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Aliases for GNPAT Gene

Aliases for GNPAT Gene

  • Glyceronephosphate O-Acyltransferase 2 3 5
  • Glycerone-Phosphate O-Acyltransferase 2 3 4
  • Acyl-CoA:Dihydroxyacetonephosphateacyltransferase 3 4
  • Dihydroxyacetone Phosphate Acyltransferase 2 3
  • EC 4 56
  • DHAP-AT 3 4
  • DAP-AT 3 4
  • DHAPAT 3 4
  • DAPAT 3 4
  • EC 2.3.1 56
  • RCDP2 3

External Ids for GNPAT Gene

Previous GeneCards Identifiers for GNPAT Gene

  • GC01P229823
  • GC01P227116
  • GC01P227850
  • GC01P228411
  • GC01P227683
  • GC01P229443
  • GC01P231376
  • GC01P201860

Summaries for GNPAT Gene

Entrez Gene Summary for GNPAT Gene

  • This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

GeneCards Summary for GNPAT Gene

GNPAT (Glyceronephosphate O-Acyltransferase) is a Protein Coding gene. Diseases associated with GNPAT include Rhizomelic Chondrodysplasia Punctata, Type 2 and Rhizomelic Chondrodysplasia Punctata. Among its related pathways are Peroxisomal lipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include receptor binding and palmitoyl-CoA hydrolase activity. An important paralog of this gene is GPAM.

Additional gene information for GNPAT Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GNPAT Gene

Genomics for GNPAT Gene

GeneHancer (GH) Regulatory Elements for GNPAT Gene

Promoters and enhancers for GNPAT Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I231240 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 574.9 +0.4 359 2.9 PKNOX1 SMAD1 FOXA2 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 GNPAT C1orf131 GC01P231282
GH01I231210 Enhancer 1.4 FANTOM5 Ensembl ENCODE 16.8 -29.2 -29237 2 ARID4B SIN3A ZNF2 IRF4 ZNF48 GLIS2 ZNF213 ELK1 ARID2 ZNF143 C1orf131 COG2 GNPAT FAM89A MIR1182 LOC644006 LOC101927604 C1orf198 SPRTN LOC149373
GH01I231527 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 5.5 +287.9 287876 3.9 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B TSNAX TSNAX-DISC1 ENSG00000233461 C1orf131 COG2 DISC1 GNPAT EXOC8 SPRTN GC01P231515
GH01I231603 Enhancer 1.1 Ensembl ENCODE 9.8 +363.0 362985 1.2 PKNOX1 ARID4B SIN3A ZNF2 ZNF213 ARID2 ZNF143 KLF13 REST TSHZ1 C1orf131 DISC1 EGLN1 COG2 GNPAT SPRTN LINC00582 GC01P231590 GC01P231591 TSNAX-DISC1
GH01I231231 Enhancer 1.1 ENCODE dbSUPER 7.6 -6.6 -6594 5.9 PKNOX1 FOXA2 MLX ZFP64 ARID4B ETS1 ZNF121 ATF7 RXRA ZHX2 GNPAT C1orf131 LOC149373
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GNPAT on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for GNPAT Gene

Genomic Locations for GNPAT Gene
36,801 bases
Plus strand

Genomic View for GNPAT Gene

Genes around GNPAT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for GNPAT Gene

Proteins for GNPAT Gene

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

    Protein Symbol:
    Recommended name:
    Dihydroxyacetone phosphate acyltransferase
    Protein Accession:
    Secondary Accessions:
    • B4DNM9
    • Q5TBH7
    • Q9BWC2

    Protein attributes for GNPAT Gene

    680 amino acids
    Molecular mass:
    77188 Da
    Quaternary structure:
    • May be part of a heterotrimeric complex composed of DAP-AT, ADAP-S and a modified form of DAP-AT.

    Alternative splice isoforms for GNPAT Gene


neXtProt entry for GNPAT Gene

Selected DME Specific Peptides for GNPAT Gene


Post-translational modifications for GNPAT Gene

  • Ubiquitination at isoforms=2113
  • Modification sites at PhosphoSitePlus

Other Protein References for GNPAT Gene

Domains & Families for GNPAT Gene

Gene Families for GNPAT Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for GNPAT Gene

Graphical View of Domain Structure for InterPro Entry



  • The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphate.
  • Belongs to the GPAT/DAPAT family.
  • The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphate.
  • Belongs to the GPAT/DAPAT family.
genes like me logo Genes that share domains with GNPAT: view

Function for GNPAT Gene

Molecular function for GNPAT Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Acyl-CoA + glycerone phosphate = CoA + acylglycerone phosphate.

