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BDH1 Gene(Protein Coding)

3-Hydroxybutyrate Dehydrogenase 1

GCID:
GC03M197529
GIFtS:
53
Genes Participants
UDN Logo

Aliases for BDH1 Gene

Aliases for BDH1 Gene

  • 3-Hydroxybutyrate Dehydrogenase 1 2 3 5
  • 3-Hydroxybutyrate Dehydrogenase (Heart, Mitochondrial) 2 3
  • Short Chain Dehydrogenase/Reductase Family 9C Member 1 3 4
  • 3-Hydroxybutyrate Dehydrogenase, Type 1 2 3
  • EC 1.1.1.30 4 56
  • SDR9C1 3 4
  • BDH 3 4
  • Short Chain Dehydrogenase/Reductase Family 9C, Member 1 2
  • D-Beta-Hydroxybutyrate Dehydrogenase, Mitochondrial 3
  • (R)-3-Hydroxybutyrate Dehydrogenase 3
  • 3-Hydroxybutyrate Dehydrogenase 4
  • EC 1.1.1 56

External Ids for BDH1 Gene

Previous HGNC Symbols for BDH1 Gene

  • BDH

Previous GeneCards Identifiers for BDH1 Gene

  • GC03M198727
  • GC03M197236
  • GC03M194539
  • GC03M197510
  • GC03M197512
  • GC03M197516
  • GC03M197519
  • GC03M197521
  • GC03M197523
  • GC03M197526

Summaries for BDH1 Gene

Entrez Gene Summary for BDH1 Gene

  • This gene encodes a member of the short-chain dehydrogenase/reductase gene family. The encoded protein forms a homotetrameric lipid-requiring enzyme of the mitochondrial membrane and has a specific requirement for phosphatidylcholine for optimal enzymatic activity. The encoded protein catalyzes the interconversion of acetoacetate and (R)-3-hydroxybutyrate, the two major ketone bodies produced during fatty acid catabolism. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2008]

GeneCards Summary for BDH1 Gene

BDH1 (3-Hydroxybutyrate Dehydrogenase 1) is a Protein Coding gene. Diseases associated with BDH1 include 3-Hydroxy-3-Methylglutaryl-Coa Lyase Deficiency and Chromosome 3Q29 Duplication Syndrome. Among its related pathways are Ketone body metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity and 3-hydroxybutyrate dehydrogenase activity. An important paralog of this gene is HSD17B6.

Gene Wiki entry for BDH1 Gene

Additional gene information for BDH1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BDH1 Gene

Genomics for BDH1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for BDH1 Gene

Promoters and enhancers for BDH1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH03I197553 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 563.5 +18.2 18187 2.5 HDGF PKNOX1 SIN3A ZNF2 ZBTB7B BRCA1 GLIS2 ZNF143 RUNX3 DEK BDH1 MELTF-AS1 ENSG00000249626 SENP5 LOC220729 GC03P197515
GH03I197572 Promoter/Enhancer 1.4 EPDnew ENCODE 567.1 -0.9 -917 3.4 FOXA2 MLX ARID4B DMAP1 ZNF48 ETS1 YY1 SLC30A9 RXRA SP5 BDH1 MIR922 RPL36P7 GC03P197515
GH03I197568 Promoter 0.5 EPDnew 550.4 +5.2 5162 0.1 BDH1 MIR922 GC03P197515
GH03I197559 Enhancer 0.8 ENCODE dbSUPER 19.3 +13.4 13440 0.8 FOXA2 JUND RXRA MAX SMAD4 HNF4A RAD21 FOXA1 BDH1 NRROS GC03P197515
GH03I197598 Enhancer 1 Ensembl ENCODE 11.7 -25.9 -25918 1.2 HDGF RB1 ARID4B KLF17 SIN3A ZNF2 ZNF48 RAD21 RFX5 GLIS2 LOC220729 BDH1 RPL36P7 PIR46687 GC03P197515
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around BDH1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BDH1 gene promoter:

Genomic Locations for BDH1 Gene

Genomic Locations for BDH1 Gene
chr3:197,509,783-197,573,323
(GRCh38/hg38)
Size:
63,541 bases
Orientation:
Minus strand
chr3:197,236,654-197,300,194
(GRCh37/hg19)

Genomic View for BDH1 Gene

Genes around BDH1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BDH1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BDH1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for BDH1 Gene

Proteins for BDH1 Gene

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  • Protein details for BDH1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q02338-BDH_HUMAN
    Recommended name:
    D-beta-hydroxybutyrate dehydrogenase, mitochondrial
    Protein Accession:
    Q02338
    Secondary Accessions:
    • D3DXC0
    • Q96ET1
    • Q9BRZ4

    Protein attributes for BDH1 Gene

    Size:
    343 amino acids
    Molecular mass:
    38157 Da
    Quaternary structure:
    • Homotetramer.
    SequenceCaution:
    • Sequence=AAA58352.1; Type=Frameshift; Positions=124, 134; Evidence={ECO:0000305};

neXtProt entry for BDH1 Gene

Protein Expression for BDH1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for BDH1 Gene

