LAMC1

laminin subunit gamma 1, the group of Laminin subunits

Basic information

Region (hg38): 1:183023419-183145592

Previous symbols: [ "LAMB2" ]

Links

ENSG00000135862 ∙ NCBI:3915 ∙ OMIM:150290 ∙ HGNC:6492 ∙ Uniprot:P11047 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LAMC1 gene.

• not provided (116 variants)
• Inborn genetic diseases (60 variants)
• LAMC1-related autism spectrum disorder (1 variants)
• LAMC1-associated syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAMC1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	12	16
missense			62	3	6	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1	1	2
non coding					88	88
Total	0	0	63	7	106

Variants in LAMC1

This is a list of pathogenic ClinVar variants found in the LAMC1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-183023599-A-G			Benign (May 13, 2021)
1-183023804-G-T		not specified	Uncertain significance (Apr 11, 2023)
1-183023811-G-C		not specified	Uncertain significance (Jun 10, 2022)
1-183023816-C-G		not specified	Uncertain significance (Jun 18, 2021)
1-183023855-C-G		not specified	Uncertain significance (Apr 07, 2023)
1-183023883-A-G		not specified	Uncertain significance (Feb 17, 2022)
1-183023890-C-T			Benign (May 04, 2021)
1-183023895-A-G		not specified	Uncertain significance (Dec 22, 2023)
1-183023897-G-C		not specified	Uncertain significance (Dec 07, 2021)
1-183023906-G-C		not specified	Uncertain significance (Oct 30, 2023)
1-183023936-G-C		not specified	Uncertain significance (Feb 17, 2024)
1-183023948-G-A		not specified	Uncertain significance (Jan 31, 2023)
1-183024024-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-183024092-G-C		not specified	Uncertain significance (Sep 29, 2023)
1-183024108-G-A		not specified	Likely benign (Apr 07, 2023)
1-183024223-G-T			Benign (May 13, 2021)
1-183024246-C-G			Benign (May 13, 2021)
1-183024303-T-C			Benign (May 12, 2021)
1-183103376-G-A		not specified	Uncertain significance (Oct 26, 2022)
1-183103416-C-T		LAMC1-related disorder	Likely benign (Dec 05, 2019)
1-183103462-A-G		not specified	Uncertain significance (Dec 11, 2023)
1-183103481-G-A		not specified	Uncertain significance (Apr 22, 2022)
1-183103493-G-A		not specified	Uncertain significance (Aug 08, 2023)
1-183103530-T-G		not specified	Uncertain significance (Oct 25, 2022)
1-183103566-C-T			Benign (May 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAMC1	protein_coding	protein_coding	ENST00000258341	28	122133

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.16e-7	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	786	921	0.853	0.0000513	10636
Missense in Polyphen		278	392.14	0.70893		4330
Synonymous	-0.944	370	348	1.06	0.0000200	3024
Loss of Function	7.33	9	79.5	0.113	0.00000428	936

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000959	0.0000924
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000141	0.000131
Other	0.00	0.00

dbNSFP

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.
• Pathway: 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);Amoebiasis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Alpha 6 Beta 4 signaling pathway;Human Complement System;Endoderm Differentiation;miRNA targets in ECM and membrane receptors;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Inflammatory Response Pathway;Developmental Biology;Signal Transduction;prion pathway;Post-translational protein phosphorylation;Alpha6Beta4Integrin;Laminin interactions;Post-translational protein modification;Metabolism of proteins;Extracellular matrix organization;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Beta3 integrin cell surface interactions;agrin in postsynaptic differentiation;Degradation of the extracellular matrix;a6b1 and a6b4 Integrin signaling;L1CAM interactions;Non-integrin membrane-ECM interactions;Axon guidance;ECM proteoglycans;MET activates PTK2 signaling;MET promotes cell motility;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Beta1 integrin cell surface interactions;Alpha6 beta4 integrin-ligand interactions;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.388

Intolerance Scores

• loftool: 0.326
• rvis_EVS: -2.49
• rvis_percentile_EVS: 0.94

Haploinsufficiency Scores

• pHI: 0.172
• hipred: Y
• hipred_score: 0.685
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.603

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lamc1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; respiratory system phenotype; embryo phenotype; renal/urinary system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: lamc1
• Affected structure: fast muscle myoblast
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: cell adhesion;endoderm development;cell migration;extracellular matrix disassembly;extracellular matrix organization;hemidesmosome assembly;substrate adhesion-dependent cell spreading;post-translational protein modification;cellular protein metabolic process;positive regulation of epithelial cell proliferation;protein-containing complex assembly
• Cellular component: extracellular region;basement membrane;laminin-1 complex;extracellular space;endoplasmic reticulum lumen;laminin-10 complex;laminin-11 complex;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: extracellular matrix structural constituent