Enzyme Numbers (IUBMB) for GNPAT Gene

Phenotypes From GWAS Catalog for GNPAT Gene

Gene Ontology (GO) - Molecular Function for GNPAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding IPI 20178365
GO:0008374 O-acyltransferase activity IEA --
GO:0016287 glycerone-phosphate O-acyltransferase activity TAS --
GO:0016290 palmitoyl-CoA hydrolase activity IDA 8186247
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with GNPAT: view
genes like me logo Genes that share phenotypes with GNPAT: view

Human Phenotype Ontology for GNPAT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GNPAT Gene

MGI Knock Outs for GNPAT:

miRNA for GNPAT Gene

miRTarBase miRNAs that target GNPAT

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for GNPAT Gene

Localization for GNPAT Gene

Subcellular locations from UniProtKB/Swiss-Prot for GNPAT Gene

Peroxisome membrane; Peripheral membrane protein; Matrix side. Note=Exclusively localized to the lumenal side of the peroxisomal membrane. {ECO:0000250}.

Subcellular locations from

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 GNPAT gene
Compartment Confidence
peroxisome 5
mitochondrion 3
cytoskeleton 2
nucleus 2
cytosol 2
plasma membrane 1
extracellular 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for GNPAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005777 peroxisome NAS 9459311
GO:0005778 peroxisomal membrane TAS --
GO:0005782 peroxisomal matrix TAS --
GO:0016020 membrane IEA,HDA 19946888
genes like me logo Genes that share ontologies with GNPAT: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GNPAT Gene

Pathways & Interactions for GNPAT Gene

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

UniProtKB/Swiss-Prot O15228-GNPAT_HUMAN

  • Pathway: Membrane lipid metabolism; glycerophospholipid metabolism.

Gene Ontology (GO) - Biological Process for GNPAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006650 glycerophospholipid metabolic process IEA --
GO:0006654 phosphatidic acid biosynthetic process TAS --
GO:0007416 synapse assembly IEA --
GO:0007584 response to nutrient IEA --
GO:0008152 metabolic process IEA --
genes like me logo Genes that share ontologies with GNPAT: view

No data available for SIGNOR curated interactions for GNPAT Gene

Drugs & Compounds for GNPAT Gene

(5) Drugs for GNPAT Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Hexanoyl-CoA Experimental Pharma 0
Propanoyl-CoA Experimental Pharma 0
Dihydroxyacetone phosphate Investigational Pharma 0
Coenzyme A Investigational Nutra 0

(39) Additional Compounds for GNPAT Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (E)-S-2-decenoate
  • (E)-S-2-decenoate CoA
  • (E)-S-2-decenoate Coenzyme A
  • (E)-S-2-decenoic acid
  • 2-trans-Decenoyl-CoA
  • (2E)-Dodec-2-enoyl-CoA
  • (2E)-Dodec-2-enoyl-Coenzyme A
  • 2-trans-Dodecenoyl-CoA
  • 2-trans-Dodecenoyl-Coenzyme A
  • (2E)-Hexadecenoyl-CoA
  • (2E)-Hexadecenoyl-Coenzyme A
  • trans-2-Hexadecenoyl-CoA
  • trans-2-Hexadecenoyl-Coenzyme A
  • (E)-S-2-octenoate
  • (E)-S-2-octenoate CoA
  • (E)-S-2-octenoate Coenzyme A
  • (E)-S-2-octenoic acid
  • 2,3-trans-Octenoyl coenzyme A
  • (2E)-Tetradecenoyl-CoA
  • (2E)-Tetradecenoyl-Coenzyme A
  • Trans-tetra-dec-2-enoyl-CoA
  • Trans-tetra-dec-2-enoyl-CoA.
  • Trans-tetra-dec-2-enoyl-Coenzyme A
genes like me logo Genes that share compounds with GNPAT: view

Transcripts for GNPAT Gene

Unigene Clusters for GNPAT Gene

Glyceronephosphate O-acyltransferase:
Representative Sequences:

Clone Products

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

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14a · 14b ^
SP1: - - - - -
SP2: - - - - -
SP3: - - -
SP4: - - -
SP5: - -
SP7: -
SP10: - - - -

ExUns: 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19 ^ 20a · 20b
SP1: - -

Relevant External Links for GNPAT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for GNPAT Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GNPAT Gene

This gene is overexpressed in Muscle - Skeletal (x4.2).

Protein differential expression in normal tissues from HIPED for GNPAT Gene

This gene is overexpressed in Breast (43.4) and Peripheral blood mononuclear cells (9.8).

