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Aliases for GMDS Gene

Aliases for GMDS Gene

  • GDP-Mannose 4,6-Dehydratase 2 3 5
  • Short Chain Dehydrogenase/Reductase Family 3E, Member 1 2 3
  • GDP-D-Mannose Dehydratase 3 4
  • EC 4.2.1.47 4 61
  • GMD 3 4
  • GDP-Mannose 4,6 Dehydratase 3
  • SDR3E1 3

External Ids for GMDS Gene

Previous GeneCards Identifiers for GMDS Gene

  • GC06M001609
  • GC06M001570
  • GC06M001571
  • GC06M001572
  • GC06M001493

Summaries for GMDS Gene

Entrez Gene Summary for GMDS Gene

  • GDP-mannose 4,6-dehydratase (GMD; EC 4.2.1.47) catalyzes the conversion of GDP-mannose to GDP-4-keto-6-deoxymannose, the first step in the synthesis of GDP-fucose from GDP-mannose, using NADP+ as a cofactor. The second and third steps of the pathway are catalyzed by a single enzyme, GDP-keto-6-deoxymannose 3,5-epimerase, 4-reductase, designated FX in humans (MIM 137020).[supplied by OMIM, Aug 2009]

GeneCards Summary for GMDS Gene

GMDS (GDP-Mannose 4,6-Dehydratase) is a Protein Coding gene. Diseases associated with GMDS include Congenital Disorder Of Glycosylation, Type Iic and Leukocyte Adhesion Deficiency. Among its related pathways are Transport to the Golgi and subsequent modification and Amino sugar and nucleotide sugar metabolism. GO annotations related to this gene include coenzyme binding and NADP+ binding.

UniProtKB/Swiss-Prot for GMDS Gene

  • Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.

Gene Wiki entry for GMDS Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GMDS Gene

Genomics for GMDS Gene

Regulatory Elements for GMDS Gene

Enhancers for GMDS Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F002274 0.2 ENCODE 20.7 -29.8 -29771 1.5 BHLHE40 GMDS GMDS-AS1 GC06P002272 GC06P002289
GH06F002221 0.9 Ensembl ENCODE 17 +23.4 23392 1.4 SOX13 PKNOX1 ASH2L CEBPG RBBP5 ZSCAN9 SCRT2 PRDM10 GATAD2A TEAD1 GMDS GMDS-AS1 LOC105379642
GH06F002257 0.8 ENCODE 10.9 -13.2 -13165 3.5 ELF3 ATF1 MLX ZFP64 ARID4B THRB RAD21 ZBTB40 RARA YY1 GMDS GMDS-AS1 ENSG00000272465 GC06P002272
GH06F002351 0.2 ENCODE 9.7 -106.5 -106471 0.6 FOS GMDS LINC01600 LOC105374885 GMDS-AS1 GC06M002323 GC06P002345
GH06F002244 0.5 ENCODE 9.6 +0.0 3 2.8 HDGF CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 YY1 ZNF207 FOS KLF13 FAM136BP ENSG00000228365 RN7SL352P GMDS GMDS-AS1 LOC105379642
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around GMDS on UCSC Golden Path with GeneCards custom track

Promoters for GMDS Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001208968 292 2801 HDGF MLX CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF207

Genomic Location for GMDS Gene

Chromosome:
6
Start:
1,623,800 bp from pter
End:
2,245,692 bp from pter
Size:
621,893 bases
Orientation:
Minus strand

Genomic View for GMDS Gene

Genes around GMDS on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for GMDS Gene

Proteins for GMDS Gene

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

    Protein Symbol:
    O60547-GMDS_HUMAN
    Recommended name:
    GDP-mannose 4,6 dehydratase
    Protein Accession:
    O60547
    Secondary Accessions:
    • E9PI88
    • O75357
    • Q5T954
    • Q6FH09
    • Q9UGZ3
    • Q9UJK9

    Protein attributes for GMDS Gene

    Size:
    372 amino acids
    Molecular mass:
    41950 Da
    Cofactor:
    Name=NADP(+); Xref=ChEBI:CHEBI:58349;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC24501.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for GMDS Gene

    Alternative splice isoforms for GMDS Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GMDS Gene

Post-translational modifications for GMDS Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for GMDS

Domains & Families for GMDS Gene

Gene Families for GMDS Gene

Suggested Antigen Peptide Sequences for GMDS Gene

Graphical View of Domain Structure for InterPro Entry

O60547

UniProtKB/Swiss-Prot:

GMDS_HUMAN :
  • Belongs to the NAD(P)-dependent epimerase/dehydratase family. GDP-mannose 4,6-dehydratase subfamily.
Family:
  • Belongs to the NAD(P)-dependent epimerase/dehydratase family. GDP-mannose 4,6-dehydratase subfamily.
genes like me logo Genes that share domains with GMDS: view

Function for GMDS Gene

Molecular function for GMDS Gene

GENATLAS Biochemistry:
GDP-mannose 4,6-dehydratase homolog,first enzyme in the pathway,converting GDP-mannose to GDP-fructose
UniProtKB/Swiss-Prot CatalyticActivity:
GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H(2)O.
UniProtKB/Swiss-Prot Function:
Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.

Enzyme Numbers (IUBMB) for GMDS Gene

Gene Ontology (GO) - Molecular Function for GMDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0008446 GDP-mannose 4,6-dehydratase activity IGI,TAS --
GO:0016829 lyase activity IEA --
GO:0042802 identical protein binding IPI 16189514
GO:0070401 NADP+ binding IDA 9525924
genes like me logo Genes that share ontologies with GMDS: view
genes like me logo Genes that share phenotypes with GMDS: view

Animal Models for GMDS Gene

MGI Knock Outs for GMDS:
  • Gmds tm1a(KOMP)Wtsi

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for GMDS Gene

Localization for GMDS Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for GMDS Gene COMPARTMENTS Subcellular localization image for GMDS gene
Compartment Confidence
cytosol 5
extracellular 5
cytoskeleton 2
mitochondrion 2
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for GMDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IC 9525924
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 19199708
genes like me logo Genes that share ontologies with GMDS: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for GMDS Gene

Pathways & Interactions for GMDS Gene

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

UniProtKB/Swiss-Prot O60547-GMDS_HUMAN

  • Pathway: Nucleotide-sugar biosynthesis; GDP-L-fucose biosynthesis via de novo pathway; GDP-L-fucose from GDP-alpha-D-mannose: step 1/2.

Gene Ontology (GO) - Biological Process for GMDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007219 Notch signaling pathway ISS --
GO:0019673 GDP-mannose metabolic process IEA,IGI 9603974
GO:0042351 de novo GDP-L-fucose biosynthetic process IEA --
genes like me logo Genes that share ontologies with GMDS: view

No data available for SIGNOR curated interactions for GMDS Gene

Drugs & Compounds for GMDS Gene

(21) Drugs for GMDS Gene - From: DrugBank, ClinicalTrials, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
leucovorin Approved Pharma 1089
Levoleucovorin Approved Pharma 711
Folic Acid Approved, Vet_approved Nutra 4279
Water Approved Pharma 0
Guanosine diphosphate Experimental Pharma Target 0

(7) Additional Compounds for GMDS Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
GDP-4-Dehydro-6-deoxy-D-mannose
  • GDP-4-Dehydro-6-deoxy-D-mannose
  • GDP-4-Dehydro-6-deoxy-D-talose
  • GDP-4-Dehydro-D-rhamnose
  • GDP-4-Keto-6-D-deoxymannose
  • GDP-4-Keto-6-deoxy-D-mannose
18186-48-6
Guanosine diphosphate mannose
  • GDP Mannose
  • GDP-D-Mannose
  • GDP-Glucose
  • GDP-Mannose
  • Guanosine Diphosphate Mannose
3123-67-9
NADP
  • Adenine-nicotinamide dinucleotide phosphate
  • b-NADP
  • b-Nicotinamide adenine dinucleotide phosphate
  • b-TPN
  • beta-NADP
53-59-8
genes like me logo Genes that share compounds with GMDS: view

Transcripts for GMDS Gene

Unigene Clusters for GMDS Gene

GDP-mannose 4,6-dehydratase:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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

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

Relevant External Links for GMDS Gene

GeneLoc Exon Structure for
GMDS
ECgene alternative splicing isoforms for
GMDS

Expression for GMDS Gene

mRNA expression in normal human tissues for GMDS Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Colon - Transverse (x5.3).

Protein differential expression in normal tissues from HIPED for GMDS Gene

This gene is overexpressed in Skin (16.4) and Salivary gland (12.3).

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



Protein tissue co-expression partners for GMDS Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GMDS Gene:

GMDS

SOURCE GeneReport for Unigene cluster for GMDS Gene:

Hs.144496
genes like me logo Genes that share expression patterns with GMDS: view

Primer Products

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

Orthologs for GMDS Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GMDS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GMDS 35
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GMDS 35
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gmds 34 16 35
  • 89.7 (n)
rat
(Rattus norvegicus)
Mammalia Gmds 34
  • 89.34 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GMDS 35
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia GMDS 34 35
  • 88.75 (n)
cow
(Bos Taurus)
Mammalia GMDS 34 35
  • 86.11 (n)
chicken
(Gallus gallus)
Aves GMDS 34 35
  • 82.27 (n)
lizard
(Anolis carolinensis)
Reptilia GMDS 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gmds 34
  • 78.68 (n)
LOC394693 34
zebrafish
(Danio rerio)
Actinopterygii gmds 34 35
  • 74.21 (n)
-- 34
fruit fly
(Drosophila melanogaster)
Insecta Gmd 36 34 35
  • 66.11 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006783 34
  • 64.62 (n)
worm
(Caenorhabditis elegans)
Secernentea F56H6.5 36
  • 66 (a)
gmd-2 34 35
  • 63.15 (n)
C53B4.7a 36
  • 62 (a)
C53B4.7b 36
  • 62 (a)
bre-1 35
  • 59 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons MUR1 34
  • 58.51 (n)
rice
(Oryza sativa)
Liliopsida Os06g0137700 34
  • 56.93 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5147 35
  • 68 (a)
OneToOne
Species where no ortholog for GMDS was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • bread mold (Neurospora crassa)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GMDS Gene

ENSEMBL:
Gene Tree for GMDS (if available)
TreeFam:
Gene Tree for GMDS (if available)

Paralogs for GMDS Gene

No data available for Paralogs for GMDS Gene

Variants for GMDS Gene

Sequence variations from dbSNP and Humsavar for GMDS Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1004779 -- 2,093,198(-) CTCAA(C/T)AAGAA intron-variant
rs1006019 -- 2,174,952(-) TGAAG(A/G)CTTCT intron-variant
rs1006883 -- 1,628,124(-) CAGCC(A/G)AACAT intron-variant
rs10080724 -- 1,781,105(+) ACACC(A/G)AGAAG intron-variant
rs1013064 -- 1,731,458(+) ctgaa(A/G)cactt intron-variant

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

Variant ID Type Subtype PubMed ID
dgv3253n106 CNV deletion 24896259
dgv3254n106 CNV duplication 24896259
dgv3442e59 CNV duplication 20981092
dgv367n21 CNV loss 19592680
dgv368n21 CNV loss 19592680
dgv982e201 CNV deletion 23290073
dgv992n67 CNV gain 20364138
esv1079731 CNV deletion 17803354
esv1276389 CNV insertion 17803354
esv1420337 CNV insertion 17803354
esv1680278 CNV insertion 17803354
esv1726903 CNV insertion 17803354
esv1790287 CNV insertion 17803354
esv1975015 CNV deletion 18987734
esv2088179 CNV deletion 18987734
esv2309535 CNV deletion 18987734
esv2501581 CNV insertion 19546169
esv25056 CNV gain 19812545
esv2522446 CNV deletion 19546169
esv25592 CNV loss 19812545
esv2661700 CNV deletion 23128226
esv2672691 CNV deletion 23128226
esv2678398 CNV deletion 23128226
esv2731438 CNV deletion 23290073
esv2731440 CNV deletion 23290073
esv2731441 CNV deletion 23290073
esv2731442 CNV deletion 23290073
esv2731443 CNV deletion 23290073
esv2731444 CNV deletion 23290073
esv2731447 CNV deletion 23290073
esv2731448 CNV deletion 23290073
esv2731449 CNV deletion 23290073
esv2731451 CNV deletion 23290073
esv2731452 CNV deletion 23290073
esv2731453 CNV deletion 23290073
esv2731454 CNV deletion 23290073
esv2731455 CNV deletion 23290073
esv2731456 CNV deletion 23290073
esv2763525 CNV loss 21179565
esv2763526 CNV loss 21179565
esv3305375 CNV mobile element insertion 20981092
esv3307631 CNV mobile element insertion 20981092
esv3330791 CNV duplication 20981092
esv3333870 CNV duplication 20981092
esv3340170 CNV insertion 20981092
esv3346789 CNV insertion 20981092
esv3349773 CNV duplication 20981092
esv3353333 CNV duplication 20981092
esv3391213 CNV duplication 20981092
esv3402980 CNV insertion 20981092
esv3567156 CNV deletion 23714750
esv3567164 CNV deletion 23714750
esv3607894 CNV loss 21293372
esv3607897 CNV loss 21293372
esv3607898 CNV loss 21293372
esv3607899 CNV loss 21293372
esv3607900 CNV gain 21293372
esv3607901 CNV gain 21293372
esv3607903 CNV loss 21293372
esv3607905 CNV loss 21293372
esv3607906 CNV loss 21293372
esv5149 CNV loss 18987735
esv5411 CNV loss 18987735
esv6042 CNV loss 19470904
esv994377 CNV deletion 20482838
esv994574 CNV deletion 20482838
nsv1016859 CNV gain 25217958
nsv1019895 CNV loss 25217958
nsv1026678 CNV gain 25217958
nsv1032149 CNV loss 25217958
nsv1072592 CNV deletion 25765185
nsv1076594 CNV duplication 25765185
nsv1125868 CNV tandem duplication 24896259
nsv1133369 CNV tandem duplication 24896259
nsv1142636 CNV deletion 24896259
nsv1145087 CNV deletion 24896259
nsv1148622 CNV deletion 26484159
nsv1148720 CNV deletion 26484159
nsv1152080 CNV duplication 26484159
nsv1153023 CNV deletion 26484159
nsv1153825 CNV deletion 26484159
nsv1161332 CNV duplication 26073780
nsv349305 CNV deletion 16902084
nsv350018 CNV deletion 16902084
nsv462611 CNV loss 19166990
nsv474186 CNV novel sequence insertion 20440878
nsv474513 CNV novel sequence insertion 20440878
nsv516745 CNV loss 19592680
nsv5175 CNV insertion 18451855
nsv519587 CNV loss 19592680
nsv522608 CNV gain 19592680
nsv527735 CNV loss 19592680
nsv528906 CNV gain 19592680
nsv600808 CNV loss 21841781
nsv600809 CNV loss 21841781
nsv830573 CNV gain 17160897
nsv950757 CNV duplication 24416366
nsv950758 CNV deletion 24416366
nsv950759 CNV duplication 24416366
nsv956548 CNV deletion 24416366

Variation tolerance for GMDS Gene

Residual Variation Intolerance Score: 24.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.46; 10.03% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GMDS Gene

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

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

Disorders for GMDS Gene

MalaCards: The human disease database

(2) MalaCards diseases for GMDS Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
congenital disorder of glycosylation, type iic
  • leukocyte adhesion deficiency type ii
leukocyte adhesion deficiency
  • leukocyte adhesion deficiency, type i
- elite association - COSMIC cancer census association via MalaCards
Search GMDS in MalaCards View complete list of genes associated with diseases

Relevant External Links for GMDS

Genetic Association Database (GAD)
GMDS
Human Genome Epidemiology (HuGE) Navigator
GMDS
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GMDS
genes like me logo Genes that share disorders with GMDS: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GMDS Gene

Publications for GMDS Gene

  1. Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro. (PMID: 9525924) Sullivan F.X. … Cumming D.A. (J. Biol. Chem. 1998) 2 3 4 64
  2. Molecular cloning and expression of GDP-D-mannose-4,6-dehydratase, a key enzyme for fucose metabolism defective in Lec13 cells. (PMID: 9603974) Ohyama C. … Fukuda M. (J. Biol. Chem. 1998) 3 4 22 64
  3. Discovery and replication of dopamine-related gene effects on caudate volume in young and elderly populations (N=1198) using genome-wide search. (PMID: 21502949) Stein J.L. … Thompson P.M. (Mol. Psychiatry 2011) 3 46 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. (PMID: 19027726) Persson B. … Oppermann U. (Chem. Biol. Interact. 2009) 2 3 64

Products for GMDS Gene

Sources for GMDS Gene

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