LAMC2
protein-codinglaminin 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]
- EBR2
- LAMB2T
- LAMNB2
- EBR2A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~58.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0030749
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0030748
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009182
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0017612
Submitter: Myriad Women's Health
Inheritance Pattern: AR
Disease ID:MONDO:0009182
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0009182
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0019307
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009180
Submitter: Genomics England PanelApp
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LAMC2 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | 464 | 5 | 475 | ||
| missense | 1 | 1 | 213 | 34 | 6 | 255 |
| nonsense | 43 | 46 | 89 | |||
| start loss | 1 | 2 | 3 | |||
| frameshift | 73 | 49 | 1 | 123 | ||
| splice donor/acceptor (+/-2bp) | 7 | 40 | 7 | 54 | ||
| Total | 125 | 138 | 227 | 498 | 11 | 999 |
Highest pathogenic variant AF is 0.000043779364
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005553.2 | 23 | MANE Select | |
| Ensembl | ENSP00000264144.4 | 23 | MANE Select | |
| RefSeq | NP_061486.2 | 22 | Standard | |
| Ensembl | ENSP00000432063.1 | 22 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.346 | 627 | 652 | 0.962 | 0.0000367 | 7819 |
| Missense (PolyPhen) | 189 | 222.92 | 0.84783 | 2706 | ||
| Synonymous | 0.611 | 234 | 246 | 0.951 | 0.0000138 | 2285 |
| Loss of Function | 3.83 | 30 | 62.8 | 0.478 | 0.00000366 | 724 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00049 | 0.00049 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00045 | 0.00045 | rare |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |