Tbio LMNA Prelamin-A/C

Protein Summary

Description

Lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane, which is thought to provide a framework for the nuclear envelope and may also interact with chromatin. Lamin A and C are present in equal amounts in the lamina of mammals. Plays an important role in nuclear assembly, chromatin organization, nuclear membrane and telomere dynamics. Required for normal development of peripheral nervous system and skeletal muscle and for muscle satellite cell proliferation (PubMed:10080180, PubMed:22431096, PubMed:10814726, PubMed:11799477, PubMed:18551513). Required for osteoblastogenesis and bone formation (PubMed:12075506, PubMed:15317753, PubMed:18611980). Also prevents fat infiltration of muscle and bone marrow, helping to maintain the volume and strength of skeletal muscle and bone (PubMed:10587585). Required for cardiac homeostasis (PubMed:10580070, PubMed:12927431, PubMed:18611980, PubMed:23666920). Prelamin-A/C can accelerate smooth muscle cell senescence. It acts to disrupt mitosis and induce DNA damage in vascular smooth muscle cells (VSMCs), leading to mitotic failure, genomic instability, and premature senescence. The nuclear lamina consists of a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly conserved in evolution. During mitosis, the lamina matrix is reversibly disassembled as the lamin proteins are phosphorylated. Lamin proteins are thought to be involved in nuclear stability, chromatin structure and gene expression. Vertebrate lamins consist of two types, A and B. Alternative splicing results in multiple transcript variants. Mutations in this gene lead to several diseases: Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, Charcot-Marie-Tooth disease, and Hutchinson-Gilford progeria syndrome. [provided by RefSeq, Apr 2012]

Uniprot Accession IDs

• P02545
• B4DI32
• D3DVB0
• D6RAQ3
• E7EUI9
• P02546
• Q5I6Y4
• Q5I6Y6
• Q5TCJ2
• Q5TCJ3
• Q6UYC3
• Q969I8
• Q96JA2

Gene Name

• LMNA

Ensembl ID

• ENST00000347559
• ENSP00000292304
• ENSG00000160789
• ENST00000368299
• ENSP00000357282
• ENST00000368300
• ENSP00000357283
• ENST00000368301
• ENSP00000357284
• ENST00000448611
• ENSP00000395597
• ENST00000473598
• ENSP00000421821

Symbol

• LMN1
• FPL
• IDC
• LFP
• CDDC
• EMD2
• FPLD
• HGPS
• LDP1
• LMN1
• LMNC
• MADA
• PRO1
• CDCD1
• CMD1A
• FPLD2
• LMNL1
• CMT2B1
• LGMD1B

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
hub protein	1
interacting protein	1
ligand (protein) perturbation	1
transcription factor perturbation	1
biological process	0.97

Related Tools

Target Illumination GWAS Analytics (TIGA)

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 2198.86   (req: < 5)

Gene RIFs: 495   (req: <= 3)

Antibodies: 1465   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 2198.86   (req: >= 5)

Gene RIFs: 495   (req: > 3)

Antibodies: 1465   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 24

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

GWAS Traits (5)

• Explore on Target Illumination GWAS Analytics (TIGA)

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GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
appendicular lean mass	EFO_0004980	3	1	3		89.1
myeloid white cell count	EFO_0007988	1	1	1		63.3
neutrophil count	EFO_0004833	2	2	2		63
leukocyte count	EFO_0004308	1	1	1		2.7
platelet count	EFO_0004309	1	1	1		0.3

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
appendicular lean mass	EFO_0004980	3		89.1
myeloid white cell count	EFO_0007988	1		63.3
neutrophil count	EFO_0004833	2		63
leukocyte count	EFO_0004308	1		2.7
platelet count	EFO_0004309	1		0.3

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Orthologs (13)

1 – 5 of 13

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	lamin A/C	VGNC:11515	457385
Macaque	lamin A/C		719414
Mouse	lamin A	MGI:96794	16905
Rat	lamin A/C	RGD:620456	60374
Dog	lamin A/C	VGNC:42717	480124

