The protein encoded by this gene is a member of the lipin family of proteins, and all family members share strong homology in their C-terminal region. This protein is thought to form hetero-oligomers with other lipin family members, while one family member, lipin 1, can also form homo-oligomers. This protein contains conserved motifs for phosphatidate phosphatase 1 (PAP1) activ... See more...

Aliases for LPIN3 Gene

Aliases for LPIN3 Gene

  • Lipin 3 2 3 5
  • Phosphatidate Phosphatase LPIN3 3 4
  • LIPN3L 3 4
  • SMP2 2 3
  • Lipin 3-Like 2
  • Lipin-3-Like 4
  • DJ620E11.2 3
  • EC 3.1.3.4 4
  • Lipin-3 4
  • LPIN3 5

External Ids for LPIN3 Gene

Previous HGNC Symbols for LPIN3 Gene

  • LIPN3L

Previous GeneCards Identifiers for LPIN3 Gene

  • GC20U990061
  • GC20M039662
  • GC20P040612
  • GC20P040659
  • GC20P039402
  • GC20P039969
  • GC20P036707

Summaries for LPIN3 Gene

Entrez Gene Summary for LPIN3 Gene

  • The protein encoded by this gene is a member of the lipin family of proteins, and all family members share strong homology in their C-terminal region. This protein is thought to form hetero-oligomers with other lipin family members, while one family member, lipin 1, can also form homo-oligomers. This protein contains conserved motifs for phosphatidate phosphatase 1 (PAP1) activity as well as a domain that interacts with a transcriptional co-activator. Lipin complexes act in the cytoplasm to catalyze the dephosphorylation of phosphatidic acid to produce diacylglycerol, which is the precursor of both triglycerides and phospholipids. Lipin complexes are also thought to regulate gene expression as transcriptional co-activators in the nucleus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014]

GeneCards Summary for LPIN3 Gene

LPIN3 (Lipin 3) is a Protein Coding gene. Diseases associated with LPIN3 include Nemaline Myopathy 1. Among its related pathways are Mitotic Prophase and Glycerolipid metabolism. Gene Ontology (GO) annotations related to this gene include transcription coactivator activity and phosphatidate phosphatase activity. An important paralog of this gene is LPIN2.

UniProtKB/Swiss-Prot Summary for LPIN3 Gene

  • Regulates fatty acid metabolism. Magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis (By similarity).

Additional gene information for LPIN3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LPIN3 Gene

Genomics for LPIN3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LPIN3 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
GH20J041339 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 619.6 +0.8 788 4.3 HNRNPL CREB1 GATAD2A CTCF PRDM10 TFE3 IKZF1 NFKBIZ KDM1A RCOR2 LPIN3 TOP1 PLCG1 NONHSAG031795.2 EMILIN3
GH20J041145 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 26.7 -187.7 -187688 15.3 SP1 GATAD2A ATF7 YBX1 ZNF629 LEF1 IKZF1 NFKBIZ RCOR2 JUND LPIN3 EMILIN3 ZHX3 PLCG1 CHD6 MIR6871 PLCG1-AS1
GH20J041027 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 17.2 -310.6 -310554 5.6 CEBPG SP1 HNRNPL CREB1 REST ZNF629 TFE3 LEF1 IKZF1 NFKBIZ TOP1 NONHSAG031788.2 lnc-ZHX3-7 LPIN3 lnc-PLCG1-2 PLCG1
GH20J041136 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 15.2 -200.9 -200853 7.5 SP1 CREB1 GATAD2A PRDM10 TFE3 NFKBIZ ZNF692 RCOR2 POLR2A ZNF7 PLCG1 PLCG1-AS1 TOP1 CHD6 LPIN3 MIR6871 ZHX3
GH20J041231 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 24 -107.7 -107652 4.3 CEBPG CREB1 GATAD2A TFE3 RFX1 NFKBIZ CTCF RCOR2 TARDBP RXRB LPIN3 ZHX3 piR-61101-412 FJ601684-273 lnc-ZHX3-4 PLCG1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LPIN3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LPIN3

