LAMC1

protein-coding

laminin subunit gamma 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, 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 1. The gamma 1 chain, formerly thought to be a beta chain, contains structural domains similar to beta chains, however, lacks the short alpha region separating domains I and II. The structural organization of this gene also suggested that it had diverged considerably from the beta chain genes. Embryos of transgenic mice in which both alleles of the gamma 1 chain gene were inactivated by homologous recombination, lacked basement membranes, indicating that laminin, gamma 1 chain is necessary for laminin heterotrimer assembly. It has been inferred by analogy with the strikingly similar 3' UTR sequence in mouse laminin gamma 1 cDNA, that multiple polyadenylation sites are utilized in human to generate the 2 different sized mRNAs (5.5 and 7.5 kb) seen on Northern analysis. [provided by RefSeq, Aug 2011]

Previous symbols:
  • LAMB2

MANE transcript

NM_002293.4

Inheritance

—

ClinVar variants

U:218B:42

Top phenotype

LAMC1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr1:183,023,420-183,145,592

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~122.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LAMC1 variants in ClinVar

7 Conditions Cataloged
not specifiedTotal: 202
not providedTotal: 35
LAMC1-related disorderTotal: 28
Wolff-Parkinson-White patternTotal: 1
LAMC1-associated syndromeTotal: 1
Variant of unknown significanceTotal: 1
LAMC1-related autism spectrum disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002293.4. 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
5
clinvar
20
clinvar
8
clinvar
33
missense
207
clinvar
11
clinvar
3
clinvar
221
nonsense
2
clinvar
2
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total002183111260
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002293.4RefSeqNP_002284.328MANE Select
ENST00000258341.5EnsemblENSP00000258341.328MANE Select
ENST00000484114.2EnsemblENSP00000473583.11Standard
ENST00000920737.1EnsemblENSP00000590796.129Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
lamc1Danio rerio

Structure: fast muscle myoblast

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Prion diseases - Homo sapiens (human)
  • 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)

Biological Process

  • cell adhesion
  • endoderm development
  • cell migration
  • extracellular matrix disassembly
  • extracellular matrix organization

Molecular Function

  • extracellular matrix structural constituent

Cellular Component

  • extracellular region
  • basement membrane
  • laminin-1 complex
  • extracellular space
  • endoplasmic reticulum lumen

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000258341
Coding exons
28
Length
122133
Individuals with no LoFs
125726
Homozygous LoFs
0
Heterozygous LoFs
21
Defined
125747
p
0.0000835
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.587869210.8530.000051310636
Missense (PolyPhen)278392.140.708934330
Synonymous-0.9443703481.060.00002003024
Loss of Function7.33979.50.1130.00000428936

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish0.0000960.000092rare
European (Non-Finnish)0.0000880.000088rare
South Asian0.000140.00013rare
Other00.0absent

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.;

Recessive Scores

pRec
0.388

Intolerance Scores

LoFtool
0.326
RVIS EVS
-2.49
RVIS percentile EVS
0.94

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.603

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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