U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LPIN3 lipin 3 [ Homo sapiens (human) ]

Gene ID: 64900, updated on 5-Mar-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
20q12
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (41340821..41360582)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (43072623..43092380)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

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. 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
  3. Lipin proteins form homo- and hetero-oligomers. Liu GH, et al. Biochem J, 2010 Nov 15. PMID 20735359, Free PMC Article
  4. Study of LPIN1, LPIN2 and LPIN3 in rhabdomyolysis and exercise-induced myalgia. Michot C, et al. J Inherit Metab Dis, 2012 Nov. PMID 22481384
  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 (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of lipidomic profiles associated with drug-resistant prostate cancer cells.
    Title: Identification of lipidomic profiles associated with drug-resistant prostate cancer cells.
  2. 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.
  3. 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.
  4. 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

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

NEW Try the new Transcript table

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_2023_10

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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous