Aliases for HDHD3 Gene

Aliases for HDHD3 Gene

  • Haloacid Dehalogenase Like Hydrolase Domain Containing 3 2 3 5
  • Haloacid Dehalogenase-Like Hydrolase Domain-Containing Protein 3 3 4
  • C9orf158 3 4
  • Haloacid Dehalogenase-Like Hydrolase Domain Containing 3 2
  • Chromosome 9 Open Reading Frame 158 2
  • 2810435D12Rik 3
  • MGC12904 2
  • HDHD3 5

External Ids for HDHD3 Gene

Previous HGNC Symbols for HDHD3 Gene

  • C9orf158

Previous GeneCards Identifiers for HDHD3 Gene

  • GC09M113215
  • GC09M115175
  • GC09M116135
  • GC09M085742

Summaries for HDHD3 Gene

GeneCards Summary for HDHD3 Gene

HDHD3 (Haloacid Dehalogenase Like Hydrolase Domain Containing 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include hydrolase activity. An important paralog of this gene is NANP.

Additional gene information for HDHD3 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HDHD3 Gene

Genomics for HDHD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HDHD3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J113372 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 621.1 -1.0 -1001 11.9 ARHGAP35 SP1 GATAD2A REST TFE3 ZNF512 IKZF1 NFKBIZ ZNF692 POLR2A HDHD3 lnc-ALAD-2 piR-30350-065 RGS3 PRPF4 C9orf43 POLE3 RNF183 ALAD CDC26
GH09J113343 Enhancer 1.1 Ensembl ENCODE dbSUPER 21.5 +33.0 32998 1.6 PRDM10 ZNF629 ZNF692 PHF21A ZIC2 PKNOX1 PATZ1 REST HDAC1 SOX6 RF00017-7837 BSPRY HDHD3 WDR31 lnc-BSPRY-1
GH09J113356 Enhancer 0.5 dbSUPER 20.4 +20.1 20087 0.8 ZNF629 ZIC2 ZFHX2 FEZF1 GLIS1 ZNF398 ATF2 EGR2 HDHD3 WDR31 ALAD RNF183 POLE3 C9orf43 BSPRY lnc-C9orf43-3 lnc-ALAD-2
GH09J113339 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 4.8 +36.9 36898 1.8 BRCA1 SP1 HNRNPL GATAD2A PRDM10 REST ZNF629 TFE3 RFX1 SIX5 WDR31 lnc-BSPRY-1 PRPF4 CDC26 BSPRY RNF183 ALAD C9orf43 POLE3 HDHD3
GH09J113186 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 6.1 +188.8 188774 3.2 CEBPB FOS GABPA JUND FOSL1 MAX NR2F2 POLR2A BHLHE40 SPI1 SLC31A1 lnc-CDC26-3 PRPF4 SLC31A2 FKBP15 RNF183 BSPRY HDHD3 piR-30843 RF00017-7837
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HDHD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HDHD3

Top Transcription factor binding sites by QIAGEN in the HDHD3 gene promoter:
  • deltaCREB
  • GR
  • GR-alpha
  • HEN1
  • PPAR-gamma1
  • PPAR-gamma2
  • SRF
  • SRF (504 AA)

Genomic Locations for HDHD3 Gene

Genomic Locations for HDHD3 Gene
3,584 bases
Minus strand
3,582 bases
Minus strand

Genomic View for HDHD3 Gene

Genes around HDHD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDHD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDHD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HDHD3 Gene

Proteins for HDHD3 Gene

  • Protein details for HDHD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Haloacid dehalogenase-like hydrolase domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • B2RD47

    Protein attributes for HDHD3 Gene

    251 amino acids
    Molecular mass:
    28000 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for HDHD3 Gene

neXtProt entry for HDHD3 Gene

Post-translational modifications for HDHD3 Gene

  • Ubiquitination at Lys15
  • Modification sites at PhosphoSitePlus

Other Protein References for HDHD3 Gene

No data available for DME Specific Peptides for HDHD3 Gene

Domains & Families for HDHD3 Gene

Gene Families for HDHD3 Gene

Protein Domains for HDHD3 Gene

  • Haloacid dehalogenase/epoxide hydrolase family signature

Suggested Antigen Peptide Sequences for HDHD3 Gene

GenScript: Design optimal peptide antigens:
  • Haloacid dehalogenase-like hydrolase domain-containing protein 3 (HDHD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the HAD-like hydrolase superfamily.
  • Belongs to the HAD-like hydrolase superfamily.
genes like me logo Genes that share domains with HDHD3: view

