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Aliases for LEMD3 Gene

Aliases for LEMD3 Gene

  • LEM Domain Containing 3 2 3 5
  • LEM Domain-Containing Protein 3 3 4
  • MAN1 3 4
  • Integral Inner Nuclear Membrane Protein 3
  • Inner Nuclear Membrane Protein Man1 3
  • LEMD3/MKX Fusion 3

External Ids for LEMD3 Gene

Previous GeneCards Identifiers for LEMD3 Gene

  • GC12P063850
  • GC12P065563
  • GC12P062615

Summaries for LEMD3 Gene

Entrez Gene Summary for LEMD3 Gene

  • This locus encodes a LEM domain-containing protein. The encoded protein functions to antagonize transforming growth factor-beta signaling at the inner nuclear membrane. Two transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis.[provided by RefSeq, Nov 2009]

GeneCards Summary for LEMD3 Gene

LEMD3 (LEM Domain Containing 3) is a Protein Coding gene. Diseases associated with LEMD3 include Buschke-Ollendorff Syndrome and Melorheostosis With Osteopoikilosis. Among its related pathways are Mitotic Prophase and DNA Damage/Telomere Stress Induced Senescence. Gene Ontology (GO) annotations related to this gene include nucleotide binding. An important paralog of this gene is LEMD2.

UniProtKB/Swiss-Prot for LEMD3 Gene

  • Can function as a specific repressor of TGF-beta, activin, and BMP signaling through its interaction with the R-SMAD proteins. Antagonizes TGF-beta-induced cell proliferation arrest.

Additional gene information for LEMD3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LEMD3 Gene

Genomics for LEMD3 Gene

GeneHancer (GH) Regulatory Elements for LEMD3 Gene

Promoters and enhancers for LEMD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12I065168 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 570.4 +0.9 893 3.9 HDGF PKNOX1 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 LEMD3 ENSG00000276853 ENSG00000250280 TBK1 MSRB3
GH12I065821 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 56 +656.8 656821 10.3 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZNF213 RPSAP52 HMGA2 GC12M065825 LEMD3 LOC100129940 TMBIM4 ENSG00000250280 ENSG00000256083 ENSG00000277945
GH12I064403 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 40 -764.8 -764786 3 CLOCK FEZF1 DMAP1 YY1 ZNF143 ZNF548 SP3 ZFP41 ZNF610 GLIS1 XPOT LEMD3 TBK1 SRGAP1 ENSG00000250280 PABPC1P4 C12orf56 LOC100420899
GH12I066168 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 34.7 +1,000.0 999963 2.7 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF263 SP3 ENSG00000228144 TMBIM4 LEMD3 LLPH-AS1 LLPH
GH12I064664 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 29.3 -494.3 -494265 21.8 HDGF PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B NEUROD1 SIN3A FEZF1 LEMD3 TBK1 RASSF3 LOC100420899 LOC105369804 MIR548C ENSG00000223294 GNS C12orf66 ENSG00000280320
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LEMD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LEMD3 gene promoter:

Genomic Locations for LEMD3 Gene

Genomic Locations for LEMD3 Gene
chr12:65,169,571-65,248,361
(GRCh38/hg38)
Size:
78,791 bases
Orientation:
Plus strand
chr12:65,563,351-65,642,141
(GRCh37/hg19)

Genomic View for LEMD3 Gene

Genes around LEMD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LEMD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LEMD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LEMD3 Gene

Proteins for LEMD3 Gene

  • Protein details for LEMD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2U8-MAN1_HUMAN
    Recommended name:
    Inner nuclear membrane protein Man1
    Protein Accession:
    Q9Y2U8
    Secondary Accessions:
    • Q9NT47
    • Q9NYA5

    Protein attributes for LEMD3 Gene

    Size:
    911 amino acids
    Molecular mass:
    99997 Da
    Quaternary structure:
    • Interacts with SMAD1, SMAD2, SMAD3 and SMAD5. Binds to both phosphorylated and unphosphorylated R-SMADS.

