Gene Gene information from NCBI Gene database.
Entrez ID 8443
Gene name Glyceronephosphate O-acyltransferase
Gene symbol GNPAT
Synonyms (NCBI Gene)
DAP-ATDAPATDHAPATRCDP2
Chromosome 1
Chromosome location 1q42.2
Summary 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 isoform
SNPs SNP information provided by dbSNP.
10
SNP ID Visualize variation Clinical significance Consequence
rs121434439 G>A Pathogenic Missense variant, coding sequence variant
rs121434440 C>T Pathogenic Missense variant, coding sequence variant
rs777894746 C>T Likely-pathogenic Coding sequence variant, stop gained
rs1442079596 C>T Likely-pathogenic Coding sequence variant, missense variant
rs1558334598 ->A Likely-pathogenic Frameshift variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
115
miRTarBase ID miRNA Experiments Reference
MIRT030370 hsa-miR-24-3p Microarray 19748357
MIRT043262 hsa-miR-331-3p CLASH 23622248
MIRT1025045 hsa-miR-1208 CLIP-seq
MIRT1025046 hsa-miR-1236 CLIP-seq
MIRT1025047 hsa-miR-1266 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
33
GO ID Ontology Definition Evidence Reference
GO:0003824 Function Catalytic activity IEA
GO:0005777 Component Peroxisome IDA 15687349
GO:0005777 Component Peroxisome IEA
GO:0005777 Component Peroxisome NAS 9459311
GO:0005778 Component Peroxisomal membrane HDA 21525035
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
602744 4416 ENSG00000116906
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O15228
Protein name Dihydroxyacetone phosphate acyltransferase (DAP-AT) (DAPAT) (DHAP-AT) (EC 2.3.1.42) (Acyl-CoA:dihydroxyacetonephosphateacyltransferase) (Glycerone-phosphate O-acyltransferase)
Protein function Dihydroxyacetonephosphate acyltransferase catalyzing the first step in the biosynthesis of plasmalogens, a subset of phospholipids that differ from other glycerolipids by having an alkyl chain attached through a vinyl ether linkage at the sn-1 p
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01553 Acyltransferase 138 283 Acyltransferase Family
Sequence
MESSSSSNSYFSVGPTSPSAVVLLYSKELKKWDEFEDILEERRHVSDLKFAMKCYTPLVY
KGITPCKPIDIKCSVLNSEEIHYVIKQLSKESLQSVDVLREEVSEILDEMSHKLRLGAIR
FCAFTLSKVFKQIFSKVCVNEEGIQKLQRAIQEHPVVLLPSHRSYIDFLMLSFLLYNYDL
PVPVIAAGMDFLGMKMVGELLRMSGAFFMRRTFGGNKLYWAVFSEYVKTMLRNGYAPVEF
FLEGTRSRSAKTLTPKFGLLNIVMEPFFKREVFDTYLVPISIS
YDKILEETLYVYELLGV
PKPKESTTGLLKARKILSENFGSIHVYFGDPVSLRSLAAGRMSRSSYNLVPRYIPQKQSE
DMHAFVTEVAYKMELLQIENMVLSPWTLIVAVLLQNRPSMDFDALVEKTLWLKGLTQAFG
GFLIWPDNKPAEEVVPASILLHSNIASLVKDQVILKVDSGDSEVVDGLMLQHITLLMCSA
YRNQLLNIFVRPSLVAVALQMTPGFRKEDVYSCFRFLRDVFADEFIFLPGNTLKDFEEGC
YLLCKSEAIQVTTKDILVTEKGNTVLEFLVGLFKPFVESYQIICKYLLSEEEDHFSEEQY
LAAVRKFTSQLLDQGTSQCYDVLSSDVQKNALAACVRLGVVEKKKINNNCIFNVNEPATT
KLEEMLGCKTPIGKPATAKL
Sequence length 680
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Glycerophospholipid metabolism
Peroxisome
  Synthesis of PA
Plasmalogen biosynthesis
Peroxisomal protein import
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
21
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
GNPAT-related disorder Likely pathogenic rs777894746 RCV003411694
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rhizomelic chondrodysplasia punctata Pathogenic; Likely pathogenic rs2102825068, rs121434440 RCV001526991
RCV003234895
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rhizomelic chondrodysplasia punctata type 2 Pathogenic; Likely pathogenic rs745869264, rs1685194348, rs749069446, rs1283169932, rs121434439, rs121434440, rs1558334625, rs1571950208, rs1571957148, rs2527028635, rs1185964193, rs2527044284, rs2527024495, rs2526967162, rs2527024941
View all (22 more)
RCV001844353
RCV001782213
RCV004571718
RCV004571191
RCV000007243
View all (32 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Likely benign; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Likely benign; Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CHONDRODYSPLASIA PUNCTATA, RHIZOMELIC Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Attention Deficit Disorder Attention Deficit Hyperactivity Disorder BEFREE 16997000
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder BEFREE 16997000, 30759250
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism BEFREE 30759250
★☆☆☆☆
Found in Text Mining only
Byzanthine arch palate High palate HPO_DG
★☆☆☆☆
Found in Text Mining only
Cataract Cataract HPO_DG
★☆☆☆☆
Found in Text Mining only
Chondrodysplasia Punctata Rhizomelic Chondrodysplasia Pubtator 10553003 Inhibit
★☆☆☆☆
Found in Text Mining only
Chondrodysplasia Punctata Rhizomelic Chondrodysplasia Pubtator 25439727, 34110102, 8466247 Associate
★☆☆☆☆
Found in Text Mining only
Chondrodysplasia Punctata, Rhizomelic Chondrodysplasia Punctata BEFREE 20583171, 21990100, 22008564, 25439727
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Chondrodysplasia Punctata, Rhizomelic Chondrodysplasia Punctata GENOMICS_ENGLAND_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Chondrodysplasia punctata, X-linked dominant type Chondrodysplasia Punctata BEFREE 8832947
★☆☆☆☆
Found in Text Mining only