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

Gene ID: 23483, updated on 11-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (94574054..94596273, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (93777561..93799780, complement)
105.20220307 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
  • 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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
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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 

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_2023_10

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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