    Three dimensional structures from OCA and Proteopedia for LEMD3 Gene

neXtProt entry for LEMD3 Gene

Post-translational modifications for LEMD3 Gene

Other Protein References for LEMD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LEMD3 Gene

Domains & Families for LEMD3 Gene

Gene Families for LEMD3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for LEMD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LEMD3: view

No data available for UniProtKB/Swiss-Prot for LEMD3 Gene

Function for LEMD3 Gene

Molecular function for LEMD3 Gene

UniProtKB/Swiss-Prot Function:
Can function as a specific repressor of TGF-beta, activin, and BMP signaling through its interaction with the R-SMAD proteins. Antagonizes TGF-beta-induced cell proliferation arrest.

Phenotypes From GWAS Catalog for LEMD3 Gene

Gene Ontology (GO) - Molecular Function for LEMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 15231748
GO:0031490 chromatin DNA binding IBA --
genes like me logo Genes that share ontologies with LEMD3: view

Phenotypes for LEMD3 Gene

genes like me logo Genes that share phenotypes with LEMD3: view

Human Phenotype Ontology for LEMD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for LEMD3 Gene

Localization for LEMD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LEMD3 Gene

Nucleus inner membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LEMD3 gene
Compartment Confidence
nucleus 5
plasma membrane 3
extracellular 2
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LEMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005637 nuclear inner membrane IDA 15647271
GO:0005639 integral component of nuclear inner membrane IBA,TAS --
GO:0016020 membrane TAS 10671519
GO:0016021 integral component of membrane IDA 10671519
genes like me logo Genes that share ontologies with LEMD3: view

Pathways & Interactions for LEMD3 Gene

genes like me logo Genes that share pathways with LEMD3: view

Gene Ontology (GO) - Biological Process for LEMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IEA --
GO:0006997 nucleus organization IEA --
GO:0006998 nuclear envelope organization IBA --
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway IDA 15647271
GO:0030514 negative regulation of BMP signaling pathway IDA 15647271
genes like me logo Genes that share ontologies with LEMD3: view

No data available for SIGNOR curated interactions for LEMD3 Gene

Drugs & Compounds for LEMD3 Gene

No Compound Related Data Available

Transcripts for LEMD3 Gene

Unigene Clusters for LEMD3 Gene

LEM domain containing 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for LEMD3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b
SP1: -
SP2:

Relevant External Links for LEMD3 Gene

GeneLoc Exon Structure for
LEMD3
ECgene alternative splicing isoforms for
LEMD3

Expression for LEMD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LEMD3 Gene

Protein differential expression in normal tissues from HIPED for LEMD3 Gene

This gene is overexpressed in Testis (15.5), Peripheral blood mononuclear cells (11.0), and Pancreas (9.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LEMD3 Gene



Protein tissue co-expression partners for LEMD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LEMD3 Gene:

LEMD3

SOURCE GeneReport for Unigene cluster for LEMD3 Gene:

Hs.744150

mRNA Expression by UniProt/SwissProt for LEMD3 Gene:

Q9Y2U8-MAN1_HUMAN
Tissue specificity: Heart, brain, placenta, lung, liver and skeletal muscle.

Evidence on tissue expression from TISSUES for LEMD3 Gene

  • Liver(4.1)
  • Skin(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LEMD3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • sinus
  • skull
  • tooth
  • vocal cord
Thorax:
  • aorta
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • lymph node
  • lymph vessel
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with LEMD3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for LEMD3 Gene

Orthologs for LEMD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LEMD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LEMD3 33 34
  • 99.74 (n)
cow
(Bos Taurus)
Mammalia LEMD3 33 34
  • 92.85 (n)
dog
(Canis familiaris)
Mammalia LEMD3 33 34
  • 88.53 (n)
rat
(Rattus norvegicus)
Mammalia Lemd3 33
  • 86.5 (n)
mouse
(Mus musculus)
Mammalia Lemd3 33 16 34
  • 86.23 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LEMD3 34
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves LEMD3 33 34
  • 80.45 (n)
lizard
(Anolis carolinensis)
Reptilia LEMD3 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lemd3 33
  • 66.82 (n)
African clawed frog
(Xenopus laevis)
Amphibia XMAN1 33
zebrafish
(Danio rerio)
Actinopterygii lemd3 33 34
  • 64.46 (n)
worm
(Caenorhabditis elegans)
Secernentea lem-2 34
  • 20 (a)
OneToOne
Species where no ortholog for LEMD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LEMD3 Gene