Top Transcription factor binding sites by QIAGEN in the LPIN3 gene promoter:
  • AP-4
  • Bach2
  • Elk-1
  • FOXL1
  • NF-1
  • NF-1/L
  • Olf-1
  • SRF
  • SRF (504 AA)
  • STAT3

Genomic Locations for LPIN3 Gene

Genomic Locations for LPIN3 Gene
chr20:41,340,779-41,360,583
(GRCh38/hg38)
Size:
19,805 bases
Orientation:
Plus strand
chr20:39,969,560-39,989,222
(GRCh37/hg19)
Size:
19,663 bases
Orientation:
Plus strand

Genomic View for LPIN3 Gene

Genes around LPIN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LPIN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LPIN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LPIN3 Gene

Proteins for LPIN3 Gene

  • Protein details for LPIN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BQK8-LPIN3_HUMAN
    Recommended name:
    Phosphatidate phosphatase LPIN3
    Protein Accession:
    Q9BQK8
    Secondary Accessions:
    • B2RTT5
    • Q5TDB9
    • Q9NPY8
    • Q9UJE5

    Protein attributes for LPIN3 Gene

    Size:
    851 amino acids
    Molecular mass:
    93614 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LPIN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LPIN3 Gene

Post-translational modifications for LPIN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LPIN3 Gene

Domains & Families for LPIN3 Gene

Gene Families for LPIN3 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for LPIN3 Gene

InterPro:
Blocks:
  • Lipin, N-terminal conserved region
ProtoNet:

Suggested Antigen Peptide Sequences for LPIN3 Gene

GenScript: Design optimal peptide antigens:
  • Lipin-3-like (LPIN3_HUMAN)
  • Lipin 3 (Q5JYP6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BQK8

UniProtKB/Swiss-Prot:

LPIN3_HUMAN :
  • Contains 1 Asp-Xaa-Asp-Xaa-Thr (DXDXT) motif, a catalytic motif known to be essential for phosphatidate phosphatase activity.
  • Belongs to the lipin family.
Domain:
  • Contains 1 Asp-Xaa-Asp-Xaa-Thr (DXDXT) motif, a catalytic motif known to be essential for phosphatidate phosphatase activity.
  • Contains one Leu-Xaa-Xaa-Ile-Leu (LXXIL) motif, a motif known to be a transcriptional binding motif.
Family:
  • Belongs to the lipin family.
genes like me logo Genes that share domains with LPIN3: view

Function for LPIN3 Gene

Molecular function for LPIN3 Gene

UniProtKB/Swiss-Prot Function:
Regulates fatty acid metabolism. Magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 1,2-diacyl-sn-glycero-3-phosphate + H2O = a 1,2-diacyl-sn-glycerol + phosphate; Xref=Rhea:RHEA:27429, ChEBI:CHEBI:15377, ChEBI:CHEBI:17815, ChEBI:CHEBI:43474, ChEBI:CHEBI:58608; EC=3.1.3.4;.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by N-ethylmaleimide.

Enzyme Numbers (IUBMB) for LPIN3 Gene

Phenotypes From GWAS Catalog for LPIN3 Gene

Gene Ontology (GO) - Molecular Function for LPIN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IBA 21873635
GO:0008195 phosphatidate phosphatase activity IEA,IBA 21873635
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with LPIN3: view
genes like me logo Genes that share phenotypes with LPIN3: view

Animal Models for LPIN3 Gene

MGI Knock Outs for LPIN3:
  • Lpin3 Lpin3<tm1b(KOMP)Wtsi>
  • Lpin3 Lpin3<tm1Reue>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LPIN3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LPIN3 Gene

Localization for LPIN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LPIN3 Gene

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 LPIN3 gene
Compartment Confidence
nucleus 4
endoplasmic reticulum 4
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LPIN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005789 endoplasmic reticulum membrane TAS --
genes like me logo Genes that share ontologies with LPIN3: view

Pathways & Interactions for LPIN3 Gene

genes like me logo Genes that share pathways with LPIN3: view

Gene Ontology (GO) - Biological Process for LPIN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006631 fatty acid metabolic process IEA --
GO:0006646 phosphatidylethanolamine biosynthetic process TAS --
GO:0006656 phosphatidylcholine biosynthetic process TAS --
GO:0009062 fatty acid catabolic process IBA 21873635
genes like me logo Genes that share ontologies with LPIN3: view