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

Protein tissue co-expression partners for GNPAT Gene

NURSA nuclear receptor signaling pathways regulating expression of GNPAT Gene:


SOURCE GeneReport for Unigene cluster for GNPAT Gene:


Evidence on tissue expression from TISSUES for GNPAT Gene

  • Nervous system(4.9)
  • Lung(4.7)
  • Liver(2.2)
  • Kidney(2.1)
  • Skin(2.1)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • chin
  • eye
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • skull
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with GNPAT: view

No data available for mRNA Expression by UniProt/SwissProt for GNPAT Gene

Orthologs for GNPAT Gene

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

Orthologs for GNPAT Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia GNPAT 33 34
  • 99.36 (n)
(Canis familiaris)
Mammalia GNPAT 33 34
  • 89.92 (n)
(Bos Taurus)
Mammalia GNPAT 33 34
  • 88.77 (n)
(Mus musculus)
Mammalia Gnpat 33 16 34
  • 81.48 (n)
(Rattus norvegicus)
Mammalia Gnpat 33
  • 81.43 (n)
(Monodelphis domestica)
Mammalia GNPAT 34
  • 73 (a)
(Ornithorhynchus anatinus)
Mammalia GNPAT 34
  • 70 (a)
(Gallus gallus)
Aves GNPAT 33 34
  • 69.96 (n)
(Anolis carolinensis)
Reptilia GNPAT 34
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia gnpat 33
  • 63.29 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.4034 33
(Danio rerio)
Actinopterygii gnpat 33 34
  • 60.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta Dhap-at 33 34
  • 42.95 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001908 33
  • 42.74 (n)
(Caenorhabditis elegans)
Secernentea acl-7 33 34
  • 46.36 (n)
Y46G5A.21 35
  • 45 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU11282 33
  • 43.13 (n)
Species where no ortholog for GNPAT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GNPAT Gene

Gene Tree for GNPAT (if available)
Gene Tree for GNPAT (if available)

Paralogs for GNPAT Gene

Paralogs for GNPAT Gene

(1) SIMAP similar genes for GNPAT Gene using alignment to 4 proteins: Pseudogenes for GNPAT Gene

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

Variants for GNPAT Gene

Sequence variations from dbSNP and Humsavar for GNPAT Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs11122266 likely-benign, Rhizomelic chondrodysplasia punctata 231,270,961(+) G/A coding_sequence_variant, missense_variant
rs112452735 likely-benign, Rhizomelic chondrodysplasia punctata 231,241,295(+) C/G/T 5_prime_UTR_variant
rs113480953 benign, likely-benign, not specified, Rhizomelic chondrodysplasia punctata 231,241,404(+) C/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs113752547 uncertain-significance, Rhizomelic chondrodysplasia punctata 231,241,234(+) G/A/C 5_prime_UTR_variant
rs11558492 pathogenic, benign, likely-benign, Rhizomelic chondrodysplasia punctata type 2, not specified, Rhizomelic chondrodysplasia punctata, Rhizomelic chondrodysplasia punctata 2 (RCDP2) [MIM:222765] 231,272,345(+) A/G/T coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
esv3589093 CNV gain 21293372
esv3589106 CNV gain 21293372
nsv1000488 CNV gain 25217958
nsv1011066 CNV gain 25217958

Variation tolerance for GNPAT Gene

Residual Variation Intolerance Score: 25.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.25; 76.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GNPAT Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for GNPAT Gene

MalaCards: The human disease database

(11) MalaCards diseases for GNPAT Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search GNPAT in MalaCards View complete list of genes associated with diseases


  • Rhizomelic chondrodysplasia punctata 2 (RCDP2) [MIM:222765]: A form of rhizomelic chondrodysplasia punctata, a disease characterized by severely disturbed endochondral bone formation, rhizomelic shortening of femur and humerus, vertebral disorders, dwarfism, cataract, cutaneous lesions, facial dysmorphism, and severe mental retardation with spasticity. {ECO:0000269 PubMed:11152660, ECO:0000269 PubMed:21990100, ECO:0000269 PubMed:9536089}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GNPAT

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GNPAT: view

No data available for Genatlas for GNPAT Gene

Publications for GNPAT Gene

  1. Acyl-CoA:dihydroxyacetonephosphate acyltransferase: cloning of the human cDNA and resolution of the molecular basis in rhizomelic chondrodysplasia punctata type 2. (PMID: 9536089) Ofman R … Wanders RJ (Human molecular genetics 1998) 2 3 4 22 58
  2. A single nucleotide polymorphism fine mapping study of chromosome 1q42.1 reveals the vulnerability genes for schizophrenia, GNPAT and DISC1: Association with impairment of sustained attention. (PMID: 16997000) Liu YL … Hwu HG (Biological psychiatry 2006) 3 22 44 58
  3. Etherphospholipid biosynthesis and dihydroxyactetone-phosphate acyltransferase: resolution of the genomic organization of the human gnpat gene and its use in the identification of novel mutations. (PMID: 11237722) Ofman R … Wanders RJ (Biochemical and biophysical research communications 2001) 3 4 22 58
  4. Ether lipid biosynthesis: isolation and molecular characterization of human dihydroxyacetonephosphate acyltransferase. (PMID: 9459311) Thai TP … Just WW (FEBS letters 1997) 2 3 4 58
  5. Functional characterization of novel mutations in GNPAT and AGPS, causing rhizomelic chondrodysplasia punctata (RCDP) types 2 and 3. (PMID: 21990100) Itzkovitz B … Braverman N (Human mutation 2012) 3 4 58

Products for GNPAT Gene

Sources for GNPAT Gene

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