ENSEMBL:
Gene Tree for LEMD3 (if available)
TreeFam:
Gene Tree for LEMD3 (if available)

Paralogs for LEMD3 Gene

Paralogs for LEMD3 Gene

genes like me logo Genes that share paralogs with LEMD3: view

Variants for LEMD3 Gene

Sequence variations from dbSNP and Humsavar for LEMD3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs11175678 likely-benign, Dermatofibrosis lenticularis disseminata 65,210,914(+) C/T intron_variant
rs11175698 likely-benign, Dermatofibrosis lenticularis disseminata 65,247,481(+) G/A 3_prime_UTR_variant
rs11175699 likely-benign, Dermatofibrosis lenticularis disseminata 65,248,276(+) C/T 3_prime_UTR_variant
rs113095916 uncertain-significance, Dermatofibrosis lenticularis disseminata 65,247,806(+) C/T 3_prime_UTR_variant
rs117013092 likely-benign, Dermatofibrosis lenticularis disseminata 65,247,240(+) G/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for LEMD3 Gene

Variant ID Type Subtype PubMed ID
nsv952197 CNV duplication 24416366
nsv832445 CNV gain 17160897
nsv522671 CNV loss 19592680
nsv1144631 CNV deletion 24896259

Variation tolerance for LEMD3 Gene

Residual Variation Intolerance Score: 22.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.85; 34.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LEMD3 Gene

Human Gene Mutation Database (HGMD)
LEMD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LEMD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LEMD3 Gene

Disorders for LEMD3 Gene

MalaCards: The human disease database

(12) MalaCards diseases for LEMD3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
buschke-ollendorff syndrome
  • bos
melorheostosis with osteopoikilosis
  • mixed sclerosing bone dystrophy
osteopoikilosis
  • osteopathia condensans disseminata
melorheostosis
elastoma
  • juvenile elastoma without osteopoikilosis
- elite association - COSMIC cancer census association via MalaCards
Search LEMD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

MAN1_HUMAN
  • Buschke-Ollendorff syndrome (BOS) [MIM:166700]: A disease characterized by osteopoikilosis and disseminated connective-tissue nevi. Osteopoikilosis is a skeletal dysplasia characterized by a symmetric but unequal distribution of multiple hyperostotic areas in different parts of the skeleton. Elastic-type nevi (juvenile elastoma) and collagen-type nevi (dermatofibrosis lenticularis disseminata) have been described in BOS. Skin or bony lesions can be absent in some family members, whereas other relatives may have both. {ECO:0000269 PubMed:15489854}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Melorheostosis (MEL) [MIM:155950]: Rare mesenchymal dysplasia and one of the sclerosing bone disorders. It is caused by a developmental error, with a sclerotomal distribution, frequently involving one limb. It may be asymptomatic, but pain, stiffness with limitation of motion, leg-length discrepancy and limb deformity may occur. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for LEMD3

genes like me logo Genes that share disorders with LEMD3: view

No data available for Genatlas for LEMD3 Gene

Publications for LEMD3 Gene

  1. MAN1, an inner nuclear membrane protein that shares the LEM domain with lamina-associated polypeptide 2 and emerin. (PMID: 10671519) Lin F … Worman HJ (The Journal of biological chemistry 2000) 2 3 4 22 58
  2. The carboxyl-terminal nucleoplasmic region of MAN1 exhibits a DNA binding winged helix domain. (PMID: 16648637) Caputo S … Zinn-Justin S (The Journal of biological chemistry 2006) 3 4 22 58
  3. The integral inner nuclear membrane protein MAN1 physically interacts with the R-Smad proteins to repress signaling by the transforming growth factor-{beta} superfamily of cytokines. (PMID: 15647271) Pan D … Luo K (The Journal of biological chemistry 2005) 3 4 22 58
  4. MAN1, an integral protein of the inner nuclear membrane, binds Smad2 and Smad3 and antagonizes transforming growth factor-beta signaling. (PMID: 15601644) Lin F … Worman HJ (Human molecular genetics 2005) 3 4 22 58
  5. Loss-of-function mutations in LEMD3 result in osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis. (PMID: 15489854) Hellemans J … Mortier GR (Nature genetics 2004) 2 3 4 58

Products for LEMD3 Gene

  • Addgene plasmids for LEMD3

Sources for LEMD3 Gene

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