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    LPIN3 lipin 3 [ Homo sapiens (human) ]

    Gene ID: 64900, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LPIN3provided by HGNC
    Official Full Name
    lipin 3provided by HGNC
    Primary source
    HGNC:HGNC:14451
    See related
    Ensembl:ENSG00000132793 MIM:605520; AllianceGenome:HGNC:14451
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SMP2; LIPN3L; dJ620E11.2
    Summary
    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]
    Expression
    Ubiquitous expression in duodenum (RPKM 19.3), skin (RPKM 16.1) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LPIN3 in Genome Data Viewer
    Location:
    20q12
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (41340821..41360582)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (43072623..43092380)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (39969461..39989222)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene zinc fingers and homeoboxes 3 Neighboring gene RNA, 7SL, cytoplasmic 615, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17893 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:39962705-39962931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12919 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:39975675-39976198 Neighboring gene acireductone dioxygenase 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:39986695-39987302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:39987303-39987910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:39994195-39994696 Neighboring gene uncharacterized LOC124904985 Neighboring gene elastin microfibril interfacer 3 Neighboring gene zinc finger MYM-type containing 1 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of a novel cell-penetrating peptide from human phosphatidate phosphatase LPIN3. Lim S, et al. Mol Cells, 2012 Dec. PMID 23263658, Free PMC Article
    2. Lipin proteins form homo- and hetero-oligomers. Liu GH, et al. Biochem J, 2010 Nov 15. PMID 20735359, Free PMC Article
    3. Identification of lipidomic profiles associated with drug-resistant prostate cancer cells. Ingram LM, et al. Lipids Health Dis, 2021 Feb 17. PMID 33596934, Free PMC Article
    4. Haploinsufficiency of Lipin3 leads to hypertriglyceridemia and obesity by disrupting the expression and nucleocytoplasmic localization of Lipin1. Wang F, et al. Front Med, 2024 Feb. PMID 37776435
    5. Adipose tissue deficiency, glucose intolerance, and increased atherosclerosis result from mutation in the mouse fatty liver dystrophy (fld) gene. Reue K, et al. J Lipid Res, 2000 Jul. PMID 10884287

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Haploinsufficiency of Lipin3 leads to hypertriglyceridemia and obesity by disrupting the expression and nucleocytoplasmic localization of Lipin1.
      Title: Haploinsufficiency of Lipin3 leads to hypertriglyceridemia and obesity by disrupting the expression and nucleocytoplasmic localization of Lipin1.
    2. Identification of lipidomic profiles associated with drug-resistant prostate cancer cells.
      Title: Identification of lipidomic profiles associated with drug-resistant prostate cancer cells.
    3. a newly identified novel cell-penetrating sequence (LPIN; RRKRRRRRK) from the nuclear localization sequence (NLS) of human nuclear phosphatase, LPIN3.
      Title: Identification of a novel cell-penetrating peptide from human phosphatidate phosphatase LPIN3.
    4. LPIN1-related myolysis constitutes a major cause of early-onset rhabdomyolysis and occasionally in adults. Heterozygous LPIN1 mutations may cause mild muscular symptoms. No major defects of LPIN2 or LPIN3 genes were associated with muscle manifestations.
      Title: Study of LPIN1, LPIN2 and LPIN3 in rhabdomyolysis and exercise-induced myalgia.
    5. Data revealed that lipin 1 formed stable homo-oligomers with itself and hetero-oligomers with lipin 2/3.
      Title: Lipin proteins form homo- and hetero-oligomers.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidate phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to insulin stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in fatty acid catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in triglyceride biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    phosphatidate phosphatase LPIN3
    NP_001288789.1
    NP_075047.1
    XP_005260573.1
    XP_006723926.1
    XP_011527298.1
    XP_011527299.1
    XP_011527300.1
    XP_011527301.1
    XP_011527302.1
    XP_011527303.1
    XP_011527304.1
    XP_011527305.1
    XP_011527306.1
    XP_011527307.1
    XP_011527308.1
    XP_047296339.1
    XP_047296340.1
    XP_047296341.1
    XP_047296342.1
    XP_047296343.1
    XP_047296344.1
    XP_047296345.1
    XP_054179840.1
    XP_054179841.1
    XP_054179842.1
    XP_054179843.1
    XP_054179844.1
    XP_054179845.1
    XP_054179846.1
    XP_054179847.1
    XP_054179848.1
    XP_054179849.1
    XP_054179850.1
    XP_054179851.1
    XP_054179852.1
    XP_054179853.1
    XP_054179854.1
    XP_054179855.1
    XP_054179856.1
    XP_054179857.1
    XP_054179858.1
    XP_054179859.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001301860.2 → NP_001288789.1  phosphatidate phosphatase LPIN3 isoform 1

      See identical proteins and their annotated locations for NP_001288789.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the supported protein.
      Source sequence(s)
      AL031667, AL132654, BC140806, BX647082
      Consensus CDS
      CCDS33469.2
      UniProtKB/Swiss-Prot
      Q9BQK8
      Related
      ENSP00000487971.1, ENST00000632009.1
      Conserved Domains (4) summary
      pfam03546
      Location:100 → 370
      Treacle; Treacher Collins syndrome protein Treacle
      pfam04571
      Location:1 → 107
      Lipin_N; lipin, N-terminal conserved region
      pfam08235
      Location:593 → 818
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    2. NM_022896.3 → NP_075047.1  phosphatidate phosphatase LPIN3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL031667, AL132654
      Consensus CDS
      CCDS93041.1
      UniProtKB/Swiss-Prot
      B2RTT5, Q5TDB9, Q9BQK8, Q9NPY8, Q9UJE5
      Related
      ENSP00000362354.3, ENST00000373257.8
      Conserved Domains (4) summary
      pfam03546
      Location:93 → 369
      Treacle; Treacher Collins syndrome protein Treacle
      pfam04571
      Location:1 → 107
      Lipin_N; lipin, N-terminal conserved region
      pfam08235
      Location:592 → 817
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:438 → 528
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    RNA

    1. NR_126051.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains alternate splice sites at two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD)
      Source sequence(s)
      AL031667, AL132654, BC140806, BC144598, BX647082

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      41340821..41360582
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528997.4 → XP_011527299.1  phosphatidate phosphatase LPIN3 isoform X1

      See identical proteins and their annotated locations for XP_011527299.1

      Conserved Domains (4) summary
      pfam15017
      Location:868 → 907
      AF1Q; Drug resistance and apoptosis regulator
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam08235
      Location:593 → 874
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    2. XM_047440384.1 → XP_047296340.1  phosphatidate phosphatase LPIN3 isoform X3

    3. XM_047440386.1 → XP_047296342.1  phosphatidate phosphatase LPIN3 isoform X4

      UniProtKB/Swiss-Prot
      B2RTT5, Q5TDB9, Q9BQK8, Q9NPY8, Q9UJE5

    4. XM_011528996.3 → XP_011527298.1  phosphatidate phosphatase LPIN3 isoform X1

      See identical proteins and their annotated locations for XP_011527298.1

      Conserved Domains (4) summary
      pfam15017
      Location:868 → 907
      AF1Q; Drug resistance and apoptosis regulator
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam08235
      Location:593 → 874
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    5. XM_011529001.3 → XP_011527303.1  phosphatidate phosphatase LPIN3 isoform X5

      Conserved Domains (4) summary
      pfam15017
      Location:761 → 800
      AF1Q; Drug resistance and apoptosis regulator
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam08235
      Location:593 → 767
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    6. XM_011529000.3 → XP_011527302.1  phosphatidate phosphatase LPIN3 isoform X2

      Conserved Domains (4) summary
      pfam15017
      Location:867 → 906
      AF1Q; Drug resistance and apoptosis regulator
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam08235
      Location:592 → 873
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:438 → 528
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    7. XM_047440388.1 → XP_047296344.1  phosphatidate phosphatase LPIN3 isoform X6

    8. XM_011528999.4 → XP_011527301.1  phosphatidate phosphatase LPIN3 isoform X1

      See identical proteins and their annotated locations for XP_011527301.1

      Conserved Domains (4) summary
      pfam15017
      Location:868 → 907
      AF1Q; Drug resistance and apoptosis regulator
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam08235
      Location:593 → 874
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    9. XM_011528998.4 → XP_011527300.1  phosphatidate phosphatase LPIN3 isoform X1

      See identical proteins and their annotated locations for XP_011527300.1

      Conserved Domains (4) summary
      pfam15017
      Location:868 → 907
      AF1Q; Drug resistance and apoptosis regulator
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam08235
      Location:593 → 874
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    10. XM_047440385.1 → XP_047296341.1  phosphatidate phosphatase LPIN3 isoform X3

    11. XM_047440383.1 → XP_047296339.1  phosphatidate phosphatase LPIN3 isoform X2

    12. XM_047440387.1 → XP_047296343.1  phosphatidate phosphatase LPIN3 isoform X4

      UniProtKB/Swiss-Prot
      B2RTT5, Q5TDB9, Q9BQK8, Q9NPY8, Q9UJE5

    13. XM_011529003.2 → XP_011527305.1  phosphatidate phosphatase LPIN3 isoform X8

      Conserved Domains (3) summary
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain
      cl21460
      Location:593 → 680
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    14. XM_047440389.1 → XP_047296345.1  phosphatidate phosphatase LPIN3 isoform X10

    15. XM_011529004.2 → XP_011527306.1  phosphatidate phosphatase LPIN3 isoform X9

      Conserved Domains (3) summary
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain
      cl21460
      Location:593 → 680
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    16. XM_011529005.3 → XP_011527307.1  phosphatidate phosphatase LPIN3 isoform X11

      Conserved Domains (3) summary
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region
      pfam16876
      Location:439 → 529
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain
      cl21460
      Location:593 → 683
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    17. XM_005260516.3 → XP_005260573.1  phosphatidate phosphatase LPIN3 isoform X13

      Conserved Domains (1) summary
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region

    18. XM_006723863.3 → XP_006723926.1  phosphatidate phosphatase LPIN3 isoform X12

      See identical proteins and their annotated locations for XP_006723926.1

      Conserved Domains (1) summary
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region

    19. XM_011529006.3 → XP_011527308.1  phosphatidate phosphatase LPIN3 isoform X12

      See identical proteins and their annotated locations for XP_011527308.1

      Conserved Domains (1) summary
      pfam04571
      Location:1 → 106
      Lipin_N; lipin, N-terminal conserved region

    20. XM_011529002.4 → XP_011527304.1  phosphatidate phosphatase LPIN3 isoform X7

      Conserved Domains (3) summary
      pfam15017
      Location:736 → 775
      AF1Q; Drug resistance and apoptosis regulator
      pfam08235
      Location:461 → 742
      LNS2; LNS2 (Lipin/Ned1/Smp2)
      pfam16876
      Location:307 → 397
      Lipin_mid; Lipin/Ned1/Smp2 multi-domain protein middle domain

    RNA

    1. XR_430311.2 RNA Sequence

    2. XR_007067476.1 RNA Sequence

    3. XR_936610.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      43072623..43092380
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323865.1 → XP_054179840.1  phosphatidate phosphatase LPIN3 isoform X1

    2. XM_054323867.1 → XP_054179842.1  phosphatidate phosphatase LPIN3 isoform X1

    3. XM_054323870.1 → XP_054179845.1  phosphatidate phosphatase LPIN3 isoform X2

    4. XM_054323872.1 → XP_054179847.1  phosphatidate phosphatase LPIN3 isoform X3

    5. XM_054323874.1 → XP_054179849.1  phosphatidate phosphatase LPIN3 isoform X4

      UniProtKB/Swiss-Prot
      B2RTT5, Q5TDB9, Q9BQK8, Q9NPY8, Q9UJE5

    6. XM_054323868.1 → XP_054179843.1  phosphatidate phosphatase LPIN3 isoform X1

    7. XM_054323871.1 → XP_054179846.1  phosphatidate phosphatase LPIN3 isoform X3

    8. XM_054323873.1 → XP_054179848.1  phosphatidate phosphatase LPIN3 isoform X4

      UniProtKB/Swiss-Prot
      B2RTT5, Q5TDB9, Q9BQK8, Q9NPY8, Q9UJE5

    9. XM_054323866.1 → XP_054179841.1  phosphatidate phosphatase LPIN3 isoform X1

    10. XM_054323875.1 → XP_054179850.1  phosphatidate phosphatase LPIN3 isoform X5

    11. XM_054323869.1 → XP_054179844.1  phosphatidate phosphatase LPIN3 isoform X2

    12. XM_054323876.1 → XP_054179851.1  phosphatidate phosphatase LPIN3 isoform X6

    13. XM_054323878.1 → XP_054179853.1  phosphatidate phosphatase LPIN3 isoform X8

    14. XM_054323880.1 → XP_054179855.1  phosphatidate phosphatase LPIN3 isoform X10

    15. XM_054323879.1 → XP_054179854.1  phosphatidate phosphatase LPIN3 isoform X9

    16. XM_054323881.1 → XP_054179856.1  phosphatidate phosphatase LPIN3 isoform X11

    17. XM_054323884.1 → XP_054179859.1  phosphatidate phosphatase LPIN3 isoform X13

    18. XM_054323882.1 → XP_054179857.1  phosphatidate phosphatase LPIN3 isoform X12

    19. XM_054323883.1 → XP_054179858.1  phosphatidate phosphatase LPIN3 isoform X12

    20. XM_054323877.1 → XP_054179852.1  phosphatidate phosphatase LPIN3 isoform X7

    RNA

    1. XR_008485295.1 RNA Sequence

    2. XR_008485293.1 RNA Sequence

    3. XR_008485294.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQK8.3 GenPept UniProtKB/Swiss-Prot:Q9BQK8

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