No data available for SIGNOR curated interactions for LPIN3 Gene

Drugs & Compounds for LPIN3 Gene

(2) Drugs for LPIN3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
genes like me logo Genes that share compounds with LPIN3: view

Transcripts for LPIN3 Gene

mRNA/cDNA for LPIN3 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LPIN3

Alternative Splicing Database (ASD) splice patterns (SP) for LPIN3 Gene

No ASD Table

Relevant External Links for LPIN3 Gene

GeneLoc Exon Structure for
LPIN3

Expression for LPIN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LPIN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LPIN3 Gene

This gene is overexpressed in Serum (51.0) and Bone (17.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LPIN3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LPIN3

SOURCE GeneReport for Unigene cluster for LPIN3 Gene:

Hs.25897

mRNA Expression by UniProt/SwissProt for LPIN3 Gene:

Q9BQK8-LPIN3_HUMAN
Tissue specificity: Significant expression in intestine and other regions of the gastrointestinal tract.

Evidence on tissue expression from TISSUES for LPIN3 Gene

  • Liver(2.5)
  • Skin(2.4)
  • Muscle(2.3)
  • Kidney(2)
  • Heart(2)
genes like me logo Genes that share expression patterns with LPIN3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for LPIN3 Gene

Orthologs for LPIN3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LPIN3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LPIN3 30 31
  • 99.02 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LPIN3 30 31
  • 86.21 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LPIN3 30 31
  • 85.42 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lpin3 30
  • 83.08 (n)
Mouse
(Mus musculus)
Mammalia Lpin3 30 17 31
  • 82.6 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LPIN3 31
  • 58 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LPIN3 31
  • 57 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LPIN3 31
  • 52 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii zgc:123305 31
  • 44 (a)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta Lpin 31
  • 30 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea lpin-1 31
  • 31 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PAH1 31
  • 26 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 55 (a)
ManyToMany
-- 31
  • 27 (a)
ManyToMany
Species where no ortholog for LPIN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • 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)
  • 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)
  • 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 Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for LPIN3 Gene

ENSEMBL:
Gene Tree for LPIN3 (if available)
TreeFam:
Gene Tree for LPIN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LPIN3: view image

Paralogs for LPIN3 Gene

Paralogs for LPIN3 Gene

(3) SIMAP similar genes for LPIN3 Gene using alignment to 2 proteins:

  • LPIN3_HUMAN
  • H0Y5E1_HUMAN
genes like me logo Genes that share paralogs with LPIN3: view

Variants for LPIN3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LPIN3 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
778623 Likely Benign: not provided 41,354,732(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
781901 Benign: not provided 41,345,862(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs12625565 - p.Gln679His

Additional dbSNP identifiers (rs#s) for LPIN3 Gene

Structural Variations from Database of Genomic Variants (DGV) for LPIN3 Gene

Variant ID Type Subtype PubMed ID
dgv245n21 CNV loss 19592680
esv2722419 CNV deletion 23290073
esv2722420 CNV deletion 23290073
nsv1064246 CNV loss 25217958
nsv3381 CNV deletion 18451855
nsv833984 CNV loss 17160897
nsv954039 CNV deletion 24416366

Variation tolerance for LPIN3 Gene

Residual Variation Intolerance Score: 97.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.27; 94.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LPIN3 Gene

Human Gene Mutation Database (HGMD)
LPIN3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LPIN3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LPIN3 Gene

Disorders for LPIN3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LPIN3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
nemaline myopathy 1
  • nem1
- elite association - COSMIC cancer census association via MalaCards
Search LPIN3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with LPIN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LPIN3 Gene

Publications for LPIN3 Gene

  1. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4
  2. Lipodystrophy in the fld mouse results from mutation of a new gene encoding a nuclear protein, lipin. (PMID: 11138012) Péterfy M … Reue K (Nature genetics 2001) 2 3
  3. The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. (PMID: 29845934) Faust TB … Frankel AD (eLife 2018) 3
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  5. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3

Products for LPIN3 Gene

Sources for LPIN3 Gene