Q02338:
  • GRVVNISS
  • GLVNNAG
  • GVEAFSD
  • PYTRYHPMDYYWWLRMQIMTH
  • VAEVNLWGTVR
  • VEPGNFIA
  • TGCDSGFG

Post-translational modifications for BDH1 Gene

  • Glycosylation at Ser219
  • Modification sites at PhosphoSitePlus

Other Protein References for BDH1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for BDH1 Gene

Gene Families for BDH1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Candidate cardiovascular disease genes
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for BDH1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for BDH1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q02338

UniProtKB/Swiss-Prot:

BDH_HUMAN :
  • Belongs to the short-chain dehydrogenases/reductases (SDR) family.
Family:
  • Belongs to the short-chain dehydrogenases/reductases (SDR) family.
genes like me logo Genes that share domains with BDH1: view

Function for BDH1 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
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  6. Cell Line

Molecular function for BDH1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH.
UniProtKB/Swiss-Prot EnzymeRegulation:
Requires phosphatidylcholine as an allosteric activator for enzymatic activity.

Enzyme Numbers (IUBMB) for BDH1 Gene

Phenotypes From GWAS Catalog for BDH1 Gene

Gene Ontology (GO) - Molecular Function for BDH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003858 3-hydroxybutyrate dehydrogenase activity TAS --
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with BDH1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for BDH1

Clone Products

No data available for Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for BDH1 Gene

Localization for BDH1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BDH1 Gene

Mitochondrion inner membrane. Mitochondrion matrix.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for BDH1 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for BDH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion IEA,IDA --
GO:0005743 mitochondrial inner membrane IEA --
GO:0005759 mitochondrial matrix TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with BDH1: view

Pathways & Interactions for BDH1 Gene

genes like me logo Genes that share pathways with BDH1: view

Gene Ontology (GO) - Biological Process for BDH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008152 metabolic process IEA --
GO:0046951 ketone body biosynthetic process TAS --
GO:0046952 ketone body catabolic process TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with BDH1: view

No data available for SIGNOR curated interactions for BDH1 Gene

Drugs & Compounds for BDH1 Gene

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  1. Drug

(3) Drugs for BDH1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
NADH Approved Nutra Target 0
Acetoacetic acid Experimental Pharma 0
NAD Pharma Full agonist, Agonist 0

(12) Additional Compounds for BDH1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
(R)-3-Hydroxybutyric acid
  • (R)-(-)-b-Hydroxybutyrate
  • (R)-(-)-b-Hydroxybutyric acid
  • (R)-(-)-beta-Hydroxybutyrate
  • (R)-(-)-beta-Hydroxybutyric acid
  • (R)-3-Hydroxybutanoate
 625-72-9
3-Hydroxybutyric acid
  • 3-Hydroxy-butanoate
  • 3-Hydroxy-butanoic acid
  • 3-Hydroxy-butyrate
  • 3-Hydroxy-butyric acid
  • 3-Hydroxybutanoate
 300-85-6
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
PC(18:1(9Z)e/2:0)
  • (2-acetyloxy-3-octadec-9-enoxypropyl) 2-trimethylazaniumylethyl phosphate
  • 2-Acetyl-1-(9Z-octadecenyl)-sn-glycero-3-phosphocholine
  • PC(O-18:1(9Z)/2:0)
Phosphatidylcholines Group A
  • (Z,Z)-(1)-(7-Oleoyl-4-oxido-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-enyl)trimethylammonium 4-oxide
  • (Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-Trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide hydroxide inner salt
  • 1,2-Dioleoyl-rac-glycero-3-phosphocholine
  • 1,2-Dioleoylglycerol-3-phosphorylcholine
  • 1,2-Dioleoylglyceryl-3-phosphorylcholine
 68737-67-7
genes like me logo Genes that share compounds with BDH1: view

Transcripts for BDH1 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for BDH1 Gene

(15) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(179) Selected AceView cDNA sequences:
(17) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for BDH1 Gene

3-hydroxybutyrate dehydrogenase, type 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for BDH1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b · 10c
SP1: - - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - -
SP4: - - - -
SP5: - - - - - - - - - -
SP6: - - - - - - - - -
SP7: - - - - -
SP8:
SP9:
SP10:

Relevant External Links for BDH1 Gene

GeneLoc Exon Structure for
BDH1
ECgene alternative splicing isoforms for
BDH1

Expression for BDH1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BDH1 Gene

mRNA expression in normal human tissues for BDH1 Gene
mRNA expression by BioGPS for BDH1 GenemRNA expression by GTEx for BDH1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BDH1 Gene

This gene is overexpressed in Liver (x9.3).

