LAMB1

protein-coding

laminin 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]

Previous symbols:
  • CLM

MANE transcript

NM_002291.3

Inheritance

AD, AR

ClinVar variants

P:51U:580B:234

Top phenotype

Lissencephaly 5

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr7:107,923,799-108,003,213

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~79.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cobblestone lissencephaly without muscular or ocular involvementMODERATE

Inheritance Pattern: Unknown

Disease ID:MONDO:0014077

Submitter: ClinGen

leukodystrophySTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0019046

Submitter: PanelApp Australia

cobblestone lissencephaly without muscular or ocular involvementSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014077

Submitter: PanelApp Australia

cobblestone lissencephaly without muscular or ocular involvementSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014077

Submitter: Genomics England PanelApp

cobblestone lissencephaly without muscular or ocular involvementSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014077

Submitter: G2P

cobblestone lissencephaly without muscular or ocular involvementSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014077

Submitter: Orphanet

cobblestone lissencephaly without muscular or ocular involvementMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0014077

Submitter: Ambry Genetics

cobblestone lissencephaly without muscular or ocular involvementSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014077

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Lissencephaly 5AR

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

Refs: 23472759; 25925986Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LAMB1 variants in ClinVar

12 Conditions Cataloged
not providedTotal: 810
Inborn genetic diseasesTotal: 260
not specifiedTotal: 115
LAMB1-related disorderTotal: 78
Cobblestone lissencephaly without muscular or ocular involvementTotal: 62
Leukoencephalopathy without lacunae, adult-onsetTotal: 5
Multiple sclerosisTotal: 2
Classic lissencephalyTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
183
clinvar
12
clinvar
202
missense
1
clinvar
1
clinvar
546
clinvar
34
clinvar
5
clinvar
587
nonsense
11
clinvar
4
clinvar
4
clinvar
19
start loss
0
frameshift
13
clinvar
10
clinvar
8
clinvar
31
splice donor/acceptor (+/-2bp)
2
clinvar
9
clinvar
15
clinvar
26
Total272458021717865

Highest pathogenic variant AF is 0.00011956553

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002291.3RefSeqNP_002282.233MANE Select
ENST00000222399.11EnsemblENSP00000222399.633MANE Select
ENST00000393559.2EnsemblENSP00000377189.23Standard
ENST00000393560.5EnsemblENSP00000377190.118Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
lamb1aDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5449651.01e+30.9520.000056911805
Missense (PolyPhen)327394.450.829014417
Synonymous0.1853753800.9880.00002303260
Loss of Function4.64531040.5090.000006171163

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000180.00018rare
Latino/Admixed American0.000700.00069rare
Ashkenazi Jewish0.000700.00069rare
East Asian0.000380.00038rare
Finnish0.000280.00028rare
European (Non-Finnish)0.000700.00069rare
South Asian0.000430.00042rare
Other0.000490.00049rare

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. 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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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