LAMC2

protein-coding

laminin subunit gamma 2, the group of Laminin subunits

Gene summary

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), have 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 gamma chain isoform laminin, gamma 2. The gamma 2 chain, formerly thought to be a truncated version of beta chain (B2t), is highly homologous to the gamma 1 chain; however, it lacks domain VI, and domains V, IV and III are shorter. It is expressed in several fetal tissues but differently from gamma 1, and is specifically localized to epithelial cells in skin, lung and kidney. The gamma 2 chain together with alpha 3 and beta 3 chains constitute laminin 5 (earlier known as kalinin), which is an integral part of the anchoring filaments that connect epithelial cells to the underlying basement membrane. The epithelium-specific expression of the gamma 2 chain implied its role as an epithelium attachment molecule, and mutations in this gene have been associated with junctional epidermolysis bullosa, a skin disease characterized by blisters due to disruption of the epidermal-dermal junction. Two transcript variants resulting from alternative splicing of the 3' terminal exon, and encoding different isoforms of gamma 2 chain, have been described. The two variants are differentially expressed in embryonic tissues, however, the biological significance of the two forms is not known. Transcript variants utilizing alternative polyA_signal have also been noted in literature. [provided by RefSeq, Aug 2011]

Previous symbols:
  • EBR2
  • LAMB2T
  • LAMNB2
  • EBR2A

MANE transcript

NM_005562.3

Inheritance

AR

ClinVar variants

P:263U:227B:509

Top phenotype

Epidermolysis bullosa, junctional 3A, intermediate; Epidermolysis bullosa, junctional 3B, severe

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr1:183,186,238-183,245,127

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~58.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

epidermolysis bullosa, junctional 3B, severeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030749

Submitter: PanelApp Australia

epidermolysis bullosa, junctional 3A, intermediateSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030748

Submitter: PanelApp Australia

junctional epidermolysis bullosa Herlitz typeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009182

Submitter: Labcorp Genetics (formerly Invitae)

junctional epidermolysis bullosaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0017612

Submitter: Myriad Women's Health

junctional epidermolysis bullosa Herlitz typeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009182

Submitter: Genomics England PanelApp

junctional epidermolysis bullosa Herlitz typeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009182

Submitter: Orphanet

generalized junctional epidermolysis bullosa non-Herlitz typeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019307

Submitter: Orphanet

junctional epidermolysis bullosa, non-Herlitz typeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009180

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Epidermolysis bullosa, junctional 3A, intermediate; Epidermolysis bullosa, junctional 3B, severeAR

Manifestation: Dermatologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 8012393; 11810295; 16473856; 21198797; 21801158Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LAMC2 variants in ClinVar

11 Conditions Cataloged
not providedTotal: 888
Inborn genetic diseasesTotal: 174
Junctional epidermolysis bullosaTotal: 144
Junctional epidermolysis bullosa gravis of HerlitzTotal: 118
Epidermolysis bullosa, junctional 3B, severeTotal: 57
Epidermolysis bullosa, junctional 3A, intermediateTotal: 53
not specifiedTotal: 45
LAMC2-related disorderTotal: 43

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005562.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
6
clinvar
464
clinvar
5
clinvar
475
missense
1
clinvar
1
clinvar
213
clinvar
34
clinvar
6
clinvar
255
nonsense
43
clinvar
46
clinvar
89
start loss
1
clinvar
2
clinvar
3
frameshift
73
clinvar
49
clinvar
1
clinvar
123
splice donor/acceptor (+/-2bp)
7
clinvar
40
clinvar
7
clinvar
54
Total12513822749811999

Highest pathogenic variant AF is 0.000043779364

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005562.3RefSeqNP_005553.223MANE Select
ENST00000264144.5EnsemblENSP00000264144.423MANE Select
NM_018891.3RefSeqNP_061486.222Standard
ENST00000493293.5EnsemblENSP00000432063.122Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • PI3K-Akt signaling pathway - Homo sapiens (human)
  • ECM-receptor interaction - Homo sapiens (human)
  • Focal adhesion - Homo sapiens (human)
  • Small cell lung cancer - Homo sapiens (human)
  • Amoebiasis - Homo sapiens (human)

Biological Process

  • cell adhesion
  • positive regulation of cell population proliferation
  • epidermis development
  • extracellular matrix organization
  • positive regulation of cell migration

Molecular Function

  • extracellular matrix structural constituent
  • heparin binding

Cellular Component

  • extracellular region
  • laminin-2 complex
  • extracellular space
  • cell cortex
  • membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000264144
Coding exons
23
Length
58663
Individuals with no LoFs
125669
Homozygous LoFs
0
Heterozygous LoFs
79
Defined
125748
p
0.000314
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3466276520.9620.00003677819
Missense (PolyPhen)189222.920.847832706
Synonymous0.6112342460.9510.00001382285
Loss of Function3.833062.80.4780.00000366724

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000180.00018rare
Latino/Admixed American0.000120.00012rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.000490.00049rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000450.00045rare
South Asian0.000260.00026rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
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. Ladsin exerts cell- scattering activity toward a wide variety of cells, including epithelial, endothelial, and fibroblastic cells. {ECO:0000269|PubMed:8265624}.;
Disease
DISEASE: Epidermolysis bullosa, junctional, Herlitz type (H-JEB) [MIM:226700]: An infantile and lethal form of junctional epidermolysis bullosa, a group of blistering skin diseases characterized by tissue separation which occurs within the dermo- epidermal basement In the Herlitz type, death occurs usually within the first six months of life. Occasionally, children survive to teens. It is marked by bullous lesions at birth and extensive denudation of skin and mucous membranes that may be hemorrhagic. {ECO:0000269|PubMed:11810295, ECO:0000269|PubMed:8012393}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.413

Intolerance Scores

LoFtool
0.774
RVIS EVS
0.55
RVIS percentile EVS
81.39

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.352

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.