LAMA3

gene
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Also known as nicein-150kDakalinin-165kDaBM600-150kDaepiligrin

Summary

LAMA3 (laminin subunit alpha 3, HGNC:6483) is a protein-coding gene on chromosome 18q11.2, encoding Laminin subunit alpha-3 (Q16787). 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.

The protein encoded by this gene belongs to the laminin family of secreted molecules. Laminins are heterotrimeric molecules that consist of alpha, beta, and gamma subunits that assemble through a coiled-coil domain. Laminins are essential for formation and function of the basement membrane and have additional functions in regulating cell migration and mechanical signal transduction. This gene encodes an alpha subunit and is responsive to several epithelial-mesenchymal regulators including keratinocyte growth factor, epidermal growth factor and insulin-like growth factor. Mutations in this gene have been identified as the cause of Herlitz type junctional epidermolysis bullosa and laryngoonychocutaneous syndrome. Alternative splicing and alternative promoter usage result in multiple transcript variants.

Source: NCBI Gene 3909 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): junctional epidermolysis bullosa (Definitive, GenCC) — +6 more curated relationships
  • Clinical variants (ClinVar): 2,289 total — 126 pathogenic, 134 likely-pathogenic
  • Phenotypes (HPO): 98
  • Druggable target: yes
  • MANE Select transcript: NM_198129

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6483
Approved symbolLAMA3
Namelaminin subunit alpha 3
Location18q11.2
Locus typegene with protein product
StatusApproved
Aliasesnicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin
Ensembl geneENSG00000053747
Ensembl biotypeprotein_coding
OMIM600805
Entrez3909

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 3 retained_intron, 1 non_stop_decay, 1 protein_coding_CDS_not_defined

ENST00000269217, ENST00000313654, ENST00000399516, ENST00000585600, ENST00000586709, ENST00000586751, ENST00000587184, ENST00000588004, ENST00000588164, ENST00000588770, ENST00000590104, ENST00000591749, ENST00000592442, ENST00000592519, ENST00000649721

RefSeq mRNA: 4 — MANE Select: NM_198129 NM_000227, NM_001127717, NM_001127718, NM_198129

CCDS: CCDS11880, CCDS42419, CCDS45838, CCDS59307

Canonical transcript exons

ENST00000313654 — 75 exons

ExonStartEnd
ENSE000009153022375091823751088
ENSE000009153032375372123753812
ENSE000009486082388193623882045
ENSE000009486132387629423876407
ENSE000009486592386783423867917
ENSE000011096642383978523839929
ENSE000011096652381440323814502
ENSE000011096672385868923858829
ENSE000011096682382670223826799
ENSE000011096692376340523763523
ENSE000011096712377349723773587
ENSE000011096732374942823749546
ENSE000011096742381546823815573
ENSE000011096762381984123819997
ENSE000011096772381036623810503
ENSE000011096792381518823815240
ENSE000011096822377755723777619
ENSE000011096832382225223822375
ENSE000011096852381638823816487
ENSE000011096862382731423827467
ENSE000011096882382442323824565
ENSE000011096892384500923845124
ENSE000011096922384746423847668
ENSE000011096932384239523842521
ENSE000011096952371392023714072
ENSE000011096972375839623758511
ENSE000011096992385784423857988
ENSE000011097012374794323748060
ENSE000011097022383878123838878
ENSE000011097032378402323784157
ENSE000011097042377579223775923
ENSE000011097092381305723813103
ENSE000011097112384261123842750
ENSE000011097672389490723895058
ENSE000011097702389429823894348
ENSE000011364672388477323884853
ENSE000011460142387143123871661
ENSE000011460202386478523864883
ENSE000011790542395450323955066
ENSE000012221032383698123837089
ENSE000014135542389001123890117
ENSE000014260772384629723846508
ENSE000027121662386164623861807
ENSE000028196772368945323689977
ENSE000034639452389895423899065
ENSE000034990002389928823899455
ENSE000035080282391271123912881
ENSE000035160192390393323904087
ENSE000035236522394614423946284
ENSE000035421942392145223921585
ENSE000035470452393106223931201
ENSE000035503602394976523949924
ENSE000035554132391528923915422
ENSE000035575752390455323904694
ENSE000035583182393216023932291
ENSE000035636472391469823914860
ENSE000035666982390112723901323
ENSE000035762902394378823943971
ENSE000035793452389873823898848
ENSE000035873082392093523921054
ENSE000035946742392862523928765
ENSE000035961262392812323928240
ENSE000036036392390755023907666
ENSE000036197472390775623907935
ENSE000036254312395299023953109
ENSE000036254652391655123916695
ENSE000036268762390300923903125
ENSE000036303612391441023914561
ENSE000036385482383382823833988
ENSE000036437142395168423951777
ENSE000036543972390915323909295
ENSE000036707322395002923950159
ENSE000036829892390552223905624
ENSE000036837652393922323939386
ENSE000036903482393378223933935

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 94.54.

FANTOM5 (CAGE): breadth broad, TPM avg 28.4891 / max 5394.6643, expressed in 866 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter IDTPM avgSamples expressed
16969223.6465251
1696911.5008111
1696781.0584467
1696820.8530370
1696770.4008201
1696790.3233154
1696830.2435124
1696800.089620
2085180.073230
1697100.055925

Top tissues by expression

292 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right lungUBERON:000216794.54gold quality
skin of legUBERON:000151193.94gold quality
skin of abdomenUBERON:000141693.88gold quality
periodontal ligamentUBERON:000826693.88gold quality
mucosa of sigmoid colonUBERON:000499393.72gold quality
colonic mucosaUBERON:000031793.39gold quality
jejunal mucosaUBERON:000039993.22gold quality
deciduaUBERON:000245093.20gold quality
sural nerveUBERON:001548892.75gold quality
zone of skinUBERON:000001492.21gold quality
upper lobe of left lungUBERON:000895291.61gold quality
minor salivary glandUBERON:000183091.37gold quality
hair follicleUBERON:000207390.99gold quality
upper lobe of lungUBERON:000894890.70gold quality
body of uterusUBERON:000985390.69gold quality
ileal mucosaUBERON:000033190.39gold quality
vaginaUBERON:000099690.37gold quality
mouth mucosaUBERON:000372990.03gold quality
pancreatic ductal cellCL:000207989.51silver quality
ectocervixUBERON:001224989.11gold quality
saliva-secreting glandUBERON:000104489.09gold quality
right uterine tubeUBERON:000130289.09gold quality
tibial nerveUBERON:000132388.75gold quality
calcaneal tendonUBERON:000370188.48gold quality
duodenumUBERON:000211488.18gold quality
mucosa of transverse colonUBERON:000499188.18gold quality
lungUBERON:000204888.14gold quality
olfactory segment of nasal mucosaUBERON:000538687.96gold quality
left uterine tubeUBERON:000130387.77gold quality
endocervixUBERON:000045887.71gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-ENAD-21yes1891.77
E-CURD-7yes1843.65
E-MTAB-7249yes1222.92
E-MTAB-10855yes1110.30
E-GEOD-86618yes798.53
E-MTAB-8559yes444.74
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EP300, FOSL2, GDNF, KLF4, MSX2, SMAD4, SP1, USF1

miRNA regulators (miRDB)

52 targeting LAMA3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-477599.9875.006394
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-302E99.9670.742669
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-302A-3P99.8971.231777
HSA-MIR-302B-3P99.8971.231777
HSA-MIR-302C-3P99.8971.201778
HSA-MIR-302D-3P99.8971.251777
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-612499.8769.783551
HSA-MIR-373-3P99.8470.681668
HSA-MIR-520E-3P99.8470.551698
HSA-MIR-372-3P99.8370.581691
HSA-MIR-520A-3P99.8370.591687
HSA-MIR-520B-3P99.8370.561699
HSA-MIR-520C-3P99.8370.561699
HSA-MIR-520D-3P99.8370.781676
HSA-MIR-520F-3P99.8271.321216
HSA-MIR-3681-5P99.8266.88387
HSA-MIR-3617-5P99.7569.411968
HSA-MIR-64199.7569.351975

Literature-anchored findings (GeneRIF, showing 40)

  • Regulatory implications of a novel mode of interaction of calmodulin with a double IQ-motif target sequence from murine dilute myosin V. (PMID:12441389)
  • null behavioral phenotype originates in the nervous system and involves a calmodulin function that requires calcium binding to all four sites of the protein (PMID:14668380)
  • the direct interaction of melatonin with intact calcium-saturated CaM is calcium-dependent; Molecular dynamics simulations follow the dynamics of melatonin in the binding pocket of CaM (PMID:15498938)
  • potential functional role for calmodulin in regulation of the glycolytic pathway (PMID:15527800)
  • A mutation to the gene encoding calmodulin deregulates muscle contraction. (PMID:15557269)
  • Drosophila CaM is able to fully activate inducible nitric oxide synthase (iNOS); moreover, iNOS activation by CaM, like neuronal NOS, is not dependent on Ca2+ being bound to all four Ca2+-binding sites, but has specific and distinct requirements. (PMID:15896003)
  • Calmodulin/CAMTA/Fbxl4 may mediate a long-term feedback regulation of the activity of Ca(2+)-stimulating G protein-coupled receptor, which could prevent cell damage due to extra Ca(2+) influx. (PMID:17110341)
  • Thus, Calmodulin and Abelson tyrosine kinase are key signaling molecules working synergistically to transduce both midline attractive and repulsive cues. (PMID:18243630)
  • characterized the interdomain motions in the calcium-bound state of calmodulin (Ca(2+)-CaM) using NMR chemical shifts as replica-averaged structural restraints in molecular dynamics simulations (PMID:24530797)
  • Basal body formation in the male testes and the production of functional sperm does not rely on the PLP-CaM interaction, whereas production of functional mechanosensory neurons does. (PMID:25031429)
  • Asp-CaM complex has a critical role in centrosome-pole cohesion and centrosome inheritance in neural stem cells (PMID:26620907)
  • Calmodulin binds to Drosophila TRP with an unexpected mode. (PMID:33326749)
  • Characterization of morphological and cytoskeletal changes in MCF10A breast epithelial cells plated on laminin-5: comparison with breast cancer cell line MCF7. (PMID:11775027)
  • Neurite outgrowth promoting sites have been identified on the laminin alpha 3 chain LG4 module. (PMID:12196012)
  • In all developing organs investigated, the mRNA of the alpha3 chain of laminin is strictly of epithelial origin and the corresponding protein localised in the underlying basement membrane zones (PMID:12382139)
  • These results suggest that the G3 domain of laminin 5 alpha 3 contains two distinct regions that differently regulate cell adhesion and migration. (PMID:12532327)
  • laminin alpha 3 LG4 module may play an important role in tissue remodeling by inducing MMP-1 expression during wound healing (PMID:12826666)
  • a missense mutation in the adhesion G domain of laminin-5 causes mild junctional epidermolysis bullosa (PMID:12943669)
  • results demonstrate that the laminin alpha3 LG4/5 modules within unprocessed laminin-5 permit its cell binding activity through heparan and chondroitin sulfate chains of syndecan-1 (PMID:12947106)
  • proteolytic processing of laminin-5 influences its interaction with alpha3beta1 integrin (PMID:14612440)
  • LAMA3 promoter methylation is associated with increased breast tumor stage and tumor size (PMID:14695139)
  • Characterization of laminin 5B and NH2-terminal proteolytic fragment of its alpha3B chain (PMID:15044476)
  • co-cultures of epithelial cells and fibroblasts were studied to analyse the processing of laminin 5 alpha3, beta3, and gamma2 chains (PMID:15149852)
  • The G4/5 domain in the alpha3 chain facilitates deposition of precursor laminin 5 into the PBM in epidermal wounds (PMID:15316072)
  • Premature termination codon mutations in both alleles of LAMB3 or LAMC2 genes were found in nine of the 11 H junctional epidermolysis bullosa patients (PMID:15373767)
  • the LG4-5 domain synergistically enhances integrin signaling as it is released from the precursor LN5 (PMID:15695818)
  • the absolute mRNA levels generated from the laminin 5 genes do not determine the translated protein levels of the laminin 5 chains in keratinocytes; the expression of the laminin 5 genes may be controlled by common regulation mechanisms (PMID:15854126)
  • The uncoordinated production of chains of ln-5 in allergic asthma could have a bearing on the poor epithelial cell anchorage in these patients. (PMID:16179086)
  • Suppression of laminin-5 alpha 3-chain expression in human mammary epithelial cells results in loss of reconstituted extracellular matrix-mediated growth control and apoptosis. (PMID:16219677)
  • The hinge region between subdomains G3 and G4 of laminin alpha 3 carries the proteolytic cleavage sites but proteolytic processing plays no role in kerocyte migration. (PMID:16297184)
  • tumor cell migration on laminin-5 is inhibited by HYD1, a biologically active integrin-targeting peptide (PMID:16537560)
  • Ln-5 is an important regulator of ADPKD cell proliferation and cystogenesis; Ln-5 gamma(2) chain and Ln-5-alpha(6)beta(4) integrin interaction both contribute to these phenotypic changes (PMID:16870608)
  • The major contributions of laminin-5 to the resistance of the epidermis against frictional stress but also for basement membrane regeneration and repair of damaged skin are reflected by the phenotype of Herlitz junctional epidermolysis bullosa. (PMID:17000025)
  • Laminin-5 may contribute to the development of bone tissues by promoting the proliferation and by suppressing the chondrogenic differentiation of MSCs. (PMID:17071854)
  • Laminin-5 alone stimulates global changes in gene/protein expression in mesenchymal stem cells that lead to commitment of these cells to the osteogenic phenotype, and this correlates with extracellular matrix production. (PMID:17137774)
  • These results suggest a new possible approach to repairing SCI and, in general, a model which will be useful for other multidisciplinary procedures for complex neurological situations. (PMID:17466943)
  • LM-332 is a crucial motility-promoting factor for B-CLL lymphocytes and is a potential constituent favoring the dissemination of B-CLL lymphocytes through vascular basement membranes and possibly lymph node compartments. (PMID:17482449)
  • These results suggest that Crk is required for early attachment to laminin, cell motility, and growth of glioblastoma cell line KMG4. (PMID:17825249)
  • the alpha3 chain can assemble with only beta3-gamma2 heterodimer to form a heterotrimer via disulfide bonds (PMID:18603785)
  • Smad4 mediates transcriptional regulation through three mechanisms: Smad4 binding to a functional SBE site in the LAMA3 promoter, Smad4 binding to AP1 (and Sp1) sites via interaction with AP1 family, and Smad4 impact on transcription of AP1 factors (PMID:18664273)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosi:ch211-241e1.3ENSDARG00000022615
danio_reriolama3ENSDARG00000071462
mus_musculusLama3ENSMUSG00000024421
rattus_norvegicusLama3ENSRNOG00000011300

Paralogs (27): USH2A (ENSG00000042781), LAMC3 (ENSG00000050555), LAMC2 (ENSG00000058085), NTN1 (ENSG00000065320), NTN4 (ENSG00000074527), ATRN (ENSG00000088812), LAMB4 (ENSG00000091128), LAMB1 (ENSG00000091136), LAMA1 (ENSG00000101680), MEGF8 (ENSG00000105429), MEGF9 (ENSG00000106780), ATRNL1 (ENSG00000107518), LAMA4 (ENSG00000112769), LAMA5 (ENSG00000130702), LAMC1 (ENSG00000135862), NTN5 (ENSG00000142233), HSPG2 (ENSG00000142798), TMEFF2 (ENSG00000144339), NTN3 (ENSG00000162068), NTNG1 (ENSG00000162631), EGFLAM (ENSG00000164318), LAMB2 (ENSG00000172037), AGRN (ENSG00000188157), NTNG2 (ENSG00000196358), LAMA2 (ENSG00000196569), LAMB3 (ENSG00000196878), TMEFF1 (ENSG00000241697)

Protein

Protein identifiers

Laminin subunit alpha-3Q16787 (reviewed: Q16787)

Alternative names: Epiligrin 170 kDa subunit, Epiligrin subunit alpha, Kalinin subunit alpha, Laminin-5 subunit alpha, Laminin-6 subunit alpha, Laminin-7 subunit alpha, Nicein subunit alpha

All UniProt accessions (11): A0A075B783, A0A0A0MSA0, A0A0A0MTS5, A0A0A6YYF2, A0A3B3ITG1, Q16787, K7EIP4, K7EMU9, K7EPP3, K7EQ42, K7ERM0

UniProt curated annotations — full annotation on UniProt →

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. Laminin-5 is thought to be involved in (1) cell adhesion via integrin alpha-3/beta-1 in focal adhesion and integrin alpha-6/beta-4 in hemidesmosomes, (2) signal transduction via tyrosine phosphorylation of pp125-FAK and p80, (3) differentiation of keratinocytes.

Subunit / interactions. 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. Alpha-3 is a subunit of laminin-5 (laminin-332 or epiligrin/kalinin/nicein), laminin-6 (laminin-311 or K-laminin) and laminin-7 (laminin-321 or KS-laminin).

Subcellular location. Secreted. Extracellular space. Extracellular matrix. Basement membrane.

Tissue specificity. Skin; respiratory, urinary, and digestive epithelia and in other specialized tissues with prominent secretory or protective functions. Epithelial basement membrane, and epithelial cell tongue that migrates into a wound bed. A differential and focal expression of the subunit alpha-3 is observed in the CNS.

Disease relevance. Epidermolysis bullosa, junctional 2A, intermediate (JEB2A) [MIM:619783] A form of epidermolysis bullosa, a genodermatosis characterized by recurrent blistering, fragility of the skin and mucosal epithelia, and erosions caused by minor mechanical trauma. JEB2A is an autosomal recessive, intermediate form in which blistering lesions occur between the epidermis and the dermis at the lamina lucida level of the basement membrane zone. In intermediate forms of junctional epidermolysis bullosa, blistering does not lead to the formation of chronic granulation tissue and does not affect the lifespan of affected individuals. Nail dystrophy and dental enamel defects are present. Scarring or non-scarring alopecia and diffuse hair loss may occur. The disease is caused by variants affecting the gene represented in this entry. Epidermolysis bullosa, junctional 2B, severe (JEB2B) [MIM:619784] A form of epidermolysis bullosa, a genodermatosis characterized by recurrent blistering, fragility of the skin and mucosal epithelia, and erosions caused by minor mechanical trauma. JEB2B is an autosomal recessive form in which blistering lesions occur between the epidermis and the dermis at the lamina lucida level of the basement membrane zone. It belongs to the severe spectrum of junctional epidermolysis bullosa (previously known as generalized severe or Herlitz type), characterized by onset of blistering over large regions of the body at birth or in early infancy. Blistering also affects the mucous membranes, such as the moist lining of the mouth and digestive tract, which can make it difficult to eat and digest food. The extensive blistering leads to scarring and the formation of red, bumpy patches called granulation tissue. Other complications can include fusion of the fingers and toes, abnormalities of the fingernails and toenails, joint deformities, dental enamel defects, and alopecia. Severe, junctional forms are associated with death in the first 6 to 24 months of life. The disease is caused by variants affecting the gene represented in this entry. Epidermolysis bullosa, junctional 2C, laryngoonychocutaneous (JEB2C) [MIM:245660] A form of epidermolysis bullosa, a genodermatosis characterized by recurrent blistering, fragility of the skin and mucosal epithelia, and erosions caused by minor mechanical trauma. JEB2C is an autosomal recessive, severe form in which blistering lesions occur between the epidermis and the dermis at the lamina lucida level of the basement membrane zone. JEB2C manifestations appear in early infancy and include hoarse cry, skin ulceration, nail dystrophy with recurrent loss of toenails and fingernails, and conjunctival scarring. Some patients have amelogenesis imperfecta. Death in childhood is common. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The alpha-helical domains I and II are thought to interact with other laminin chains to form a coiled coil structure. Domain G is globular.

Induction. Laminin-5 is up-regulated in wound sites of human skin.

Isoforms (4)

UniProt IDNamesCanonical?
Q16787-22, Byes
Q16787-11, A
Q16787-33
Q16787-44

RefSeq proteins (4): NP_000218, NP_001121189, NP_001121190, NP_937762* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000034Laminin_IVDomain
IPR000742EGFDomain
IPR001791Laminin_GDomain
IPR002049LE_domDomain
IPR008211Laminin_NDomain
IPR009254Laminin_aIDomain
IPR010307Laminin_dom_IIDomain
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR050440Laminin/Netrin_ECMFamily
IPR056863LMN_ATRN_NET-like_EGFDomain

Pfam: PF00052, PF00053, PF00055, PF02210, PF06008, PF06009, PF24973

UniProt features (118 total): disulfide bond 60, domain 22, sequence variant 8, sequence conflict 7, splice variant 5, region of interest 5, glycosylation site 5, coiled-coil region 3, signal peptide 1, chain 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q16787 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (60): 299–308, 301–319, 321–330, 333–353, 356–365, 358–390, 393–402, 405–423, 426–436, 428–443, 445–454, 457–467, 491–503, 493–509, 511–520, 523–533, 536–548, 538–555, 557–566, 569–586 …

Glycosylation sites (5): 142, 242, 2365, 2502, 2584

Function

Pathways and Gene Ontology

Reactome pathways

19 pathways

IDPathway
R-HSA-1474228Degradation of the extracellular matrix
R-HSA-2022090Assembly of collagen fibrils and other multimeric structures
R-HSA-2214320Anchoring fibril formation
R-HSA-3000157Laminin interactions
R-HSA-3000171Non-integrin membrane-ECM interactions
R-HSA-3000178ECM proteoglycans
R-HSA-446107Type I hemidesmosome assembly
R-HSA-8874081MET activates PTK2 signaling
R-HSA-9638630Attachment of bacteria to epithelial cells
R-HSA-9913351Formation of the dystrophin-glycoprotein complex (DGC)
R-HSA-9925563Developmental Lineage of Pancreatic Ductal Cells
R-HSA-1474244Extracellular matrix organization
R-HSA-1474290Collagen formation
R-HSA-1500931Cell-Cell communication
R-HSA-162582Signal Transduction
R-HSA-446728Cell junction organization
R-HSA-6806834Signaling by MET
R-HSA-8875878MET promotes cell motility
R-HSA-9006934Signaling by Receptor Tyrosine Kinases

MSigDB gene sets: 468 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, AP1_01, XU_GH1_AUTOCRINE_TARGETS_UP, GOBP_FORMATION_OF_PRIMARY_GERM_LAYER, JAEGER_METASTASIS_DN, LI_PROSTATE_CANCER_EPIGENETIC, SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER, NAGASHIMA_NRG1_SIGNALING_UP, HATADA_METHYLATED_IN_LUNG_CANCER_DN, CHANG_IMMORTALIZED_BY_HPV31_DN, GOBP_CELL_CELL_ADHESION, CAIRO_HEPATOBLASTOMA_CLASSES_DN, GOBP_HEMIDESMOSOME_ASSEMBLY, GOBP_CELL_JUNCTION_ORGANIZATION, AP1_Q4_01

GO Biological Process (9): epidermis development (GO:0008544), regulation of cell adhesion (GO:0030155), regulation of cell migration (GO:0030334), hemidesmosome assembly (GO:0031581), endodermal cell differentiation (GO:0035987), regulation of embryonic development (GO:0045995), cell-cell adhesion (GO:0098609), cell adhesion (GO:0007155), anatomical structure morphogenesis (GO:0009653)

GO Molecular Function (3): signaling receptor binding (GO:0005102), structural molecule activity (GO:0005198), extracellular matrix structural constituent (GO:0005201)

GO Cellular Component (10): extracellular region (GO:0005576), basement membrane (GO:0005604), laminin-121 trimer (GO:0005608), laminin-332 trimer (GO:0005610), endoplasmic reticulum (GO:0005783), adherens junction (GO:0005912), hemidesmosome (GO:0030056), extracellular matrix (GO:0031012), extracellular exosome (GO:0070062), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-12 pathways:

CategoryPathways
Extracellular matrix organization5
Collagen formation1
Assembly of collagen fibrils and other multimeric structures1
Cell junction organization1
MET promotes cell motility1
Biofilm formation1
Non-integrin membrane-ECM interactions1
Developmental Cell Lineages of the Exocrine Pancreas1
Cell-Cell communication1
Signaling by Receptor Tyrosine Kinases1
Signaling by MET1
Signal Transduction1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell adhesion2
extracellular matrix2
cellular anatomical structure2
laminin trimer2
tissue development1
regulation of cellular process1
cell migration1
regulation of cell motility1
cell-substrate junction assembly1
endoderm formation1
cell differentiation1
embryo development1
regulation of multicellular organismal development1
cellular process1
developmental process1
anatomical structure development1
protein binding1
molecular_function1
structural molecule activity1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cell-cell junction1
cell-substrate junction1
external encapsulating structure1
extracellular vesicle1

Protein interactions and networks

STRING

2066 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LAMA3LAMB3Q13751985
LAMA3LAMC2Q13753982
LAMA3COL17A1Q9UMD9936
LAMA3ITGB4P16144830
LAMA3ITGA6P23229785
LAMA3ITGA3P26006736
LAMA3DSTQ03001675
LAMA3COL7A1Q02388647
LAMA3TLL2Q9Y6L7639
LAMA3COL4A1P02462637
LAMA3COL4A2P08572636
LAMA3ITGA5P08648613
LAMA3LAMB1P07942612
LAMA3NID1P14543611
LAMA3COL6A1P12109573

IntAct

57 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
SPINK4PLXNA2psi-mi:“MI:0914”(association)0.530
DEFA1MANBApsi-mi:“MI:0914”(association)0.530
SCGB1D4EGFRpsi-mi:“MI:0914”(association)0.530
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
OS9AGRNpsi-mi:“MI:0914”(association)0.530
CFTRCNOT1psi-mi:“MI:0914”(association)0.480
LAMA3SDC1psi-mi:“MI:0915”(physical association)0.400
SIRT1KPNA3psi-mi:“MI:0915”(physical association)0.400
LAMA3KDM3Apsi-mi:“MI:0915”(physical association)0.400
VWA8psi-mi:“MI:0914”(association)0.350
SCGB2A2GXYLT2psi-mi:“MI:0914”(association)0.350
TSHRPOTEFpsi-mi:“MI:0914”(association)0.350
CD44TCAF2psi-mi:“MI:0914”(association)0.350
PTPRKMANBApsi-mi:“MI:0914”(association)0.350
TAZMANBApsi-mi:“MI:0914”(association)0.350
SLAMF1RTCApsi-mi:“MI:0914”(association)0.350
GMLCLSTN1psi-mi:“MI:0914”(association)0.350
HRASRPL7psi-mi:“MI:0914”(association)0.350
CFTRMYH7Bpsi-mi:“MI:0914”(association)0.350
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
OS9GXYLT2psi-mi:“MI:0914”(association)0.350
CDH23GTPBP10psi-mi:“MI:0914”(association)0.350

BioGRID (72): LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), PLG (Reconstituted Complex), PLAT (Reconstituted Complex), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS), LAMA3 (Affinity Capture-MS)

ESM2 similar proteins: A0JP86, A1A5Y0, A4D0S4, G5ECE3, O15230, P11046, P15215, P15800, P16144, P18563, P18564, P19137, P24043, P25391, P26010, P26011, P55268, P58459, P97607, Q13751, Q13753, Q16787, Q1EHB3, Q1RPR6, Q2KIT5, Q2QI47, Q5RB89, Q60438, Q60675, Q61001, Q61087, Q61092, Q61292, Q61789, Q68SA9, Q6AYF4, Q75N90, Q863C4, Q8BG22, Q8HZI9

Diamond homologs: A0JP86, A2ASQ1, G5ECE3, O00468, O00634, O09118, O15230, O75445, O75882, O95631, P02468, P11047, P15215, P19137, P24043, P25304, P25391, P31696, P34710, P97927, Q00174, Q01635, Q13751, Q13753, Q16363, Q16787, Q18823, Q19981, Q1LVF0, Q24567, Q24568, Q27262, Q2HXW4, Q2QI47, Q5RB89, Q5VV63, Q60675, Q61001, Q61087, Q61092

SIGNOR signaling

2 interactions.

AEffectBMechanism
GDNF“up-regulates quantity by expression”LAMA3“transcriptional regulation”
LAMA3“form complex”Laminin-5binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

2289 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic126
Likely pathogenic134
Uncertain significance626
Likely benign1111
Benign144

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1047960NM_198129.4(LAMA3):c.6319-1G>TPathogenic
1047961NM_198129.4(LAMA3):c.6348_6352delinsCTGGCAAGA (p.Glu2117fs)Pathogenic
1047962NM_198129.4(LAMA3):c.9856G>T (p.Ala3286Ser)Pathogenic
1068548NM_198129.4(LAMA3):c.6469G>T (p.Glu2157Ter)Pathogenic
1069997NM_198129.4(LAMA3):c.5622_5635del (p.Leu1874fs)Pathogenic
1070832NM_198129.4(LAMA3):c.8145T>A (p.Tyr2715Ter)Pathogenic
1070853NC_000018.9:g.(?21478692)(21479039_?)delPathogenic
1071930NM_198129.4(LAMA3):c.6100A>T (p.Lys2034Ter)Pathogenic
1071950NM_198129.4(LAMA3):c.9887G>A (p.Trp3296Ter)Pathogenic
1072339NM_198129.4(LAMA3):c.5394T>A (p.Cys1798Ter)Pathogenic
1072501NM_198129.4(LAMA3):c.6847_6854del (p.Ala2283fs)Pathogenic
1074803NC_000018.9:g.(?21484507)(21485598_?)delPathogenic
1075696NM_198129.4(LAMA3):c.5568dup (p.Leu1857fs)Pathogenic
1252054NM_198129.4(LAMA3):c.8302C>T (p.Arg2768Ter)Pathogenic
1321416NM_198129.4(LAMA3):c.7204C>T (p.Arg2402Ter)Pathogenic
1323177NM_198129.4(LAMA3):c.5000_5003del (p.Gly1667fs)Pathogenic
1323178NM_198129.4(LAMA3):c.8087_8090delinsTGC (p.Asn2696fs)Pathogenic
1350464NM_198129.4(LAMA3):c.9617T>G (p.Leu3206Ter)Pathogenic
1361060NM_198129.4(LAMA3):c.9893C>A (p.Ser3298Ter)Pathogenic
1369957NM_198129.4(LAMA3):c.8755A>T (p.Lys2919Ter)Pathogenic
1371125NM_198129.4(LAMA3):c.7738del (p.Thr2580fs)Pathogenic
1379401NM_198129.4(LAMA3):c.5137G>T (p.Glu1713Ter)Pathogenic
1400822NM_198129.4(LAMA3):c.9236dup (p.Arg3081fs)Pathogenic
1404615NM_198129.4(LAMA3):c.5728C>T (p.Gln1910Ter)Pathogenic
1412135NM_198129.4(LAMA3):c.5992G>T (p.Glu1998Ter)Pathogenic
1412583NM_198129.4(LAMA3):c.6778G>T (p.Glu2260Ter)Pathogenic
1417958NM_198129.4(LAMA3):c.8284del (p.Glu2762fs)Pathogenic
1422229NM_198129.4(LAMA3):c.8911C>T (p.Gln2971Ter)Pathogenic
1422425NM_198129.4(LAMA3):c.6199C>T (p.Gln2067Ter)Pathogenic
1441309NM_198129.4(LAMA3):c.5119C>T (p.Gln1707Ter)Pathogenic

SpliceAI

11506 predictions. Top by Δscore:

VariantEffectΔscore
18:23713916:TCAG:Tacceptor_loss1.0000
18:23713917:CAGG:Cacceptor_loss1.0000
18:23713918:A:AGacceptor_gain1.0000
18:23713918:AG:Aacceptor_gain1.0000
18:23713919:G:GTacceptor_gain1.0000
18:23713919:GG:Gacceptor_gain1.0000
18:23713919:GGGCC:Gacceptor_gain1.0000
18:23714070:CAGGT:Cdonor_loss1.0000
18:23714071:AGGTG:Adonor_loss1.0000
18:23714073:GTG:Gdonor_loss1.0000
18:23714074:T:Gdonor_loss1.0000
18:23747937:TATCA:Tacceptor_loss1.0000
18:23747938:ATCAG:Aacceptor_loss1.0000
18:23747939:TCAG:Tacceptor_loss1.0000
18:23747940:CAGC:Cacceptor_loss1.0000
18:23747941:A:AGacceptor_gain1.0000
18:23747941:AGC:Aacceptor_loss1.0000
18:23747942:G:Aacceptor_loss1.0000
18:23747942:G:GAacceptor_gain1.0000
18:23748056:TGCTC:Tdonor_gain1.0000
18:23748057:GCTC:Gdonor_gain1.0000
18:23748057:GCTCG:Gdonor_gain1.0000
18:23748058:CTC:Cdonor_gain1.0000
18:23748059:TC:Tdonor_gain1.0000
18:23748060:CG:Cdonor_loss1.0000
18:23748061:G:GGdonor_gain1.0000
18:23748061:GT:Gdonor_loss1.0000
18:23748062:TAAG:Tdonor_loss1.0000
18:23748063:A:ATdonor_loss1.0000
18:23748064:AGT:Adonor_loss1.0000

AlphaMissense

21889 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:23909264:T:CL2376P0.998
18:23909275:G:CA2380P0.998
18:23861664:T:AW1481R0.996
18:23861664:T:CW1481R0.996
18:23928151:G:CG2736R0.996
18:23928154:T:AC2737S0.996
18:23928155:G:CC2737S0.996
18:23928223:T:CC2760R0.996
18:23714006:G:CW127C0.995
18:23714006:G:TW127C0.995
18:23714010:A:CS129R0.995
18:23714012:C:AS129R0.995
18:23714012:C:GS129R0.995
18:23928154:T:CC2737R0.995
18:23928223:T:AC2760S0.995
18:23928224:G:CC2760S0.995
18:23689927:T:AC82S0.994
18:23689928:G:CC82S0.994
18:23689929:C:GC82W0.994
18:23713929:T:AC102S0.994
18:23713930:G:CC102S0.994
18:23714004:T:AW127R0.994
18:23714004:T:CW127R0.994
18:23915361:A:CS2573R0.994
18:23915363:C:AS2573R0.994
18:23915363:C:GS2573R0.994
18:23916580:T:GF2603C0.994
18:23920951:T:CL2647P0.994
18:23921558:G:AG2717E0.994
18:23928152:G:AG2736D0.994

dbSNP variants (sampled 300 via entrez): RS1000004758 (18:23925781 G>T), RS1000008419 (18:23846639 T>C), RS1000009756 (18:23809926 T>C), RS1000011371 (18:23744686 G>A), RS1000013857 (18:23853186 AAAAT>A,AAAATAAAT), RS1000024389 (18:23837372 G>C,T), RS1000025785 (18:23698276 G>A,C), RS1000030198 (18:23840560 A>T), RS1000054308 (18:23937609 G>T), RS1000055444 (18:23729888 C>T), RS1000058071 (18:23695159 A>G), RS1000067236 (18:23701369 T>C), RS1000071294 (18:23906581 A>G), RS1000102051 (18:23906025 A>G), RS1000108879 (18:23795837 A>T)

Disease associations

OMIM: gene MIM:600805 | disease phenotypes: MIM:226650, MIM:226700, MIM:245660, MIM:619783, MIM:619784, MIM:178500

GenCC curated gene-disease

DiseaseClassificationInheritance
laryngo-onycho-cutaneous syndromeDefinitiveAutosomal recessive
junctional epidermolysis bullosaDefinitiveAutosomal recessive
junctional epidermolysis bullosa, non-Herlitz typeStrongAutosomal recessive
junctional epidermolysis bullosa Herlitz typeStrongAutosomal recessive
epidermolysis bullosa, junctional 2A, intermediateStrongAutosomal recessive
epidermolysis bullosa, junctional 2B, severeStrongAutosomal recessive
generalized junctional epidermolysis bullosa non-Herlitz typeSupportiveAutosomal recessive

Mondo (8): junctional epidermolysis bullosa, non-Herlitz type (MONDO:0009180), junctional epidermolysis bullosa (MONDO:0017612), junctional epidermolysis bullosa Herlitz type (MONDO:0009182), laryngo-onycho-cutaneous syndrome (MONDO:0009513), epidermolysis bullosa, junctional 2A, intermediate (MONDO:0030746), epidermolysis bullosa, junctional 2B, severe (MONDO:0030747), interstitial lung disease 2 (MONDO:0800497), generalized junctional epidermolysis bullosa non-Herlitz type (MONDO:0019307)

Orphanet (9): Localized junctional epidermolysis bullosa (Orphanet:251393), Intermediate generalized junctional epidermolysis bullosa (Orphanet:79402), Junctional epidermolysis bullosa inversa (Orphanet:79405), OBSOLETE: Junctional epidermolysis bullosa, non-Herlitz type (Orphanet:89840), Junctional epidermolysis bullosa (Orphanet:305), Laryngo-onycho-cutaneous syndrome (Orphanet:2407), Severe generalized junctional epidermolysis bullosa (Orphanet:79404), Idiopathic pulmonary fibrosis (Orphanet:2032), Acute interstitial pneumonia (Orphanet:79126)

HPO phenotypes

98 total (30 of 98 shown, HPO-id order):

HPOTerm
HP:0000003Multicystic kidney dysplasia
HP:0000007Autosomal recessive inheritance
HP:0000010Recurrent urinary tract infections
HP:0000014Abnormality of the bladder
HP:0000016Urinary retention
HP:0000070Ureterocele
HP:0000072Hydroureter
HP:0000081Duplicated collecting system
HP:0000107Renal cyst
HP:0000126Hydronephrosis
HP:0000421Epistaxis
HP:0000481Abnormal cornea morphology
HP:0000505Visual impairment
HP:0000670Carious teeth
HP:0000684Delayed eruption of teeth
HP:0000691Microdontia
HP:0000705Amelogenesis imperfecta
HP:0000939Osteoporosis
HP:0000969Edema
HP:0000982Palmoplantar keratoderma
HP:0000999Pyoderma
HP:0001000Abnormality of skin pigmentation
HP:0001030Fragile skin
HP:0001056Milia
HP:0001057Aplasia cutis congenita
HP:0001075Atrophic scars
HP:0001159Syndactyly
HP:0001211Abnormal fingertip morphology
HP:0001250Seizure
HP:0001508Failure to thrive

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

DescriptorNameTree numbers
D016109Epidermolysis Bullosa, JunctionalC16.131.831.493.170; C16.320.850.275.170; C17.800.804.493.170; C17.800.827.275.170; C17.800.865.410.170
C537032Laryngo onycho cutaneous syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2364187 (PROTEIN COMPLEX GROUP)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

82 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Estradiolaffects expression, affects cotreatment, increases expression, decreases expression5
sodium arseniteaffects expression, affects methylation, increases expression3
Zoledronic Acidincreases expression3
Air Pollutantsaffects cotreatment, decreases expression, increases abundance, increases oxidation, increases expression3
Tetrachlorodibenzodioxinaffects cotreatment, increases expression, decreases expression3
bisphenol Aincreases methylation, increases expression, affects cotreatment2
chloropicrinaffects expression, decreases expression2
Benzo(a)pyreneincreases expression, affects methylation, decreases methylation2
Cisplatindecreases expression, increases expression2
Formaldehydedecreases expression, increases expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
Tretinoindecreases expression, increases expression2
Cyclosporinedecreases expression, affects expression2
Aflatoxin B1increases expression, increases methylation2
Cadmium Chlorideaffects expression, decreases expression2
Particulate Matterincreases expression, affects cotreatment, increases abundance2
4-oxoretinoic aciddecreases expression1
chloroacetaldehydeaffects expression1
alpha-pinenedecreases expression, increases oxidation, increases abundance, affects cotreatment1
pyrogallol 1,3-dimethyl etheraffects localization, affects cotreatment, increases expression, decreases expression1
2,4,5,2’,4’,5’-hexachlorobiphenylincreases expression1
beta-lapachoneincreases expression1
butyraldehydedecreases expression1
benzo(e)pyreneaffects methylation, increases methylation1
cupric chlorideincreases expression1
phenanthreneincreases expression1
lysophosphatidic acidincreases expression1
benazol Paffects expression1
methacrylaldehydeincreases oxidation, increases abundance, affects cotreatment, decreases expression1
brequinarincreases expression1

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1VHAbcam HeLa LAMA3 KOCancer cell lineFemale
CVCL_D9I7Ubigene HEK293 LAMA3 KOTransformed cell lineFemale

Clinical trials (associated diseases)

17 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00587223PHASE3TERMINATEDSafety and Efficacy of Apligraf in Nonhealing Wounds of Subjects With Junctional or Dystrophic Epidermolysis Bullosa (EB)
NCT06917690PHASE3RECRUITINGA Study to Learn About the Safety and Efficacy of the Drug Oleogel-S10 in Japanese Patients With Epidermolysis Bullosa
NCT03578029PHASE2TERMINATEDEvaluation of the Safety and Efficacy Study of RGN-137 Topical Gel for Junctional and Dystrophic Epidermolysis Bullosa
NCT04908215PHASE2COMPLETEDINM-755 (Cannabinol) Cream for Treatment of Epidermolysis Bullosa
NCT06594393PHASE2RECRUITINGA Phase 2 Study of TCP-25 Gel in Patients With Epidermolysis Bullosa, STEP-study
NCT03472287PHASE1COMPLETEDTo Evaluate the Pharmacokinetic of Diacerein and Rhein After Maximum Use in Patients With Epidermolysis Bullosa (EB)
NCT06713434PHASE1ACTIVE_NOT_RECRUITINGPilot Study of ELK-003 Eye Drops for Treating Ocular Manifestations of Epidermolysis Bullosa
NCT04727268Not specifiedUNKNOWNGenotype-phenotype Correlation in Junctional Epidermolysis Bullosa
NCT03490331PHASE1/PHASE2TERMINATEDClinical Trial to Assess Safety and Efficacy of Autologous Cultured Epidermal Grafts Containing Epidermal Stem Cells Genetically Modified in Patients With JEB (HOLOGENE17)
NCT03526159PHASE1/PHASE2RECRUITINGGentamicin for Junctional Epidermolysis Bullosa
NCT04140786PHASE1/PHASE2UNKNOWNOptimizing IV Gentamicin in JEB
NCT03269474Not specifiedUNKNOWNComputational Drug Repurposing for All EBS Cases
NCT05033574Not specifiedUNKNOWNThe State of Sexual Development in Children With Inherited Epidermolysis Bullosa
NCT06007235Not specifiedUNKNOWNCACIPLIQ20 in Wound Healing in Subjects With Epidermolysis Bullosa
NCT06423573Not specifiedRECRUITINGA Study to Assess the Incidence of Skin Cancers in Patients With Epidermolysis Bullosa Receiving Filsuvez
NCT06372353Not specifiedCOMPLETEDThe Effect Of Baduanjin Exercises In Patients With Idiopathic Pulmonary Fibrosis
NCT06644144Not specifiedRECRUITINGP4O2 ILD Extension