Species	Name	OMA	EggNOG	Inparanoid
Chimp	lamin A/C
Macaque	lamin A/C
Mouse	lamin A
Rat	lamin A/C
Dog	lamin A/C

Protein Data Bank (10)

1 – 5 of 10

PDB Structure Id	Ligand	Method	Resolution (Å)	M.W. (kDa)	Pub Year	Title

PDB Structure Id	M.W.	Resolution	Pub Year

Pathways (46)

Reactome (28)

KEGG (4)

PathwayCommons (2)

WikiPathways (12)

Apoptosis (R-HSA-109581)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Apoptosis	177 targets	R-HSA-109581
Reactome	Apoptotic cleavage of cellular proteins	38 targets	R-HSA-111465
Reactome	Apoptotic execution phase	52 targets	R-HSA-75153
Reactome	Breakdown of the nuclear lamina	3 targets	R-HSA-352238
Reactome	Cell Cycle	597 targets	R-HSA-1640170

Name	Explore in Pharos	Explore in Source
Apoptosis	177 targets	R-HSA-109581
Apoptotic cleavage of cellular proteins	38 targets	R-HSA-111465
Apoptotic execution phase	52 targets	R-HSA-75153
Breakdown of the nuclear lamina	3 targets	R-HSA-352238
Cell Cycle	597 targets	R-HSA-1640170

Gene Ontology Terms (34)

Functions (2)

Components (10)

Processes (22)

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10

1 – 2 of 2

GO Term	Evidence	Assigned by
identical protein binding	Inferred from Physical Interaction (IPI)	IntAct
structural molecule activity	Traceable Author Statement (TAS)	UniProtKB

Protein-Protein Interactions (316)

Explore Interacting Targets

1 – 10 of 316

• See Interactions on String-DB

FGFR1OP2

Tbio

Novelty: 0.1082136

p_int: 0.97285252

p_ni: 0.027147481

Data Source: BioPlex

SYCE1

Tbio

Novelty: 0.05038876

p_int: 0.967521733

p_ni: 0.032478267

Data Source: BioPlex

KPNA6

Tbio

Novelty: 0.03516499

p_int: 0.848269915

p_ni: 0.151730085

Score: 0.421

Data Source: BioPlex,STRINGDB

SUN2

Tbio

Novelty: 0.01387591

p_int: 0.75000428

p_ni: 0.24999572

Score: 0.972

Data Source: BioPlex,STRINGDB

CDC5L

Tbio

Family: TF

Novelty: 0.00663599

Score: 0.98

Data Source: STRINGDB

CASP6

Tchem

Family: Enzyme

Novelty: 0.00234346

Score: 0.97

Data Source: Reactome,STRINGDB

MAPK3

Tchem

Family: Kinase

Novelty: 0.00012969

Score: 0.964

Data Source: STRINGDB

MAPK1

Tchem

Family: Kinase

Novelty: 0.00061058

Score: 0.961

Data Source: STRINGDB

LMNB2

Tbio

Novelty: 0.0019221

Score: 0.957

Data Source: STRINGDB

EMD

Tbio

Novelty: 0.00135202

Score: 0.952

Data Source: Reactome,STRINGDB

Publication Statistics

PubMed Score  2198.86

PubMed score by year

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PubTator Score  1568.26

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

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UniProt Keyword Find Similar Targets

3D-structure
Acetylation
Alternative splicing
Cardiomyopathy
Charcot-Marie-Tooth disease
Coiled coil
Complete proteome
Congenital muscular dystrophy
Direct protein sequencing
Disease mutation

GWAS Trait Find Similar Targets

appendicular lean mass
leukocyte count
myeloid white cell count
neutrophil count
platelet count

MGI Phenotype Find Similar Targets

adipose tissue phenotype
behavior/neurological phenotype
cardiovascular system phenotype
cellular phenotype
craniofacial phenotype
digestive/alimentary phenotype
endocrine/exocrine gland phenotype
growth/size/body region phenotype
hearing/vestibular/ear phenotype
hematopoietic system phenotype