Focal adhesion
hsa04512 - ECM-receptor interaction
hsa05200 - Pathways in cancer
hsa05222 - Small cell lung cancer

Reactome (by CSHL, EBI, and GO)

Protein P55268 (Reactome details) participates in the following event(s):

R-HSA-2327803 Laminins bind Nidogens 1, 2
R-HSA-2426355 NTN4 binds laminins with gamma-1, gamma-3
R-HSA-2396124 AGRN binds Laminins with gamma-1 subunit
R-HSA-2328129 Dystroglycan binds Laminins and Dystrophin
R-HSA-2396083 Laminins bind galactosyl sulfatide and related sulfated glycolipids
R-HSA-216058 Integrin alpha7beta1 binds Laminin-211, 221, 411, 512, 521
R-HSA-3907292 Integrin alpha6beta1 binds laminin-322, 512, 521, 211, 221, 411
R-HSA-4084505 Laminins bind HSPG2
R-HSA-216048 Integrins alpha3beta1, alpha6beta4 bind laminin-332, 511, 521, (211, 221)
R-HSA-8952289 FAM20C phosphorylates FAM20C substrates
R-HSA-2426450 Laminins:Nidogens binds collagen type IV networks
R-HSA-2426530 Laminins:Nidogens binds HSPG2
R-HSA-3000157 Laminin interactions
R-HSA-3000171 Non-integrin membrane-ECM interactions
R-HSA-3000178 ECM proteoglycans
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-HSA-8957275 Post-translational protein phosphorylation
R-HSA-1474244 Extracellular matrix organization
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification

-  Other Names for This Gene
  Alternate Gene Symbols: LAMB2_HUMAN, LAMS, NM_002292, NP_002283, P55268, Q16321
UCSC ID: uc003cwe.3
RefSeq Accession: NM_002292
Protein: P55268 (aka LAMB2_HUMAN or LMB2_HUMAN)
CCDS: CCDS2789.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LAMB2:
cms (Congenital Myasthenic Syndromes)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002292.3
exon count: 32CDS single in 3' UTR: no RNA size: 5817
ORF size: 5397CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 10994.00frame shift in genome: no % Coverage: 99.85
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 298# 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.