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    TGDS TDP-glucose 4,6-dehydratase [ Homo sapiens (human) ]

    Gene ID: 23483, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TGDSprovided by HGNC
    Official Full Name
    TDP-glucose 4,6-dehydrataseprovided by HGNC
    Primary source
    HGNC:HGNC:20324
    See related
    Ensembl:ENSG00000088451 MIM:616146; AllianceGenome:HGNC:20324
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TDPGD; SDR2E1; CATMANS
    Summary
    The protein encoded by this gene is a member of the short-chain dehydrogenases/reductases (SDR) superfamily, and is thought to contain a nicotinamide adenine dinucleotide (NAD) binding domain. This large SDR family of enzymes is involved in the metabolism of a variety of compounds, including prostaglandins, retinoids, lipids, steroid hormones, and xenobiotics. Mutations in this gene have been associated with Catel-Manzke syndrome, which is characterized by Pierre Robin sequence, and radial deviation of the index finger due to the presence of an accessory bone between the index finger and its proximal phalanx. Pierre Robin sequence is defined by an undersized jaw, backwards displacement of the tongue base that causes an obstruction of the airways, and can also be associated with a cleft palate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
    Expression
    Ubiquitous expression in thyroid (RPKM 7.9), liver (RPKM 6.7) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See TGDS in Genome Data Viewer
    Location:
    13q32.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (94574054..94596273, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (93777561..93799780, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (95226308..95248406, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene dopachrome tautomerase Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:95143673-95144872 Neighboring gene uncharacterized LOC124903191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5434 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:95202297-95202796 Neighboring gene tRNA-Phe (anticodon GAA) 1-5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7866 Neighboring gene Sharpr-MPRA regulatory region 4462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:95256499-95256998 Neighboring gene G protein-coupled receptor 180 Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 pseudogene 5 Neighboring gene RNA, 5S ribosomal pseudogene 36

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Catel-Manzke syndrome without Manzke dysostosis. Miller DE, et al. Am J Med Genet A, 2020 Mar. PMID 31833187
    2. TGDS pathogenic variants cause Catel-Manzke syndrome without hyperphalangy. Boschann F, et al. Am J Med Genet A, 2020 Mar. PMID 31769200
    3. Mutations in TGDS associated with additional malformations of the middle fingers and halluces: Atypical Catel-Manzke syndrome in a fetus. Schoner K, et al. Am J Med Genet A, 2017 Jun. PMID 28422407
    4. Homozygous and compound-heterozygous mutations in TGDS cause Catel-Manzke syndrome. Ehmke N, et al. Am J Hum Genet, 2014 Dec 4. PMID 25480037, Free PMC Article
    5. Coenzyme-based functional assignments of short-chain dehydrogenases/reductases (SDRs). Persson B, et al. Chem Biol Interact, 2003 Feb 1. PMID 12604213

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Catel-Manzke syndrome without Manzke dysostosis.
      Title: Catel-Manzke syndrome without Manzke dysostosis.
    2. TGDS pathogenic variants cause Catel-Manzke syndrome without hyperphalangy.
      Title: TGDS pathogenic variants cause Catel-Manzke syndrome without hyperphalangy.
    3. Our findings widen the phenotype spectrum caused by TGDS mutations and underline the phenotypic overlap with Temtamy preaxial brachydactyly syndrome. This improves our understanding of the prenatal development and the pathogenetic mechanism of Catel-Manzke syndrome.
      Title: Mutations in TGDS associated with additional malformations of the middle fingers and halluces: Atypical Catel-Manzke syndrome in a fetus.
    4. By using haplotype reconstruction we showed that the mutation c.298G>T is probably a founder mutation. Due to the spectrum of the amino acid changes, we suggest that loss of function in TGDS is the underlying mechanism of Catel-Manzke syndrome.
      Title: Homozygous and compound-heterozygous mutations in TGDS cause Catel-Manzke syndrome.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Catel-Manzke syndrome
    MedGen: C1844887 OMIM: 616145 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of TDP-glucose 4,6-dehydratase (TGDS) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables dTDP-glucose 4,6-dehydratase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in nucleotide-sugar metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    dTDP-D-glucose 4,6-dehydratase
    Names
    growth-inhibiting protein 21
    short chain dehydrogenase/reductase family 2E, member 1
    NP_001291359.1
    NP_055120.1
    XP_011519367.1
    XP_011519368.1
    XP_054230355.1
    XP_054230356.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_041837.1 RefSeqGene

      Range
      5124..27222
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001304430.2 → NP_001291359.1  dTDP-D-glucose 4,6-dehydratase isoform 2

      See identical proteins and their annotated locations for NP_001291359.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' terminal exon, and uses a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      BC033675, BI914642
      UniProtKB/Swiss-Prot
      O95455
      Conserved Domains (2) summary
      cd05246
      Location:1 → 304
      dTDP_GD_SDR_e; dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs
      TIGR01181
      Location:2 → 306
      dTDP_gluc_dehyt; dTDP-glucose 4,6-dehydratase

    2. NM_014305.4 → NP_055120.1  dTDP-D-glucose 4,6-dehydratase isoform 1

      See identical proteins and their annotated locations for NP_055120.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC033675
      Consensus CDS
      CCDS9471.1
      UniProtKB/Swiss-Prot
      O95455, Q05DQ3, Q2TU31, Q5T3Z2, Q9H1T9
      Related
      ENSP00000261296.5, ENST00000261296.7
      Conserved Domains (1) summary
      cd05246
      Location:18 → 336
      dTDP_GD_SDR_e; dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs

    RNA

    1. NR_130731.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC033675, BG702561

    2. NR_130732.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC033675, BG546428

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      94574054..94596273 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521066.3 → XP_011519368.1  dTDP-D-glucose 4,6-dehydratase isoform X1

      See identical proteins and their annotated locations for XP_011519368.1

      Conserved Domains (2) summary
      cd05246
      Location:1 → 304
      dTDP_GD_SDR_e; dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs
      TIGR01181
      Location:2 → 306
      dTDP_gluc_dehyt; dTDP-glucose 4,6-dehydratase

    2. XM_011521065.3 → XP_011519367.1  dTDP-D-glucose 4,6-dehydratase isoform X1

      See identical proteins and their annotated locations for XP_011519367.1

      Conserved Domains (2) summary
      cd05246
      Location:1 → 304
      dTDP_GD_SDR_e; dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs
      TIGR01181
      Location:2 → 306
      dTDP_gluc_dehyt; dTDP-glucose 4,6-dehydratase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      93777561..93799780 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374380.1 → XP_054230355.1  dTDP-D-glucose 4,6-dehydratase isoform X1

    2. XM_054374381.1 → XP_054230356.1  dTDP-D-glucose 4,6-dehydratase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95455.1 GenPept UniProtKB/Swiss-Prot:O95455

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