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AGPS Gene

protein-coding   GIFtS: 64
GCID: GC02P178221

Alkylglycerone Phosphate Synthase

  See AGPS-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Alkylglycerone Phosphate Synthase1 2     ADAP-S2
Aging-Associated Gene 5 Protein2 3     ADAS2
Alkyl-DHAP Synthase2 3     ADPS2
Alkylglycerone-Phosphate Synthase2 3     ALDHPSY2
EC 2.5.1.263 8     Aging-Associated Protein 52
ADHAPS2 5     Alkyldihydroxyacetonephosphate Synthase, Peroxisomal2

External Ids:    HGNC: 3271   Entrez Gene: 85402   Ensembl: ENSG000000185107   OMIM: 6030515   UniProtKB: O001163   

Export aliases for AGPS gene to outside databases

Previous GC identifers: GC02P176320 GC02P176928 GC02P178460 GC02P178083 GC02P177965 GC02P170128


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for AGPS Gene:
This gene is a member of the FAD-binding oxidoreductase/transferase type 4 family. It encodes a protein that
catalyzes the second step of ether lipid biosynthesis in which acyl-dihydroxyacetonephosphate (DHAP) is converted
to alkyl-DHAP by the addition of a long chain alcohol and the removal of a long-chain acid anion. The protein is
localized to the inner aspect of the peroxisomal membrane and requires FAD as a cofactor. Mutations in this gene
have been associated with rhizomelic chondrodysplasia punctata, type 3 and Zellweger syndrome. (provided by
RefSeq, Jul 2008)

GeneCards Summary for AGPS Gene:
AGPS (alkylglycerone phosphate synthase) is a protein-coding gene. Diseases associated with AGPS include rhizomelic chondrodysplasia punctata, type 3, and photoallergic dermatitis. GO annotations related to this gene include alkylglycerone-phosphate synthase activity and FAD binding. An important paralog of this gene is LDHD.

UniProtKB/Swiss-Prot: ADAS_HUMAN, O00116
Function: Catalyzes the exchange of an acyl for a long-chain alkyl group and the formation of the ether bond in
the biosynthesis of ether phospholipids (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the AGPS gene promoter:
         MIF-1   Evi-1   C/EBPalpha   GATA-2   AREB6   Egr-2   PPAR-gamma1   PPAR-gamma2   LyF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidAGPS promoter sequence
   Search Chromatin IP Primers for AGPS

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat AGPS


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q31.2   Ensembl cytogenetic band:  2q31.2   HGNC cytogenetic band: 2q

AGPS Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
AGPS gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P178221:  view genomic region     (about GC identifiers)

Start:
178,257,372 bp from pter      End:
178,408,564 bp from pter
Size:
151,193 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ADAS_HUMAN, O00116 (See protein sequence)
Recommended Name: Alkyldihydroxyacetonephosphate synthase, peroxisomal precursor  
Size: 658 amino acids; 72912 Da
Cofactor: FAD
Subunit: Homodimer (By similarity)
Secondary accessions: A5D8U9 Q2TU35

Explore the universe of human proteins at neXtProt for AGPS: NX_O00116

Explore proteomics data for AGPS at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys92, Lys102, Lys108, Lys456, Lys490
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for AGPS (O00116) (see all 7)
     AFPNFEQGV  YGNIEDLVV  TRASGMKKN  IIPIGGGTSV 


    See AGPS Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003650.1  
    ENSEMBL proteins: 
     ENSP00000264167   ENSP00000386688  
    Reactome Protein details: O00116

    AGPS Human Recombinant Protein Products:

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    Novus Biologicals AGPS Protein
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    Browse Sino Biological Cell Lysates
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    Cloud-Clone Corp. Proteins for AGPS

     
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    antibodies-online proteins for AGPS (4 products) 

     
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    antibodies-online antibodies for AGPS (17 products) 

    AGPS Assay Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 7):
     IPR025650 Alkyl-DHAP_Synthase
     IPR016167 FAD-bd_2_sub1
     IPR016166 FAD-bd_2
     IPR016164 FAD-linked_Oxase-like_C
     IPR006094 Oxid_FAD_bind_N

    Graphical View of Domain Structure for InterPro Entry O00116

    ProtoNet protein and cluster: O00116

    1 Blocks protein domain: IPB004113 FAD linked oxidase

    UniProtKB/Swiss-Prot: ADAS_HUMAN, O00116
    Similarity: Belongs to the FAD-binding oxidoreductase/transferase type 4 family
    Similarity: Contains 1 FAD-binding PCMH-type domain


    Find genes that share domains with AGPS           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ADAS_HUMAN, O00116
    Function: Catalyzes the exchange of an acyl for a long-chain alkyl group and the formation of the ether bond in
    the biosynthesis of ether phospholipids (By similarity)
    Catalytic activity: 1-acyl-glycerone 3-phosphate + a long-chain alcohol = an alkyl-glycerone 3-phosphate + a
    long-chain acid anion

         Enzyme Number (IUBMB): EC 2.5.1.261 2

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0008609alkylglycerone-phosphate synthase activity IDA10415121
    GO:0008762UDP-N-acetylmuramate dehydrogenase activity IEA--
    GO:0016491oxidoreductase activity ----
    GO:0016614oxidoreductase activity, acting on CH-OH group of donors ----
         
    Find genes that share ontologies with AGPS           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for AGPS:
     Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e 

         5 MGI mutant phenotypes (inferred from 1 allele(MGI details for Agps):
     endocrine/exocrine gland  homeostasis/metabolism  mortality/aging  reproductive system  vision/eye 

    Find genes that share phenotypes with AGPS           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for AGPS
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for AGPS
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    miRNA
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    miRTarBase miRNAs that target AGPS:
    hsa-mir-98-5p (MIRT027666)

    Block miRNA regulation of human, mouse, rat AGPS using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate AGPS (see all 134):
    hsa-miR-361-5p hsa-miR-520f hsa-miR-1260b hsa-miR-3653 hsa-miR-519a hsa-miR-3916 hsa-miR-510 hsa-miR-520b
    SwitchGear 3'UTR luciferase reporter plasmidAGPS 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for AGPS
    Predesigned siRNA for gene silencing in human, mouse, rat AGPS

    Gene Editing
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    GenScript: all cDNA clones in your preferred vector: AGPS (NM_003659)
    Browse Sino Biological Human cDNA Clones
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    ADAS_HUMAN, O00116: Peroxisome membrane. Note=Localized to the inner aspect of the peroxisomal membrane
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    peroxisome5
    plasma membrane3
    cytosol2
    mitochondrion2
    extracellular1
    golgi apparatus1
    nucleus1
    vacuole1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005730nucleolus IDA--
    GO:0005739mitochondrion IDA--
    GO:0005777peroxisome IDA10415121
    GO:0005778peroxisomal membrane IDA--
    GO:0005782peroxisomal matrix TAS--

    Find genes that share ontologies with AGPS           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for AGPS About    
    See pathways by source

    SuperPathContained pathways About
    1Metabolism
    Metabolism0.38
    Metabolism of lipids and lipoproteins0.37
    Metabolic pathways0.38
    2Peroxisomal lipid metabolism
    Peroxisomal lipid metabolism
    Plasmalogen biosynthesis0.00
    3Acyl chain remodelling of PC
    Ether lipid metabolism0.48
    4triacylglycerol biosynthesis
    Triacylglyceride Synthesis0.36
    5Peroxisome
    Peroxisome


    Find genes that share SuperPaths with AGPS           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for AGPS
        Triacylglyceride Synthesis

    1 Reactome Pathway for AGPS
        Plasmalogen biosynthesis


    3 Kegg Pathways  (Kegg details for AGPS):
        Ether lipid metabolism
    Metabolic pathways
    Peroxisome

    UniProtKB/Swiss-Prot: ADAS_HUMAN, O00116
    Pathway: Glycerolipid metabolism; ether lipid biosynthesis

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for AGPS
    Interactions:

        Search GeneGlobe Interaction Network for AGPS

    STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

    Selected Interacting proteins for AGPS (O001163 ENSP000002641674) via UniProtKB, MINT, STRING, and/or I2D (see all 16)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    ATG16L1Q676U53, ENSP000003758724I2D: score=3 STRING: ENSP00000375872
    GNPATO152283, ENSP000003556074I2D: score=3 STRING: ENSP00000355607
    ATG101Q9BSB43I2D: score=1 
    DDA1Q9BW613I2D: score=1 
    GBASO753233I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008610lipid biosynthetic process IDA9553082
    GO:0008611ether lipid biosynthetic process TAS--
    GO:0044255cellular lipid metabolic process TAS--
    GO:0044281small molecule metabolic process TAS--
    GO:0055114oxidation-reduction process ----

    Find genes that share ontologies with AGPS           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for AGPS (ADAS)

    10 HMDB Compounds for AGPS    About this table
    CompoundSynonyms CAS #PubMed Ids
    1-Hexadecanol1-Cetanol (see all 82)36653-82-4--
    1-Undecanol1-Hendecanol (see all 25)112-42-5--
    Arachidyl alcoholn-1-Eicosanol (see all 12)629-96-9--
    DHAP(18:0)1-Octadecanoyl-glycerone-3-phosphate (see all 3)----
    DHAP(18:0e)1-Octadecyl-glycerone-3-phosphate (see all 3)----
    Decyl alcoholRoyaltac-85 (see all 30)112-30-1--
    DodecanolLorol (see all 41)112-53-8--
    FAD1H-Purin-6-amine flavin dinucleotide (see all 21)146-14-5--
    Octadecanol1-0ctadecanol (see all 16)112-92-5--
    Tetradecanol1-Tetradecanol (see all 22)112-72-1--

    9 Novoseek inferred chemical compound relationships for AGPS gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    arabinogalactan 94 26 15346810 (2), 12177459 (2), 15675787 (1), 10588691 (1) (see all 19)
    dhap 66 3 11237722 (1), 9645070 (1), 9714777 (1)
    hydroxyproline 27.3 2 1874742 (1), 12177459 (1)
    polysaccharide 15.3 2 8727785 (1), 20129101 (1)
    threonine 8.27 2 1874742 (1), 12177459 (1)
    serine 5.21 2 1874742 (1), 12177459 (1)
    fatty acid 0 1 10972423 (1)
    alanine 0 2 1874742 (1), 12177459 (1)
    h2o2 0 2 9418056 (2)



    Find genes that share compounds with AGPS           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for AGPS gene: 
    NM_003659.3  

    Unigene Cluster for AGPS:

    Alkylglycerone phosphate synthase
    Hs.516543  [show with all ESTs]
    Unigene Representative Sequence: NM_003659
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000264167(uc002ull.2 uc010zfb.1) ENST00000409888 ENST00000460342

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate AGPS (see all 134):
    hsa-miR-361-5p hsa-miR-520f hsa-miR-1260b hsa-miR-3653 hsa-miR-519a hsa-miR-3916 hsa-miR-510 hsa-miR-520b
    SwitchGear 3'UTR luciferase reporter plasmidAGPS 3' UTR sequence
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      QuantiTect SYBR Green Assays in human, mouse, rat AGPS
      QuantiFast Probe-based Assays in human, mouse, rat AGPS

    Additional mRNA sequence: 

    AK296239.1 AK309714.1 AK314259.1 AK316240.1 AL359559.1 AY544121.1 BC141820.1 CR749699.1 
    Y09443.1 

    8 DOTS entries:

    DT.91950433  DT.95227781  DT.92421097  DT.99991754  DT.40217546  DT.426818  DT.86854796  DT.95159042 

    Selected AceView cDNA sequences (see all 224):