Function for HDHD3 Gene

Phenotypes From GWAS Catalog for HDHD3 Gene

Gene Ontology (GO) - Molecular Function for HDHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with HDHD3: view
genes like me logo Genes that share phenotypes with HDHD3: view

Animal Model Products

CRISPR Products

miRNA for HDHD3 Gene

miRTarBase miRNAs that target HDHD3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDHD3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HDHD3 Gene

Localization for HDHD3 Gene

Subcellular locations from

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 HDHD3 gene
Compartment Confidence
nucleus 5
mitochondrion 2
extracellular 1
peroxisome 1
cytosol 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for HDHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with HDHD3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for HDHD3 Gene

Pathways & Interactions for HDHD3 Gene

PathCards logo

SuperPathways for HDHD3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HDHD3 Gene


No data available for Pathways by source and SIGNOR curated interactions for HDHD3 Gene

Drugs & Compounds for HDHD3 Gene

No Compound Related Data Available

Transcripts for HDHD3 Gene

mRNA/cDNA for HDHD3 Gene

9 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDHD3

Alternative Splicing Database (ASD) splice patterns (SP) for HDHD3 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b
SP1: -
SP2: - -

Relevant External Links for HDHD3 Gene

GeneLoc Exon Structure for

Expression for HDHD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HDHD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HDHD3 Gene

This gene is overexpressed in Adrenal Gland (x6.8).

Protein differential expression in normal tissues from HIPED for HDHD3 Gene

This gene is overexpressed in Adrenal (10.5), Salivary gland (9.0), and Skin (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HDHD3 Gene

Protein tissue co-expression partners for HDHD3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HDHD3

SOURCE GeneReport for Unigene cluster for HDHD3 Gene:


Evidence on tissue expression from TISSUES for HDHD3 Gene

  • Intestine(4.5)
  • Liver(4.4)
  • Skin(4.2)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with HDHD3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HDHD3 Gene

Orthologs for HDHD3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HDHD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HDHD3 30 31
  • 98.8 (n)
(Bos Taurus)
Mammalia HDHD3 30 31
  • 85.39 (n)
(Canis familiaris)
Mammalia HDHD3 30 31
  • 84.68 (n)
(Mus musculus)
Mammalia Hdhd3 30 17 31
  • 80.72 (n)
(Rattus norvegicus)
Mammalia Hdhd3 30
  • 79.38 (n)
(Monodelphis domestica)
Mammalia HDHD3 31
  • 68 (a)
(Ornithorhynchus anatinus)
Mammalia HDHD3 31
  • 57 (a)
(Gallus gallus)
Aves LOC101747936 30
  • 64.96 (n)
HDHD3 31
  • 55 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hdhd3 30
  • 60.74 (n)
(Danio rerio)
Actinopterygii hdhd3 30 31
  • 52.16 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG15912 30 31
  • 47.39 (n)
Reg-2 31
  • 26 (a)
(Caenorhabditis elegans)
Secernentea K01G5.10 30 31
  • 42.41 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 31
  • 19 (a)
-- 33
-- 33
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G44730 30
  • 39.97 (n)
(Oryza sativa)
Liliopsida Os06g0665100 30
  • 43.69 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 25 (a)
Species where no ortholog for HDHD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Lizard (Anolis carolinensis)
  • 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for HDHD3 Gene

Gene Tree for HDHD3 (if available)
Gene Tree for HDHD3 (if available)
Evolutionary constrained regions (ECRs) for HDHD3: view image

Paralogs for HDHD3 Gene

Paralogs for HDHD3 Gene

genes like me logo Genes that share paralogs with HDHD3: view

Variants for HDHD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HDHD3 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs1043836 - p.Gly146Glu

Additional dbSNP identifiers (rs#s) for HDHD3 Gene

Structural Variations from Database of Genomic Variants (DGV) for HDHD3 Gene

Variant ID Type Subtype PubMed ID
esv3576690 CNV gain 25503493
esv3621540 CNV gain 21293372
nsv1036586 CNV gain 25217958
nsv519849 CNV gain 19592680
nsv615214 CNV gain 21841781

Variation tolerance for HDHD3 Gene

Residual Variation Intolerance Score: 67.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.57; 30.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HDHD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HDHD3 Gene

Disorders for HDHD3 Gene

No disorders were found for HDHD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HDHD3 Gene

Publications for HDHD3 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis. (PMID: 31536960) Moutaoufik MT … Babu M (iScience 2019) 3
  5. Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones. (PMID: 28515276) Malinová A … Verheggen C (The Journal of cell biology 2017) 3

Products for HDHD3 Gene

Sources for HDHD3 Gene