Protein differential expression in normal tissues from HIPED for BDH1 Gene

This gene is overexpressed in Gallbladder (18.9), Liver (16.5), and Nasal epithelium (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for BDH1 Gene



Protein tissue co-expression partners for BDH1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of BDH1 Gene:

BDH1

SOURCE GeneReport for Unigene cluster for BDH1 Gene:

Hs.274539

Evidence on tissue expression from TISSUES for BDH1 Gene

  • Liver(4.6)
  • Heart(4.4)
  • Lung(4.2)
  • Nervous system(2.9)
  • Muscle(2)
genes like me logo Genes that share expression patterns with BDH1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for BDH1 Gene

Orthologs for BDH1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for BDH1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia BDH1 33 34
  • 99.68 (n)
cow
(Bos Taurus)
 Mammalia BDH1 33 34
  • 87.13 (n)
mouse
(Mus musculus)
 Mammalia Bdh1 33 16 34
  • 86.35 (n)
dog
(Canis familiaris)
 Mammalia BDH1 33 34
  • 86.16 (n)
rat
(Rattus norvegicus)
 Mammalia Bdh1 33
  • 86.06 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia BDH1 34
  • 78 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia BDH1 34
  • 70 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves BDH1 33 34
  • 74.36 (n)
lizard
(Anolis carolinensis)
 Reptilia -- 34
  • 78 (a)
 OneToMany
-- 34
  • 66 (a)
 OneToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia bdh1 33
  • 74.61 (n)
Str.11989 33
zebrafish
(Danio rerio)
 Actinopterygii bdh1 33 34
  • 65.62 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG8888 34
  • 26 (a)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea F55E10.6 34
  • 28 (a)
 OneToMany
dhs-16 34
  • 26 (a)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes LYS2 34
  • 5 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 47 (a)
 OneToOne
Species where no ortholog for BDH1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for BDH1 Gene

ENSEMBL:
Gene Tree for BDH1 (if available)
TreeFam:
Gene Tree for BDH1 (if available)

Paralogs for BDH1 Gene

Paralogs for BDH1 Gene

(11) SIMAP similar genes for BDH1 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with BDH1: view

Variants for BDH1 Gene

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Sequence variations from dbSNP and Humsavar for BDH1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000039835 -- 197,536,143(-) T/C genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000070049 -- 197,561,177(-) C/A genic_upstream_transcript_variant, intron_variant
rs1000115054 -- 197,529,871(-) T/C genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000123170 -- 197,541,043(-) T/A genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000204530 -- 197,561,406(-) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BDH1 Gene

Variant ID Type Subtype PubMed ID
dgv5038n100 CNV gain 25217958
dgv5040n100 CNV gain 25217958
dgv5041n100 CNV gain 25217958
dgv5042n100 CNV gain 25217958
dgv635n27 CNV gain 19166990
dgv8863n54 CNV gain 21841781
esv1013303 CNV deletion 17803354
esv1109840 CNV deletion 17803354
esv1436400 CNV deletion 17803354
esv1448451 CNV deletion 17803354
esv2759214 CNV gain+loss 17122850
esv29640 CNV loss 19812545
esv3599309 CNV gain 21293372
esv3599312 CNV gain 21293372
esv3599313 CNV gain 21293372
esv3599314 CNV gain 21293372
esv3893854 CNV loss 25118596
nsv1006202 CNV gain 25217958
nsv1007506 CNV loss 25217958
nsv10399 CNV gain 18304495
nsv1136801 CNV deletion 24896259
nsv428433 CNV gain+loss 18775914
nsv461136 CNV gain 19166990
nsv471149 CNV gain 18288195
nsv507146 OTHER sequence alteration 20534489
nsv508982 CNV insertion 20534489
nsv593116 CNV gain 21841781

Variation tolerance for BDH1 Gene

Residual Variation Intolerance Score: 54.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.82; 34.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BDH1 Gene

Human Gene Mutation Database (HGMD)
BDH1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
BDH1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BDH1 Gene

Disorders for BDH1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for BDH1 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
3-hydroxy-3-methylglutaryl-coa lyase deficiency
  • hmgcld
chromosome 3q29 duplication syndrome
  • microduplication 3q29 syndrome
- elite association - COSMIC cancer census association via MalaCards
Search BDH1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BDH1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with BDH1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BDH1 Gene

Publications for BDH1 Gene

  1. Molecular cloning and characterization of (R)-3-hydroxybutyrate dehydrogenase from human heart. (PMID: 1639787) Marks AR … Fleischer S (The Journal of biological chemistry 1992) 2 3 4 58
  2. Differential utilization of ketone bodies by neurons and glioma cell lines: a rationale for ketogenic diet as experimental glioma therapy. (PMID: 21791085) Maurer GD … Rieger J (BMC cancer 2011) 2 3 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  4. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. (PMID: 19027726) Persson B … Oppermann U (Chemico-biological interactions 2009) 2 3 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

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Sources for BDH1 Gene

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