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    LDHD lactate dehydrogenase D [ Homo sapiens (human) ]

    Gene ID: 197257, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LDHDprovided by HGNC
    Official Full Name
    lactate dehydrogenase Dprovided by HGNC
    Primary source
    HGNC:HGNC:19708
    See related
    Ensembl:ENSG00000166816 MIM:607490; AllianceGenome:HGNC:19708
    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
    DLD; DLACD
    Summary
    The protein encoded by this gene belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. The similar protein in yeast has both D-lactate and D-glycerate dehydrogenase activities. Alternative splicing occurs at this locus and two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in kidney (RPKM 28.2), liver (RPKM 23.6) and 15 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LDHD in Genome Data Viewer
    Location:
    16q23.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (75111864..75116780, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81158564..81163478, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (75145762..75150678, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74905369-74905917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74908123-74908848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:74909577-74910302 Neighboring gene WD repeat domain 59 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:74997467-74997687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11112 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75020112-75020312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11115 Neighboring gene zinc and ring finger 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11116 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:75095860-75097059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75108734-75109234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75109235-75109735 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75113000-75113201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75113937-75114482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75121619-75122275 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75127186-75127378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75129219-75129949 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75129950-75130679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75136275-75136776 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11122 Neighboring gene Sharpr-MPRA regulatory region 12749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7709 Neighboring gene ZFP1 zinc finger protein Neighboring gene RPS4Y1 pseudogene 1

    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. Early-onset gout and rare deficient variants of the lactate dehydrogenase D gene. Bardin T, et al. Rheumatology (Oxford), 2023 Dec 1. PMID 37021930
    2. Prostate cancer cells metabolize d-lactate inside mitochondria via a D-lactate dehydrogenase which is more active and highly expressed than in normal cells. de Bari L, et al. FEBS Lett, 2013 Mar 1. PMID 23333299
    3. Cancer/testis antigen LDHC promotes proliferation and metastasis by activating the PI3K/Akt/GSK-3β-signaling pathway and the in lung adenocarcinoma. Chen L, et al. Exp Cell Res, 2021 Jan 15. PMID 33301764
    4. Systematic analysis of the role of LDHs subtype in pan-cancer demonstrates the importance of LDHD in the prognosis of hepatocellular carcinoma patients. Wang S, et al. BMC Cancer, 2024 Jan 31. PMID 38291366, Free PMC Article
    5. Hyperuricemia and gout caused by missense mutation in d-lactate dehydrogenase. Drabkin M, et al. J Clin Invest, 2019 Dec 2. PMID 31638601, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Systematic analysis of the role of LDHs subtype in pan-cancer demonstrates the importance of LDHD in the prognosis of hepatocellular carcinoma patients.
      Title: Systematic analysis of the role of LDHs subtype in pan-cancer demonstrates the importance of LDHD in the prognosis of hepatocellular carcinoma patients.
    2. Early-onset gout and rare deficient variants of the lactate dehydrogenase D gene.
      Title: Early-onset gout and rare deficient variants of the lactate dehydrogenase D gene.
    3. Cancer/testis antigen LDHC promotes proliferation and metastasis by activating the PI3K/Akt/GSK-3beta-signaling pathway and the in lung adenocarcinoma.
      Title: Cancer/testis antigen LDHC promotes proliferation and metastasis by activating the PI3K/Akt/GSK-3β-signaling pathway and the in lung adenocarcinoma.
    4. gout can be caused by a mutation in LDHD within the putative catalytic site of the encoded d-lactate dehydrogenase, resulting in augmented blood levels of d-lactate, a stereoisomer of l-lactate
      Title: Hyperuricemia and gout caused by missense mutation in d-lactate dehydrogenase.
    5. The activity and expression of the mitochondrial D-lactate dehydrogenase, is higher in prostate cancer versus normal prostate cells.
      Title: Prostate cancer cells metabolize d-lactate inside mitochondria via a D-lactate dehydrogenase which is more active and highly expressed than in normal cells.
    6. Elevated serum LDH isoenzymes and AST indicate a disturbance (of uncertain clinical significance) within multiple extraosseous tissues when there is CLCN7 deficiency.
      Title: Elevated serum lactate dehydrogenase isoenzymes and aspartate transaminase distinguish Albers-Schönberg disease (Chloride Channel 7 Deficiency Osteopetrosis) among the sclerosing bone disorders.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    8. identification and characterization of human and mouse D-lactate dehydrogenase (NAD) [D-LDH]
      Title: Identification of putative mammalian D-lactate dehydrogenase enzymes.
    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
    Lactic aciduria due to D-lactic acid
    MedGen: C5193006 OMIM: 245450 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
    EBI GWAS Catalog
    Multidimensional prognostic risk assessment identifies association between IL12B variation and surgery in Crohn's disease.
    EBI GWAS Catalog

    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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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120/41 (SFVenvBX08)-expressing microglia exhibit a 170% increase in lactate dehydrogenase (LDH) release PubMed
    Envelope transmembrane glycoprotein gp41 env A lentivirus lytic peptide 1 (LLP-1) corresponding to the carboxyl terminus of HIV-1 gp41 induces a significant lactate dehydrogenase (LDH, a marker of cell death) release from human neuronal and glial cell lines PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC57726

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables D-lactate dehydrogenase (cytochrome) activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables D-lactate dehydrogenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables FAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables flavin adenine dinucleotide binding 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 lactate catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lactate catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    probable D-lactate dehydrogenase, mitochondrial
    Names
    D-lactate dehydrogenase
    NP_705690.2
    NP_919417.1

    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.

    mRNA and Protein(s)

    1. NM_153486.4 → NP_705690.2  probable D-lactate dehydrogenase, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_705690.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC099508, BC040279
      Consensus CDS
      CCDS10913.1
      UniProtKB/Swiss-Prot
      Q86WU2, Q8IZK5
      Related
      ENSP00000300051.4, ENST00000300051.8
      Conserved Domains (1) summary
      cl28072
      Location:29 → 507
      FAD-oxidase_C; FAD linked oxidases, C-terminal domain

    2. NM_194436.3 → NP_919417.1  probable D-lactate dehydrogenase, mitochondrial isoform 2 precursor

      See identical proteins and their annotated locations for NP_919417.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame segment, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC099508, BC040279, BM544922
      Consensus CDS
      CCDS45529.1
      UniProtKB/Swiss-Prot
      Q86WU2
      Related
      ENSP00000417011.2, ENST00000450168.3
      Conserved Domains (3) summary
      COG0277
      Location:34 → 484
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:66 → 202
      FAD_binding_4; FAD binding domain
      pfam02913
      Location:243 → 483
      FAD-oxidase_C; FAD linked oxidases, C-terminal domain

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      75111864..75116780 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      81158564..81163478 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86WU2.1 GenPept UniProtKB/Swiss-Prot:Q86WU2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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