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] See more...

Aliases for GNPAT Gene

Aliases for GNPAT Gene

  • Glyceronephosphate O-Acyltransferase 2 3 5
  • Dihydroxyacetone Phosphate Acyltransferase 2 3 4
  • Glycerone-Phosphate O-Acyltransferase 2 3 4
  • Acyl-CoA:Dihydroxyacetonephosphateacyltransferase 3 4
  • EC 2.3.1.42 4 54
  • DHAP-AT 3 4
  • DAP-AT 3 4
  • DHAPAT 3 4
  • DAPAT 3 4
  • EC 2.3.1 54
  • 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 Peroxisome. Gene Ontology (GO) annotations related to this gene include signaling 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 Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GNPAT Gene

Genomics for GNPAT Gene

GeneHancer (GH) Regulatory Elements for GNPAT Gene

Promoters and enhancers for GNPAT Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GNPAT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GNPAT gene promoter:
  • aMEF-2
  • AML1a
  • AREB6
  • Cdc5
  • Ik-3
  • LCR-F1
  • LyF-1
  • MEF-2A
  • Pax-4a

Genomic Locations for GNPAT Gene

Genomic Locations for GNPAT Gene
chr1:231,241,173-231,277,973
(GRCh38/hg38)
Size:
36,801 bases
Orientation:
Plus strand
chr1:231,376,919-231,413,719
(GRCh37/hg19)
Size:
36,801 bases
Orientation:
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:
    O15228-GNPAT_HUMAN
    Recommended name:
    Dihydroxyacetone phosphate acyltransferase
    Protein Accession:
    O15228
    Secondary Accessions:
    • B4DNM9
    • Q5TBH7
    • Q9BWC2

    Protein attributes for GNPAT Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

neXtProt entry for GNPAT Gene

Selected DME Specific Peptides for GNPAT Gene

O15228:
  • LLPSHRSYIDFLMLSF
  • LFKPFVESYQ
  • FLEGTRSR

Post-translational modifications for GNPAT Gene

  • Ubiquitination at Lys113
  • 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

Suggested Antigen Peptide Sequences for GNPAT Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ53146, highly similar to Dihydroxyacetone phosphate acyltransferase(EC 2.3.1.42) (B4DNM9_HUMAN)
  • Glycerone-phosphate O-acyltransferase (GNPAT_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15228

UniProtKB/Swiss-Prot:

GNPAT_HUMAN :
  • 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.
Domain:
  • The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphate.
Family:
  • 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:
Reaction=an acyl-CoA + dihydroxyacetone phosphate = a 1-acylglycerone 3-phosphate + CoA; Xref=Rhea:RHEA:17657, ChEBI:CHEBI:57287, ChEBI:CHEBI:57534, ChEBI:CHEBI:57642, ChEBI:CHEBI:58342; EC=2.3.1.42;.

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: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 --
GO:0016746 transferase activity, transferring acyl groups 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:

Animal Model Products

CRISPR Products

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

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GNPAT gene
Compartment Confidence
peroxisome 5
cytosol 4
mitochondrion 3
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1
plasma membrane 0
extracellular 0
golgi apparatus 0

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,IBA --
GO:0005782 peroxisomal matrix TAS --
GO:0005829 cytosol TAS --
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:0006625 protein targeting to peroxisome TAS --
GO:0006631 fatty acid metabolic process IBA 21873635
GO:0006650 glycerophospholipid metabolic process IEA --
GO:0006654 phosphatidic acid biosynthetic process TAS --
GO:0007416 synapse assembly 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
(2E)-Decenoyl-CoA
  • (e)-S-2-Decenoate
  • (e)-S-2-Decenoate CoA
  • (e)-S-2-Decenoate coenzyme A
  • (e)-S-2-Decenoic acid
  • 2-trans-Decenoyl-CoA
10018-95-8
(2E)-Dodecenoyl-CoA
1066-12-2
(2E)-Hexadecenoyl-CoA
  • (e)-C16:1 N-14-CoA
  • (e)-Hexadec-2-enoyl-CoA tetraanion
  • (e)-Hexadec-2-enoyl-coenzyme A tetraanion
  • (e)-Hexadec-2-enoyl-coenzyme A(4-)
  • trans-2-Hexadecenoyl-CoA(4-)
4460-95-1
(2E)-Octenoyl-CoA
  • (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
10018-94-7
(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
  • trans-Tetra-dec-2-enoyl-coenzyme A.
38795-33-4
genes like me logo Genes that share compounds with GNPAT: view

Transcripts for GNPAT Gene

mRNA/cDNA for GNPAT Gene

CRISPR Products

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: - -
SP6:
SP7: -
SP8:
SP9:
SP10: - - - -
SP11:
SP12:

ExUns: 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19 ^ 20a · 20b
SP1: - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for GNPAT Gene

GeneLoc Exon Structure for
GNPAT
ECgene alternative splicing isoforms for
GNPAT

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, MaxQB, and MOPED for GNPAT Gene



Protein tissue co-expression partners for GNPAT Gene

NURSA nuclear receptor signaling pathways regulating expression of GNPAT Gene:

GNPAT

SOURCE GeneReport for Unigene cluster for GNPAT Gene:

Hs.498028

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
Systems:
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • chin
  • eye
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • skull
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • 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
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia GNPAT 33 32
  • 99.36 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GNPAT 33 32
  • 89.92 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GNPAT 33 32
  • 88.77 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gnpat 17 33 32
  • 81.48 (n)
rat
(Rattus norvegicus)
Mammalia Gnpat 32
  • 81.43 (n)
oppossum
(Monodelphis domestica)
Mammalia GNPAT 33
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GNPAT 33
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves GNPAT 33 32
  • 69.96 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GNPAT 33
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gnpat 32
  • 63.29 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.4034 32
zebrafish
(Danio rerio)
Actinopterygii gnpat 33 32
  • 60.21 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Dhap-at 33 32
  • 42.95 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001908 32
  • 42.74 (n)
worm
(Caenorhabditis elegans)
Secernentea acl-7 33 32
  • 46.36 (n)
OneToOne
Y46G5A.21 34
  • 45 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU11282 32
  • 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

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

Paralogs for GNPAT Gene

Paralogs for GNPAT Gene

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

  • GNPAT_HUMAN
  • B4DNM9_HUMAN
  • Q5TBH6_HUMAN
  • Q5TBH8_HUMAN

Pseudogenes.org 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, benign, Rhizomelic chondrodysplasia punctata, not specified, not provided, - 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, not provided, 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)
GNPAT
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GNPAT

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

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

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

UniProtKB/Swiss-Prot

GNPAT_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 23 56
  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 23 43 56
  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 23 56
  4. Ether lipid biosynthesis: isolation and molecular characterization of human dihydroxyacetonephosphate acyltransferase. (PMID: 9459311) Thai TP … Just WW (FEBS letters 1997) 2 3 4 56
  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 56

Products for GNPAT Gene

Sources for GNPAT Gene