    AI445035 AA425188 CA447814 AI611101 CR606155 AA256583 BM802768 AI341908 
    AI954149 BU735839 N20035 AW078813 AW085059 AW592481 CA431117 CA424170 
    AI261581 AA548879 AW052134 AA599191 AA999903 BM802019 AI422186 AA804873 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for AGPS    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20a · 20b
    SP1:                                            -                                                                                                   
    SP2:                    -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -                           
    SP3:                                                                                                                                                


    ECgene alternative splicing isoforms for AGPS

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    AGPS expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTGATTTTT
    AGPS Expression
    About this image


    AGPS expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
    AGPS Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    AGPS Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.516543
        Custom PCR Arrays for AGPS
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for AGPS

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for AGPS gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Agps1 , 5 alkylglycerone phosphate synthase1, 5 90.96(n)1
    93.1(a)1
      2 (44.77 cM)5
    2280611  NM_172666.31  NP_766254.21 
     758321775 
    chicken
    (Gallus gallus)
    Aves AGPS1 alkylglycerone phosphate synthase 80.5(n)
    82.52(a)
      424135  XM_421987.4  XP_421987.3 
    lizard
    (Anolis carolinensis)
    Reptilia AGPS6
    alkylglycerone phosphate synthase
    77(a)
    1 ↔ 1
    GL343411.1(365282-434575)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia agps1 alkylglycerone phosphate synthase 76.6(n)
    81.18(a)
      100145360  NM_001126829.1  NP_001120301.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufd16e062 wufd16e06 71.59(n)   386801  BC045516.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG102531 , 3 ether lipid biosynthesis
    alkylglycerone-phosphate more3
    CG102531
    52(a)3
    55.89(n)1
    55.24(a)1
      51D33
    366691  NM_001202006.11  NP_001188935.11 
    worm
    (Caenorhabditis elegans)
    Secernentea ads-11 , 3 ads-11 53(a)3
    57.13(n)1
    54.21(a)1
      III(295713-298530)3
    1751921  NM_064784.71  NP_497185.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes DLD16
    D-lactate dehydrogenase, oxidizes D-lactate to pyr...
    17(a)
    1 → many
    IV(145826-147589) YDL174C


    ENSEMBL Gene Tree for AGPS (if available)
    TreeFam Gene Tree for AGPS (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for AGPS gene
    LDHD2  

    Find genes that share paralogs with AGPS           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for AGPS (see all 2681)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0669294
    Rhizomelic chondrodysplasia punctata 3 (RCDP3)4--see VAR_0669292 R Q mis40--------
    VAR_0258954
    Rhizomelic chondrodysplasia punctata 3 (RCDP3)4--see VAR_0258952 T I mis40--------
    VAR_0669314
    Rhizomelic chondrodysplasia punctata 3 (RCDP3)4--see VAR_0669312 T M mis40--------
    VAR_0258964
    Rhizomelic chondrodysplasia punctata 3 (RCDP3)4--see VAR_0258962 L P mis40--------
    VAR_0669304
    Rhizomelic chondrodysplasia punctata 3 (RCDP3)4--see VAR_0669302 E K mis40--------
    VAR_0050024
    Rhizomelic chondrodysplasia punctata 3 (RCDP3)4--see VAR_0050022 R H mis40--------
    rs775980141,2
    C--170141328(+) GGAACT/-TTTAA 1 -- int12Minor allele frequency- -:0.00NA CSA 4
    rs113053521,2
    C--170144870(+) TTGAC-/TTTTTT 1 -- int1 trp32Minor allele frequency- T:0.00NA CSA 4
    rs777166031,2
    C,F--177644438(+) TGTCAA/GTCAGG 1 -- us2k12Minor allele frequency- G:0.08WA NA 238
    rs1839890101,2
    --177644548(+) ATTCTC/GTTTTT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for AGPS (178257372 - 178408564 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for AGPS (see all 11):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2084314CNV Deletion18987734
    esv2721181CNV Deletion23290073
    esv2665427CNV Deletion23128226
    esv2660495CNV Deletion23128226
    esv2433824CNV Deletion19546169
    esv1528872CNV Insertion17803354
    esv1690590CNV Insertion17803354
    esv267553CNV Insertion20981092
    nsv507053CNV Insertion20534489
    esv272459CNV Insertion20981092

    Human Gene Mutation Database (HGMD): AGPS
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing AGPS
    DNA2.0 Custom Variant and Variant Library Synthesis for AGPS

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 603051   
    OMIM disorders: 600121  
    UniProtKB/Swiss-Prot: ADAS_HUMAN, O00116
  • Rhizomelic chondrodysplasia punctata 3 (RCDP3) [MIM:600121]: A disease characterized by rhizomelic
    shortening of femur and humerus, vertebral disorders, cataract, cutaneous lesions and severe mental retardation.
    Note=The disease is caused by mutations affecting the gene represented in this entry

  • 5 diseases for AGPS:    
    About MalaCards
    rhizomelic chondrodysplasia punctata, type 3    photoallergic dermatitis    rhizomelic chondrodysplasia punctata    rhizomelic chondrodysplasia punctata type 2
    chondrodysplasia

    3 diseases from the University of Copenhagen DISEASES database for AGPS:
    Rhizomelic chondrodysplasia punctata     Acquired immunodeficiency syndrome     Photoallergic dermatitis

    Find genes that share disorders with AGPS           About GenesLikeMe

    3 Novoseek inferred disease relationships for AGPS gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chondrodysplasia punctata rhizomelic 86.1 1 10683770 (1)
    peroxisomal disorders 68.4 2 10683770 (1), 10384985 (1)
    zellweger syndrome 68.3 1 10683770 (1)

    Genetic Association Database (GAD): AGPS
    Human Genome Epidemiology (HuGE) Navigator: AGPS (2 documents)

    Export disorders for AGPS gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for AGPS gene, integrated from 10 sources (see all 94):
    (articles sorted by number of sources associating them with AGPS)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Alkyl-dihydroxyacetonephosphate synthase. Fate in peroxisome biogenesis disorders and identification of the point mutation underlying a single enzyme deficiency. (PubMed id 9553082)1, 2, 3 de Vet E.C.J.M....van den Bosch H. (J. Biol. Chem. 1998)
    2. Nucleotide sequence of human alkyl-dihydroxyacetonephosphate synthase cDNA reveals the presence of a peroxisomal targeting signal 2. (PubMed id 9187299)1, 2, 3 de Vet E.C.J.M.... van den Bosch H. (Biochim. Biophys. Acta 1997)
    3. Functional characterization of novel mutations in GNPAT and AGPS, causing rhizomelic chondrodysplasia punctata (RCDP) types 2 and 3. (PubMed id 21990100)1, 2 Itzkovitz B.... Braverman N. (Hum. Mutat. 2012)
    4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    6. Impaired membrane traffic in defective ether lipid biosynthesis. (PubMed id 11152660)1, 2 Thai T.P....Just W.W. (Hum. Mol. Genet. 2001)
    7. Stability of alkyl-dihydroxyacetonephosphate synthase in human control and peroxisomal disorder fibroblasts. (PubMed id 10683770)1, 9 Biermann J....van den Bosch H. (IUBMB Life 1999)
    8. Immunological analyses of alkyl-dihydroxyacetone-phosphate synthase in human peroxisomal disorders. (PubMed id 10384985)1, 9 Biermann J....van den Bosch H. (Eur. J. Cell Biol. 1999)
    9. Immunological localization and tissue distribution of alkyldihydroxyacetonephosphate synthase and deficiency of the enzyme in peroxisomal disorders. (PubMed id 9266692)1, 9 de Vet E.C....van den Bosch H. (Eur. J. Biochem. 1997)
    10. Profiling of Parkin-binding partners using tandem affinity purification. (PubMed id 24244333)1 Zanon A....Pichler I. (PLoS ONE 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 8540 HGNC: 327 AceView: AGPS Ensembl:ENSG00000018510 euGenes: HUgn8540
    ECgene: AGPS Kegg: 8540 H-InvDB: AGPS

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for AGPS Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=AGPS[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for AGPS gene:
    Search GeneIP for patents involving AGPS

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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