LAMB1
protein-codinglaminin subunit beta 1, 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 are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they 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 1. The beta 1 chain has 7 structurally distinct domains which it shares with other beta chain isomers. The C-terminal helical region containing domains I and II are separated by domain alpha, domains III and V contain several EGF-like repeats, and domains IV and VI have a globular conformation. Laminin, beta 1 is expressed in most tissues that produce basement membranes, and is one of the 3 chains constituting laminin 1, the first laminin isolated from Engelbreth-Holm-Swarm (EHS) tumor. A sequence in the beta 1 chain that is involved in cell attachment, chemotaxis, and binding to the laminin receptor was identified and shown to have the capacity to inhibit metastasis. [provided by RefSeq, Aug 2011]
- CLM
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~79.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0014077
Submitter: ClinGen
Inheritance Pattern: AD
Disease ID:MONDO:0019046
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014077
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014077
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0014077
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0014077
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014077
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014077
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Neurologic; Ophthalmologic
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 LAMB1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002291.3. 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 | 7 | 183 | 12 | 202 | ||
| missense | 1 | 1 | 546 | 34 | 5 | 587 |
| nonsense | 11 | 4 | 4 | 19 | ||
| start loss | 0 | |||||
| frameshift | 13 | 10 | 8 | 31 | ||
| splice donor/acceptor (+/-2bp) | 2 | 9 | 15 | 26 | ||
| Total | 27 | 24 | 580 | 217 | 17 | 865 |
Highest pathogenic variant AF is 0.00011956553
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002282.2 | 33 | MANE Select | |
| Ensembl | ENSP00000222399.6 | 33 | MANE Select | |
| Ensembl | ENSP00000377189.2 | 3 | Standard | |
| Ensembl | ENSP00000377190.1 | 18 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lamb1a | Danio rerio | Structure: fast muscle myoblast Quality: decreased length abnormal |
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
- neuronal-glial interaction involved in cerebral cortex radial glia guided migration
- extracellular matrix organization
- positive regulation of cell migration
- neuron projection development
Molecular Function
- structural molecule activity
- extracellular matrix structural constituent
- protein binding
Cellular Component
- extracellular region
- basement membrane
- laminin-1 complex
- laminin-2 complex
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000222399
- Coding exons
- 33
- Length
- 79457
- Individuals with no LoFs
- 125606
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 142
- Defined
- 125748
- p
- 0.000565
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.544 | 965 | 1.01e+3 | 0.952 | 0.0000569 | 11805 |
| Missense (PolyPhen) | 327 | 394.45 | 0.82901 | 4417 | ||
| Synonymous | 0.185 | 375 | 380 | 0.988 | 0.0000230 | 3260 |
| Loss of Function | 4.64 | 53 | 104 | 0.509 | 0.00000617 | 1163 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00070 | 0.00069 | rare |
| Ashkenazi Jewish | 0.00070 | 0.00069 | rare |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.00070 | 0.00069 | rare |
| South Asian | 0.00043 | 0.00042 | rare |
| Other | 0.00049 | 0.00049 | 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. Involved in the organization of the laminar architecture of cerebral cortex. It is probably required for the integrity of the basement membrane/glia limitans that serves as an anchor point for the endfeet of radial glial cells and as a physical barrier to migrating neurons. Radial glial cells play a central role in cerebral cortical development, where they act both as the proliferative unit of the cerebral cortex and a scaffold for neurons migrating toward the pial surface. {ECO:0000269|PubMed:23472759}.;
- Disease
- DISEASE: Lissencephaly 5 (LIS5) [MIM:615191]: An autosomal recessive brain malformation characterized by cobblestone changes in the cortex, more severe in the posterior region, and subcortical band heterotopia. Affected individuals have hydrocephalus, seizures, and severely delayed psychomotor development. {ECO:0000269|PubMed:23472759}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.501
Intolerance Scores
- LoFtool
- 0.631
- RVIS EVS
- -0.99
- RVIS percentile EVS
- 8.55
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.915
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |