LPIN1

gene
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Also known as KIAA0188

Summary

LPIN1 (lipin 1, HGNC:13345) is a protein-coding gene on chromosome 2p25.1, encoding Phosphatidate phosphatase LPIN1 (Q14693). Acts as a magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis and therefore controls the metabolism of fatty acids at differe….

This gene encodes a magnesium-ion-dependent phosphatidic acid phosphohydrolase enzyme that catalyzes the penultimate step in triglyceride synthesis including the dephosphorylation of phosphatidic acid to yield diacylglycerol. Expression of this gene is required for adipocyte differentiation and it also functions as a nuclear transcriptional coactivator with some peroxisome proliferator-activated receptors to modulate expression of other genes involved in lipid metabolism. Mutations in this gene are associated with metabolic syndrome, type 2 diabetes, acute recurrent rhabdomyolysis, and autosomal recessive acute recurrent myoglobinuria (ARARM). This gene is also a candidate for several human lipodystrophy syndromes.

Source: NCBI Gene 23175 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): myoglobinuria, acute recurrent, autosomal recessive (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 4
  • Clinical variants (ClinVar): 818 total — 35 pathogenic, 17 likely-pathogenic
  • Phenotypes (HPO): 41
  • MANE Select transcript: NM_001349206

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13345
Approved symbolLPIN1
Namelipin 1
Location2p25.1
Locus typegene with protein product
StatusApproved
AliasesKIAA0188
Ensembl geneENSG00000134324
Ensembl biotypeprotein_coding
OMIM605518
Entrez23175

Gene structure

Transcript identifiers

Ensembl transcripts: 49 — 38 protein_coding, 6 protein_coding_CDS_not_defined, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000256720, ENST00000396097, ENST00000396098, ENST00000396099, ENST00000404113, ENST00000423495, ENST00000425416, ENST00000441684, ENST00000449576, ENST00000454151, ENST00000460096, ENST00000464517, ENST00000464953, ENST00000475286, ENST00000475922, ENST00000480315, ENST00000487346, ENST00000487576, ENST00000495907, ENST00000674199, ENST00000852426, ENST00000852427, ENST00000852428, ENST00000852429, ENST00000852430, ENST00000852431, ENST00000852432, ENST00000852433, ENST00000852434, ENST00000852435, ENST00000852436, ENST00000852437, ENST00000852438, ENST00000852439, ENST00000852440, ENST00000852441, ENST00000852442, ENST00000914304, ENST00000961822, ENST00000961823, ENST00000961824, ENST00000961825, ENST00000961826, ENST00000961827, ENST00000961828, ENST00000961829, ENST00000961830, ENST00000961831, ENST00000961832

RefSeq mRNA: 13 — MANE Select: NM_001349206 NM_001261427, NM_001261428, NM_001349199, NM_001349200, NM_001349201, NM_001349202, NM_001349203, NM_001349204, NM_001349205, NM_001349206, NM_001349207, NM_001349208, NM_145693

CCDS: CCDS1682, CCDS58699, CCDS58701, CCDS92716

Canonical transcript exons

ENST00000674199 — 21 exons

ExonStartEnd
ENSE000015239011177608611776193
ENSE000016137081178488611785076
ENSE000017451521178382911783922
ENSE000017494411177137211771679
ENSE000017520661178220111782507
ENSE000017879581177362011773745
ENSE000017911571178707411787167
ENSE000018259611182463211827409
ENSE000034827341176553311765733
ENSE000035449371177951911779645
ENSE000035472191178838711788456
ENSE000035542061182041111820514
ENSE000037142861181508811815240
ENSE000037348151179540811795487
ENSE000037392021179191411792006
ENSE000037410601181948411819598
ENSE000037420761180290711803033
ENSE000037518241180507011805156
ENSE000037523511180442311804571
ENSE000037884411176776311767858
ENSE000038983791174663211746671

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 99.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.4436 / max 258.5051, expressed in 1815 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
1891423.70971813
189153.0108954
189090.326881
189080.239177
189170.082430
189130.03983
189120.03503

Top tissues by expression

298 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001999.91gold quality
male germ cellCL:000001599.44gold quality
lower esophagus mucosaUBERON:003583498.32gold quality
olfactory bulbUBERON:000226498.31gold quality
buccal mucosa cellCL:000233698.20gold quality
trigeminal ganglionUBERON:000167598.15gold quality
sural nerveUBERON:001548897.97gold quality
gastrocnemiusUBERON:000138897.81gold quality
dorsal root ganglionUBERON:000004497.74gold quality
tibial nerveUBERON:000132397.47gold quality
right testisUBERON:000453497.23gold quality
muscle of legUBERON:000138397.21gold quality
esophagus squamous epitheliumUBERON:000692097.18gold quality
left testisUBERON:000453396.94gold quality
muscle organUBERON:000163096.93gold quality
skeletal muscle organUBERON:001489296.93gold quality
quadriceps femorisUBERON:000137796.55gold quality
medial globus pallidusUBERON:000247796.48gold quality
vastus lateralisUBERON:000137996.44gold quality
deltoidUBERON:000147696.43gold quality
globus pallidusUBERON:000187596.21gold quality
inferior olivary complexUBERON:000212796.14gold quality
hindlimb stylopod muscleUBERON:000425296.09gold quality
lateral globus pallidusUBERON:000247695.97gold quality
body of tongueUBERON:001187695.96gold quality
skeletal muscle tissueUBERON:000113495.82gold quality
testisUBERON:000047395.56gold quality
tibialis anteriorUBERON:000138595.49gold quality
dorsal motor nucleus of vagus nerveUBERON:000287095.49gold quality
superior surface of tongueUBERON:000737195.43gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes10.68
E-GEOD-100618no1354.63
E-CURD-46no11.37
E-CURD-112no2.76

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF1, CEBPA, CEBPB, CREB3L3, EGR1, ETS2, FOXC1, HIF1A, HNF4A, KDM5D, NFATC4, NFE2L1, NFYA, NFYB, NFYC, NRF1, SREBF1, STAT3

miRNA regulators (miRDB)

100 targeting LPIN1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4533100.0069.482758
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-186-5P99.9970.833707
HSA-MIR-428299.9975.366408
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-391099.9571.132227
HSA-MIR-545-3P99.9570.742783
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-651-3P99.9473.485177
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-806399.9169.763146
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-17-5P99.8973.832665
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-153-5P99.8973.866317
HSA-MIR-106B-5P99.8874.722795

Literature-anchored findings (GeneRIF, showing 40)

  • LPIN1 mutations are not commonly seen in patients with lipodystrophy who had no mutations in known disease genes. (PMID:12111372)
  • effects of genetic variation in lipin levels on glucose homeostasis across species by analyzing lipin transcript levels in human and mouse adipose tissues (PMID:16357106)
  • human lipin 1 is a Mg2+-dependent PA phosphatase, the penultimate enzyme in the pathway to synthesize triacylglyerol (PMID:16467296)
  • Lipin 1 is an inducible amplifier of the hepatic PGC-1alpha/PPARalpha regulatory pathway (PMID:16950137)
  • These results suggest that increased adipogenesis and/or lipogenesis in subcutaneous fat, mediated by the LPIN1 gene, may prevent lipotoxicity in muscle, leading to improved insulin sensitivity (PMID:17003347)
  • Body fat accumulation is a major regulator of human adipose LPIN1 expression and suggests a role of LPIN1 in human preadipocyte as well as mature adipocyte function. (PMID:17035674)
  • insulin and epinephrine control lipin primarily by changing localization rather than intrinsic PAP activity (PMID:17105729)
  • Lipin 1beta and overexpression of peroxisome proliferator-activated receptor-gamma coactivator (PGC)-1alpha are downregulated by obesity and obesity-related metabolic perturbations in human subjects. (PMID:17563064)
  • Variants of the LPIN1 gene have significant effects in human metabolic traits and implicate lipin in the pathophysiology of the metabolic syndrome. (PMID:17940119)
  • LPIN1 messenger RNA levels positively correlated with insulin sensitivity in all subjects with obesity, NIDDM, and HIV-associated lipodystrophy (PMID:17950103)
  • Sequence variation in the LPIN1 gene contributes to variation in resting metabolic rate and obesity-related phenotypes potentially in an age-dependent manner. (PMID:18070763)
  • Lpin1 glucocorticoid response element binds to the glucocorticoid receptor (PMID:18362392)
  • Study provides further evidence that lipin 1 may play a role in blood pressure regulation, especially in men. (PMID:18437145)
  • Our data do not support a major effect of common LPIN1 variation on metabolic traits and suggest that mutations in LPIN1 are not a common cause of lipodystrophy in humans (PMID:18591397)
  • LPIN1 genetic variations can affect rosiglitazone treatment response in T2DM. (PMID:18693052)
  • distinct and non-redundant functions of lipin 1 and 2 regulate lipid production during the cell cycle and adipocyte differentiation (PMID:18694939)
  • Mutations in the LPIN1 gene cause recurrent rhabdomyolysis in childhood, and a carrier state may predispose for statin-induced myopathy (PMID:18817903)
  • Decreased expression of lipin 1 beta in visceral and subcutaneous adipose tissue appears to contribute to the pathogenesis of insulin resistance in polycystic ovary syndrome. (PMID:18829900)
  • the LPIN1 gene seemed not to be a major susceptibility gene for type 2 diabetes or related metabolic phenotypes in the Chinese population. (PMID:19543209)
  • sterol-mediated regulation of lipin 1 gene transcription modulates triglyceride accumulation (PMID:19553673)
  • A conserved serine residue is required for the phosphatidate phosphatase activity but not the transcriptional coactivator functions of lipin-1 and lipin-2. (PMID:19717560)
  • sumoylation facilitates the nuclear localization and transcriptional coactivator behavior of lipin-1alpha, which may act as a sumoylation-regulated transcriptional coactivator in brain (PMID:19753306)
  • Results showed a marked association between LPIN1 and PPARalpha gene expression both in subcutaneous and visceral adipose tissues and might suggest a possible role of LPIN1 in stress conditions that occur in chronic obesity and underlie insulin resistance (PMID:20101248)
  • LPIN1 rs33997857, rs6744682, and rs6708316 did not associate with type 2 diabetes, obesity, or related quantitative metabolic phenotypes in the Danish population examined. (PMID:20356931)
  • the low-grade proinflammatory environment and the insulin resistance associated with obesity may contribute to downregulate LPIN1 in adipose tissue (PMID:20530740)
  • Data suggest that the high frequency of the intragenic LPIN1 deletion should provide a valuable criterion for fast diagnosis, prior to muscle biopsy. (PMID:20583302)
  • Data revealed that lipin 1 formed stable homo-oligomers with itself and hetero-oligomers with lipin 2/3. (PMID:20735359)
  • PPARG and LPIN1 gene polymorphisms role of these genes in lipid metabolism and pathogenesis of type 2 diabetes and metabolic syndrome (PMID:21263402)
  • dullard shows specificity for the peptide corresponding to the insulin-dependent phosphorylation site (Ser106) of lipin (PMID:21413788)
  • The aim of present study was to investigate for the first time the association of lipin 1 gene polymorphisms with metabolic and hormonal profile in polycystic ovary syndrome patients and controls. (PMID:21448847)
  • data suggest that lipin-1 associates with lipid droplets and regulates the activation of cytosolic group IVA phospholipase A(2)alpha in monocyte-derived macrophages (PMID:21478406)
  • lipin-1gamma is the main lipin-1 isoform expressed in normal human brain, suggesting a specialized role in regulating brain lipid metabolism. (PMID:21616074)
  • reduced expression of SFRS10, as observed in tissues from obese humans, alters LPIN1 splicing, induces lipogenesis, and therefore contributes to metabolic phenotypes associated with obesity. (PMID:21803291)
  • Estrogen-related receptor gamma (ERRgamma) is a novel transcriptional regulator of phosphatidic acid phosphatase, LIPIN1, and inhibits hepatic insulin signaling (PMID:21911493)
  • Lpin1 expression in response to nutritional stress is controlled through the reactive oxygen species-ATM-p53 pathway. (PMID:22055193)
  • Lipin1 rs13412852 single nucleotide polymorphism is associated with the severity of liver damage and fibrosis progression in pediatric patients with histological NAFLD. (PMID:22157924)
  • We conclude that direct control of lipin 1 transcription by HIF-1 is an important regulatory feature of lipid metabolism and its adaptation to hypoxia. (PMID:22467849)
  • LPIN1 mutations should be considered in any child presenting with severe rhabdomyolysis. (PMID:22480698)
  • 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. (PMID:22481384)
  • Data suggests common single nucleotide polymorphisms within the LPIN1 region were associated with Type 2 diabetes and metabolic traits in the Chinese population. (PMID:22853689)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriolpin1aENSDARG00000020239
danio_reriolpin1bENSDARG00000103380
mus_musculusLpin1ENSMUSG00000020593
rattus_norvegicusLpin1ENSRNOG00000004377
drosophila_melanogasterLpinFBGN0263593
caenorhabditis_elegansWBGENE00010425

Paralogs (3): LPIN2 (ENSG00000101577), LPIN3 (ENSG00000132793), AP5Z1 (ENSG00000242802)

Protein

Protein identifiers

Phosphatidate phosphatase LPIN1Q14693 (reviewed: Q14693)

Alternative names: Lipin-1

All UniProt accessions (5): A0A0A0MS66, C9IYP2, C9J278, Q14693, H7C3T1

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis and therefore controls the metabolism of fatty acids at different levels. Is involved in adipocyte differentiation. Recruited at the mitochondrion outer membrane and is involved in mitochondrial fission by converting phosphatidic acid to diacylglycerol. Acts also as nuclear transcriptional coactivator for PPARGC1A/PPARA regulatory pathway to modulate lipid metabolism gene expression.

Subunit / interactions. Interacts (via LXXIL motif) with PPARA. Interacts with PPARGC1A. Interaction with PPARA and PPARGC1A leads to the formation of a complex that modulates gene transcription. Interacts with MEF2C.

Subcellular location. Cytoplasm. Cytosol. Endoplasmic reticulum membrane. Nucleus membrane.

Tissue specificity. Specifically expressed in skeletal muscle. Also abundant in adipose tissue. Lower levels in some portions of the digestive tract.

Post-translational modifications. Phosphorylated at multiple sites by mTOR in response to insulin, leading to its inactivation. Phosphorylation does not affect the catalytic activity but regulates the localization. Phosphorylation is decreased by epinephrine. Dephosphorylated by the CTDNEP1-CNEP1R1 complex. Dephosphorylation following mTOR inhibition promotes its activity. Acetylation at Lys-425 and Lys-595 by KAT5 in response to fatty acids promotes translocation to the endoplasmic reticulum and synthesis of diacylglycerol. Sumoylated.

Disease relevance. Myoglobinuria, acute recurrent, autosomal recessive (ARARM) [MIM:268200] Recurrent myoglobinuria is characterized by recurrent attacks of rhabdomyolysis (necrosis or disintegration of skeletal muscle) associated with muscle pain and weakness and followed by excretion of myoglobin in the urine. Renal failure may occasionally occur. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Potently inhibited by sphingolipids, in particular, the sphingoid bases sphinganine and sphingosine and ceramide-1-phosphate. Inhibited by concentrations of Mg(2+) and Mn(2+) above their optimums and by Ca(2+), Zn(2+), N-ethylmaleimide and propranolol. Sertraline and propanolol inhibit activity in dose-dependent manners with IC(50) values of 103 uM and 226 uM, respectively. Sertraline and propanolol inhibit activity in dose-dependent manners with IC(50) values of 108 uM and 271 uM, respectively. Sertraline and propanolol inhibit activity in dose-dependent manners with IC(50) values of 143 uM and 227 uM, respectively.

Cofactor. Mg(2+) and, at a lesser extent, Mn(2+).

Domain organisation. Contains one Leu-Xaa-Xaa-Ile-Leu (LXXIL), a transcriptional binding motif, which mediates interaction with PPARA. Contains 1 Asp-Xaa-Asp-Xaa-Thr (DXDXT) motif, a catalytic motif essential for phosphatidate phosphatase activity.

Miscellaneous. May represent a candidate gene for human lipodysytropy syndromes.

Similarity. Belongs to the lipin family.

Isoforms (7)

UniProt IDNamesCanonical?
Q14693-11, Alphayes
Q14693-22
Q14693-33, Beta
Q14693-44, Gamma
Q14693-55
Q14693-66
Q14693-77

RefSeq proteins (13): NP_001248356, NP_001248357, NP_001336128, NP_001336129, NP_001336130, NP_001336131, NP_001336132, NP_001336133, NP_001336134, NP_001336135, NP_001336136, NP_001336137, NP_663731 (=MANE)

Domains & families (InterPro)

IDNameType
IPR007651Lipin_NDomain
IPR013209LNS2Domain
IPR026058LIPINFamily
IPR031315LNS2/PITPDomain
IPR031703Lipin_midDomain
IPR036412HAD-like_sfHomologous_superfamily

Pfam: PF04571, PF08235, PF16876

Enzyme classification (BRENDA):

  • EC 3.1.3.4 — phosphatidate phosphatase (BRENDA: 31 organisms, 190 substrates, 196 inhibitors, 44 Km, 3 kcat entries)

Substrate kinetics (BRENDA)

10 substrates with measured Km, best-characterized 10. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
PHOSPHATIDIC ACID0.0054–1.217
LYSOPHOSPHATIDATE0.046–0.1793
PHOSPHATIDATE0.284–0.3693
SPHINGOSINE-1-PHOSPHATE0.028–0.263
CERAMIDE-1-PHOSPHATE0.022–0.0522
DIACYLGLYCEROL DIPHOSPHATE0.041–0.1042
LYSOPHOSPHATIDIC ACID0.295–0.582
1,2-DIACYL-SN-GLYCEROL-3-PHOSPHATE0.59541
2-(4,4-DIFLUORO-5,7-DIMETHYL-4-BORA-3A,4A-DIAZA-0.0241
DIOCTANOYL PHOSPHATIDIC ACID1.41

Catalyzed reactions (Rhea), 12 shown:

  • a 1,2-diacyl-sn-glycero-3-phosphate + H2O = a 1,2-diacyl-sn-glycerol + phosphate (RHEA:27429)
  • 1,2-dioctadecanoyl-sn-glycero-3-phosphate + H2O = 1,2-dioctadecanoyl-sn-glycerol + phosphate (RHEA:33335)
  • 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol + phosphate (RHEA:41255)
  • 1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O = 1,2-dihexadecanoyl-sn-glycerol + phosphate (RHEA:43236)
  • 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphate + H2O = 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycerol + phosphate (RHEA:43240)
  • 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O = 1,2-di-(9Z-octadecenoyl)-sn-glycerol + phosphate (RHEA:43244)
  • 1,2-di-(5Z,8Z,11Z,14Z)-eicosatetraenoyl-sn-glycero-3-phosphate + H2O = 1,2-di-(5Z,8Z,11Z,14Z)-eicosatetraenoyl-sn-glycerol + phosphate (RHEA:43248)
  • 1,2-di-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphate + H2O = 1,2-di-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycerol + phosphate (RHEA:43252)
  • 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphate + H2O = 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycerol + phosphate (RHEA:43256)
  • 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphate + H2O = 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycerol + phosphate (RHEA:43260)
  • 1-hexadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphate + H2O = 1-hexadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycerol + phosphate (RHEA:43280)
  • 1-octadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O = 1-octadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol + phosphate (RHEA:43284)

UniProt features (53 total): modified residue 16, region of interest 7, compositionally biased region 7, splice variant 6, sequence conflict 5, sequence variant 4, short sequence motif 3, cross-link 2, mutagenesis site 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q14693-F160.880.25

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (18): 106, 150, 252, 254, 260, 264, 294, 425, 434, 438, 449, 595, 600, 601, 887, 889, 565, 595

Mutagenesis-validated functional residues (2):

PositionPhenotype
425decreased acetylation by kat5.
595decreased acetylation by kat5.

Function

Pathways and Gene Ontology

Reactome pathways

20 pathways

IDPathway
R-HSA-1483191Synthesis of PC
R-HSA-1483213Synthesis of PE
R-HSA-4419969Depolymerization of the Nuclear Lamina
R-HSA-75109Triglyceride biosynthesis
R-HSA-9841922MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis
R-HSA-1430728Metabolism
R-HSA-1483206Glycerophospholipid biosynthesis
R-HSA-1483257Phospholipid metabolism
R-HSA-1640170Cell Cycle
R-HSA-212165Epigenetic regulation of gene expression
R-HSA-2980766Nuclear Envelope Breakdown
R-HSA-556833Metabolism of lipids
R-HSA-68875Mitotic Prophase
R-HSA-68886M Phase
R-HSA-69278Cell Cycle, Mitotic
R-HSA-74160Gene expression (Transcription)
R-HSA-8979227Triglyceride metabolism
R-HSA-9818564Epigenetic regulation of gene expression by MLL3 and MLL4 complexes
R-HSA-9851695Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes
R-HSA-9917777Epigenetic regulation by WDR5-containing histone modifying complexes

MSigDB gene sets: 488 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_FATTY_ACID_CATABOLIC_PROCESS, chr2p25, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_NEGATIVE_REGULATION_OF_LIPID_METABOLIC_PROCESS, GOBP_MEMBRANE_DISASSEMBLY, GOLDRATH_IMMUNE_MEMORY, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_NEGATIVE_REGULATION_OF_NERVOUS_SYSTEM_PROCESS

GO Biological Process (14): triglyceride mobilization (GO:0006642), mitotic nuclear membrane disassembly (GO:0007077), fatty acid catabolic process (GO:0009062), triglyceride biosynthetic process (GO:0019432), animal organ regeneration (GO:0031100), negative regulation of myelination (GO:0031642), cellular response to insulin stimulus (GO:0032869), positive regulation of transcription by RNA polymerase II (GO:0045944), phosphatidylethanolamine metabolic process (GO:0046337), phosphatidic acid metabolic process (GO:0046473), positive regulation of cold-induced thermogenesis (GO:0120162), negative regulation of phosphatidic acid biosynthetic process (GO:1905694), lipid metabolic process (GO:0006629), fatty acid metabolic process (GO:0006631)

GO Molecular Function (4): transcription coactivator activity (GO:0003713), phosphatidate phosphatase activity (GO:0008195), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (10): nucleus (GO:0005634), nuclear envelope (GO:0005635), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), mitochondrial outer membrane (GO:0005741), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), cytosol (GO:0005829), nuclear membrane (GO:0031965), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-15 pathways:

CategoryPathways
Glycerophospholipid biosynthesis2
Metabolism of lipids2
Nuclear Envelope Breakdown1
Triglyceride metabolism1
Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes1
Phospholipid metabolism1
Gene expression (Transcription)1
Mitotic Prophase1
Metabolism1
M Phase1
Cell Cycle, Mitotic1
Cell Cycle1
Epigenetic regulation by WDR5-containing histone modifying complexes1
Epigenetic regulation of gene expression by MLL3 and MLL4 complexes1
Epigenetic regulation of gene expression1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
triglyceride metabolic process2
positive regulation of DNA-templated transcription2
glycerophospholipid metabolic process2
intracellular membrane-bounded organelle2
nucleus2
endomembrane system2
cytoplasm2
organelle membrane2
mitotic cell cycle1
nuclear membrane disassembly1
mitotic cell cycle process1
fatty acid metabolic process1
lipid catabolic process1
monocarboxylic acid catabolic process1
acylglycerol biosynthetic process1
regeneration1
animal organ development1
regulation of myelination1
negative regulation of nervous system process1
myelination1
negative regulation of cellular process1
response to insulin1
cellular response to peptide hormone stimulus1
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
positive regulation of multicellular organismal process1
cold-induced thermogenesis1
regulation of cold-induced thermogenesis1
phosphatidic acid biosynthetic process1
negative regulation of phospholipid biosynthetic process1
regulation of phosphatidic acid biosynthetic process1
primary metabolic process1
lipid metabolic process1
monocarboxylic acid metabolic process1
transcription coregulator activity1
lipid phosphatase activity1
binding1
catalytic activity1
organelle envelope1

Protein interactions and networks

STRING

1852 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LPIN1PPARAQ07869964
LPIN1PPARGC1AQ9UBK2947
LPIN1PPARGP37231909
LPIN1PLPP2O43688856
LPIN1SREBF1P36956829
LPIN1AGPAT2O15120804
LPIN1HNF4AP41235740
LPIN1PLPP3O14495726
LPIN1BSCL2Q96G97713
LPIN1DGAT1O75907708
LPIN1CTDNEP1O95476688
LPIN1FASNP49327660
LPIN1GPAMQ9HCL2654
LPIN1DGAT2Q96PD7647
LPIN1ACACAQ13085644

IntAct

95 interactions, top by confidence:

ABTypeScore
LPIN3CSNK2A2psi-mi:“MI:0914”(association)0.640
YWHAERGS12psi-mi:“MI:0914”(association)0.610
YWHAESRSF10psi-mi:“MI:0914”(association)0.560
LPIN1DBHpsi-mi:“MI:0915”(physical association)0.560
DR1LPIN1psi-mi:“MI:0915”(physical association)0.560
LPIN1psi-mi:“MI:0915”(physical association)0.560
FLNALPIN1psi-mi:“MI:0915”(physical association)0.560
FOSLPIN1psi-mi:“MI:0915”(physical association)0.560
GATMLPIN1psi-mi:“MI:0915”(physical association)0.560
LPIN1GFAPpsi-mi:“MI:0915”(physical association)0.560
GRB2LPIN1psi-mi:“MI:0915”(physical association)0.560
GRNLPIN1psi-mi:“MI:0915”(physical association)0.560
GTF2BLPIN1psi-mi:“MI:0915”(physical association)0.560
HSF1LPIN1psi-mi:“MI:0915”(physical association)0.560
LPIN1HSPB1psi-mi:“MI:0915”(physical association)0.560
SRCLPIN1psi-mi:“MI:0915”(physical association)0.560
LPIN1WFS1psi-mi:“MI:0915”(physical association)0.560
LPIN1GTF3C3psi-mi:“MI:0915”(physical association)0.560
KIF1BLPIN1psi-mi:“MI:0915”(physical association)0.560
LPIN1ATXN10psi-mi:“MI:0915”(physical association)0.560
RNF11LPIN1psi-mi:“MI:0915”(physical association)0.560
PIAS4LPIN1psi-mi:“MI:0915”(physical association)0.560
LPIN1JPH3psi-mi:“MI:0915”(physical association)0.560
HTTLPIN1psi-mi:“MI:0915”(physical association)0.560

BioGRID (45): LPIN1 (Affinity Capture-MS), LPIN1 (Affinity Capture-MS), LPIN1 (Affinity Capture-MS), LPIN1 (Affinity Capture-MS), LPIN1 (Affinity Capture-MS), LPIN1 (Affinity Capture-Western), LPIN1 (Reconstituted Complex), BTRC (Affinity Capture-Western), CUL1 (Affinity Capture-Western), CSNK1E (Affinity Capture-Western), LPIN1 (Biochemical Activity), LPIN1 (Affinity Capture-MS), LPIN1 (Affinity Capture-RNA), LPIN1 (Affinity Capture-MS), BTRC (Affinity Capture-Western)

ESM2 similar proteins: A0A078CGE6, A2QHV0, A7KAX9, A7SNN5, A9RVK2, B0XPE7, B5X564, D0Z5N4, F4HYG2, F4I114, F4IRW0, F4J394, F4J6F6, F4JY37, O00444, O13839, O24527, O43065, P0CP71, P13185, P38623, P42858, P50526, Q03407, Q0CL79, Q0WPH8, Q14693, Q19192, Q2KHT3, Q2QAV0, Q4WJI7, Q5B4Z3, Q5R9Z7, Q60DG4, Q6GPD0, Q6H647, Q756Z0, Q75CH3, Q75DK7, Q75QN6

Diamond homologs: P32567, Q14693, Q7TNN8, Q91ZP3, Q92539, Q99PI4, Q99PI5, Q9BQK8, Q9FMN2, Q9SF47, Q9UUJ6

SIGNOR signaling

5 interactions.

AEffectBMechanism
CTDNEP1“up-regulates activity”LPIN1dephosphorylation
SRC“up-regulates activity”LPIN1phosphorylation
CHKA“down-regulates activity”LPIN1phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 52 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
TP53 Regulates Metabolic Genes514.8×1e-03
G2/M DNA damage checkpoint513.7×1e-03
Cell Cycle, Mitotic66.6×7e-03
Cell Cycle86.5×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

818 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic35
Likely pathogenic17
Uncertain significance323
Likely benign293
Benign83

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1205474NM_001349206.2(LPIN1):c.181C>T (p.Arg61Ter)Pathogenic
1323246NM_001349206.2(LPIN1):c.1564C>T (p.Gln522Ter)Pathogenic
1357179NM_001349206.2(LPIN1):c.2380del (p.Ser794fs)Pathogenic
1371806NM_001349206.2(LPIN1):c.1582C>T (p.Gln528Ter)Pathogenic
1456198NC_000002.11:g.(?11905668)(11955386_?)delPathogenic
1459559NC_000002.11:g.(?11959590)(11959744_?)delPathogenic
1951473NM_001349206.2(LPIN1):c.1784del (p.Gly595fs)Pathogenic
1967744NM_001349206.2(LPIN1):c.1237_1238del (p.Lys413fs)Pathogenic
1970429NM_001349206.2(LPIN1):c.2151del (p.Thr718fs)Pathogenic
2066424NM_001349206.2(LPIN1):c.844C>T (p.Arg282Ter)Pathogenic
2089945NM_001349206.2(LPIN1):c.264dup (p.Val89fs)Pathogenic
2106824NM_001349206.2(LPIN1):c.2019_2025del (p.Ser673_Leu674insTer)Pathogenic
2112231NM_001349206.2(LPIN1):c.2055_2056del (p.Phe685fs)Pathogenic
2427337NC_000002.11:g.(?11905668)(11964917_?)delPathogenic
2444342NM_001349206.2(LPIN1):c.1029del (p.Gln344fs)Pathogenic
280315NM_001349206.2(LPIN1):c.1363_1364dup (p.Asp455fs)Pathogenic
2857438NM_001349206.2(LPIN1):c.78_79del (p.Ser28fs)Pathogenic
3247590NC_000002.11:g.(?11943013)(11943179_?)delPathogenic
3653808NM_001349206.2(LPIN1):c.1841_1845del (p.Ala614fs)Pathogenic
3658701NM_001349206.2(LPIN1):c.1867C>T (p.Gln623Ter)Pathogenic
3720300NM_001349206.2(LPIN1):c.1537G>T (p.Glu513Ter)Pathogenic
3775683NM_001349206.2(LPIN1):c.288+2dupPathogenic
4080003NM_001349206.2(LPIN1):c.221_222del (p.Val74fs)Pathogenic
4281679NM_001349206.2(LPIN1):c.1520dup (p.Leu508fs)Pathogenic
4736138NM_001349206.2(LPIN1):c.283_284insCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCNNNNNNNNNNAAAAAAAAAAAAAAAGAAACAGATAATG (p.Asn94_Asp95insAlaProAlaSerAlaSerGlnSerAlaGlyIleThrGlyValSerHisArgAlaArgProXaaXaaXaaLysLysLysLysLysGluThrAspAsn)Pathogenic
4776642NM_001349206.2(LPIN1):c.227del (p.Leu76fs)Pathogenic
4781861NM_001349206.2(LPIN1):c.1735del (p.Arg579fs)Pathogenic
4910NM_001349206.2(LPIN1):c.643G>T (p.Glu215Ter)Pathogenic
4911NM_001349206.2(LPIN1):c.1270C>T (p.Arg424Ter)Pathogenic
4912NM_001349206.2(LPIN1):c.2509C>T (p.Arg837Ter)Pathogenic

SpliceAI

3422 predictions. Top by Δscore:

VariantEffectΔscore
2:11746670:CGGTG:Cdonor_loss1.0000
2:11746671:GGTG:Gdonor_loss1.0000
2:11746672:G:Cdonor_loss1.0000
2:11746672:G:GGdonor_gain1.0000
2:11746673:T:Adonor_loss1.0000
2:11765519:T:Aacceptor_gain1.0000
2:11765531:A:AGacceptor_gain1.0000
2:11765532:G:Aacceptor_loss1.0000
2:11765532:G:GGacceptor_gain1.0000
2:11765532:GGTGC:Gacceptor_gain1.0000
2:11765700:G:GTdonor_gain1.0000
2:11765700:G:Tdonor_gain1.0000
2:11765731:GTG:Gdonor_gain1.0000
2:11765733:GGT:Gdonor_loss1.0000
2:11765734:GT:Gdonor_loss1.0000
2:11765735:T:Gdonor_loss1.0000
2:11767856:CAGG:Cdonor_loss1.0000
2:11767857:AGGTA:Adonor_loss1.0000
2:11767858:GGT:Gdonor_loss1.0000
2:11767859:GTAAG:Gdonor_loss1.0000
2:11767860:T:Adonor_loss1.0000
2:11773618:A:AGacceptor_gain1.0000
2:11773618:AGAAC:Aacceptor_loss1.0000
2:11773619:G:GTacceptor_gain1.0000
2:11773619:GA:Gacceptor_gain1.0000
2:11773619:GAA:Gacceptor_gain1.0000
2:11773619:GAAC:Gacceptor_gain1.0000
2:11773619:GAACT:Gacceptor_gain1.0000
2:11773746:GT:Gdonor_loss1.0000
2:11773747:T:Gdonor_loss1.0000

AlphaMissense

6102 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:11765564:C:AA8D1.000
2:11765626:G:TG29W1.000
2:11765627:G:AG29E1.000
2:11765636:A:TD32V1.000
2:11765645:T:AV35D1.000
2:11765690:T:AV50D1.000
2:11765695:T:CF52L1.000
2:11765696:T:CF52S1.000
2:11765697:T:AF52L1.000
2:11765697:T:GF52L1.000
2:11765698:G:TG53W1.000
2:11765699:G:AG53E1.000
2:11767764:T:AV65D1.000
2:11767803:T:AM78K1.000
2:11767803:T:CM78T1.000
2:11767803:T:GM78R1.000
2:11767809:T:CL80S1.000
2:11767821:G:AG84E1.000
2:11767821:G:TG84V1.000
2:11767836:T:AV89D1.000
2:11779619:T:AW275R1.000
2:11779619:T:CW275R1.000
2:11787146:T:CL505P1.000
2:11804436:T:CL640S1.000
2:11804463:T:CF649S1.000
2:11804469:T:AV651D1.000
2:11804486:G:CG657R1.000
2:11804519:T:AW668R1.000
2:11804519:T:CW668R1.000
2:11804546:T:CS677P1.000

dbSNP variants (sampled 300 via entrez): RS1000045707 (2:11790904 A>G), RS1000067965 (2:11692203 T>C), RS1000104542 (2:11722325 C>T), RS1000109917 (2:11713460 A>C,G), RS1000110810 (2:11800159 C>T), RS1000139371 (2:11792571 C>T), RS1000146025 (2:11794006 A>G), RS1000174446 (2:11788391 T>G), RS1000213018 (2:11713516 C>T), RS1000214672 (2:11826364 T>G), RS1000240689 (2:11701161 T>C), RS1000262702 (2:11676408 C>T), RS1000269600 (2:11765166 C>T), RS1000280319 (2:11783491 GA>G), RS1000288059 (2:11747855 T>C)

Disease associations

OMIM: gene MIM:605518 | disease phenotypes: MIM:268200

GenCC curated gene-disease

DiseaseClassificationInheritance
myoglobinuria, acute recurrent, autosomal recessiveDefinitiveAutosomal recessive
hereditary recurrent myoglobinuriaSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
myoglobinuria, acute recurrent, autosomal recessiveDefinitiveAR

Mondo (2): myoglobinuria, acute recurrent, autosomal recessive (MONDO:0009992), hereditary recurrent myoglobinuria (MONDO:0020504)

Orphanet (1): Genetic recurrent myoglobinuria (Orphanet:99845)

HPO phenotypes

41 total (30 of 41 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000083Renal insufficiency
HP:0000467Neck muscle weakness
HP:0001265Hyporeflexia
HP:0001284Areflexia
HP:0001288Gait disturbance
HP:0001315Reduced tendon reflexes
HP:0001324Muscle weakness
HP:0001919Acute kidney injury
HP:0001945Fever
HP:0002153Hyperkalemia
HP:0002167Abnormal speech pattern
HP:0002901Hypocalcemia
HP:0002905Hyperphosphatemia
HP:0002910Elevated circulating hepatic transaminase concentration
HP:0002913Myoglobinuria
HP:0003236Elevated circulating creatine kinase concentration
HP:0003326Myalgia
HP:0003394Muscle spasm
HP:0003554Type 2 muscle fiber atrophy
HP:0003558Viral infection-induced rhabdomyolysis
HP:0003621Juvenile onset
HP:0003652Recurrent myoglobinuria
HP:0003738Exercise-induced myalgia
HP:0005216Impaired mastication
HP:0005521Disseminated intravascular coagulation
HP:0007340Lower limb muscle weakness
HP:0008305Exercise-induced myoglobinuria
HP:0008942Acute rhabdomyolysis
HP:0008997Proximal upper limb muscle weakness

GWAS associations

4 associations (top):

StudyTraitp-value
GCST006309_3Post bronchodilator percent predicted FEV1 in smoking4.000000e-06
GCST007576_18Chronotype3.000000e-13
GCST009391_453Metabolite levels6.000000e-06
GCST90026414_5Severe insulin-resistant type 2 diabetes6.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004314forced expiratory volume
EFO:0008328chronotype measurement
EFO:0010521phosphocreatine measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C564832Myoglobinuria, Acute Recurrent, Autosomal Recessive (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs10192566Efficacy3rosiglitazoneDiabetes Mellitus;Type 2

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs10192566LPIN132.751rosiglitazone

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Lipid phosphate phosphatases

CTD chemical–gene interactions

80 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, affects methylation, decreases expression, affects cotreatment, increases abundance5
Valproic Acidaffects expression, decreases expression, decreases methylation, increases expression5
Cyclosporineincreases expression, decreases expression3
bisphenol Adecreases methylation, increases expression2
entinostatdecreases expression, affects cotreatment2
bisphenol Sincreases expression2
Resveratrolaffects cotreatment, decreases expression, decreases degradation, decreases ubiquitination, affects reaction (+2 more)2
Air Pollutantsaffects expression, increases abundance, decreases expression2
Ethanolincreases expression, affects cotreatment, decreases expression, increases abundance, increases reaction2
Benzo(a)pyrenedecreases expression, affects methylation2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Aflatoxin B1affects methylation, decreases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment2
afuresertibincreases expression1
FR900359increases phosphorylation1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
uranyl acetateaffects expression1
lead acetatedecreases expression1
cobaltous chlorideincreases expression1
potassium chromate(VI)decreases expression1
aflatoxin B2increases methylation1
cupric chloridedecreases expression1
toosendanindecreases expression, decreases reaction1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
epigallocatechin gallateincreases expression1
avobenzoneincreases expression1
celastrolincreases expression1
tamibarotenedecreases expression1
benzyloxycarbonylleucyl-leucyl-leucine aldehydedecreases expression, decreases reaction, increases expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B5KAHAP1 LPIN1 (-) 2Cancer cell lineMale
CVCL_D1XEAbcam A-549 LPIN1 KOCancer cell lineMale
CVCL_XQ22HAP1 LPIN1 (-) 1Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.