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LDHD lactate dehydrogenase D [ Homo sapiens (human) ]

Gene ID: 197257, updated on 11-Apr-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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Location:
16q23.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (75111864..75116780, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81158564..81163478, complement)
105.20220307 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
  • 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. 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
  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. 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
  4. Identification of human D lactate dehydrogenase deficiency. Monroe GR, et al. Nat Commun, 2019 Apr 1. PMID 30931947, Free PMC Article
  5. Elevated serum lactate dehydrogenase isoenzymes and aspartate transaminase distinguish Albers-Schönberg disease (Chloride Channel 7 Deficiency Osteopetrosis) among the sclerosing bone disorders. Whyte MP, et al. J Bone Miner Res, 2010 Nov. PMID 20499337

See all (19) 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
  
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_2023_10

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

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