Aliases for HDDC2 Gene

Aliases for HDDC2 Gene

  • HD Domain Containing 2 2 3 5
  • Hepatitis C Virus NS5A-Transactivated Protein 2 3 4
  • HCV NS5A-Transactivated Protein 2 3 4
  • HD Domain-Containing Protein 2 3 4
  • 5'-Deoxynucleotidase HDDC2 3 4
  • DJ167O5.2 2 3
  • C6orf74 3 4
  • CGI-130 2 3
  • NS5ATP2 3 4
  • Chromosome 6 Open Reading Frame 74 2
  • Testicular Tissue Protein Li 83 3
  • EC 3.1.3.89 4
  • HDDC2 5

External Ids for HDDC2 Gene

Previous HGNC Symbols for HDDC2 Gene

  • C6orf74

Previous GeneCards Identifiers for HDDC2 Gene

  • GC06M125639
  • GC06M123173
  • GC06M125596

Summaries for HDDC2 Gene

GeneCards Summary for HDDC2 Gene

HDDC2 (HD Domain Containing 2) is a Protein Coding gene.

UniProtKB/Swiss-Prot Summary for HDDC2 Gene

  • Catalyzes the dephosphorylation of the nucleoside 5'-monophosphates deoxyadenosine monophosphate (dAMP), deoxycytidine monophosphate (dCMP), deoxyguanosine monophosphate (dGMP) and deoxythymidine monophosphate (dTMP).

Additional gene information for HDDC2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HDDC2 Gene

Genomics for HDDC2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HDDC2 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
GH06J125299 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 632.3 +0.4 443 4.7 HNRNPL GATAD2A TEAD4 PRDM10 TFE3 ZNF512 LEF1 IKZF1 NFKBIZ ZNF692 HDDC2 TRMT11 ENSG00000286299 TPD52L1
GH06J125445 Promoter/Enhancer 1 EPDnew Ensembl CraniofacialAtlas 600.1 -143.3 -143349 3.1 CREB1 NR2F2 ZFHX2 POLR2A RXRA SMARCA4 ATF2 EGR2 ENSG00000226409 LOC102723341 HDDC2 piR-48369-180 HEY2
GH06J125153 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 20.8 +147.8 147785 2.6 CREB1 GATAD2A CTCF HNRNPL TEAD4 PRDM10 REST ZNF629 IKZF1 KDM1A TPD52L1 HDDC2 lnc-RNF217-2 LOC100126584
GH06J125745 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.6 -447.1 -447123 9.2 RNF2 CTCF HNRNPL TEAD4 PRDM10 REST ZNF629 ZNF512 KDM1A ZNF692 HEY2 ENSG00000237742 LOC105377986 HDDC2 HINT3 NCOA7
GH06J125917 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.8 -619.5 -619513 7.6 SP1 GATAD2A PRDM10 ZNF629 REST ZNF512 LEF1 SOX13 IKZF1 ZNF692 NCOA7 HINT3 HDDC2 NCOA7-AS1 HEY2 HSALNG0053307 piR-35729-057
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HDDC2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HDDC2

Top Transcription factor binding sites by QIAGEN in the HDDC2 gene promoter:
  • Cdc5
  • FOXD1
  • LyF-1
  • Meis-1
  • Meis-1a
  • Meis-1b
  • RORalpha2
  • SRF
  • SRF (504 AA)

Genomic Locations for HDDC2 Gene

Genomic Locations for HDDC2 Gene
chr6:125,219,962-125,302,078
(GRCh38/hg38)
Size:
82,117 bases
Orientation:
Minus strand
chr6:125,541,108-125,623,282
(GRCh37/hg19)
Size:
82,175 bases
Orientation:
Minus strand

Genomic View for HDDC2 Gene

Genes around HDDC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDDC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDDC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HDDC2 Gene

Proteins for HDDC2 Gene

  • Protein details for HDDC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z4H3-HDDC2_HUMAN
    Recommended name:
    5'-deoxynucleotidase HDDC2
    Protein Accession:
    Q7Z4H3
    Secondary Accessions:
    • Q5TDQ4
    • Q6NZ49
    • Q9BTT2
    • Q9BV31
    • Q9Y3D1

    Protein attributes for HDDC2 Gene

    Size:
    204 amino acids
    Molecular mass:
    23390 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Cofactor:
    Name=Co(2+); Xref=ChEBI:CHEBI:48828;
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer.
    SequenceCaution:
    • Sequence=AAD34125.1; Type=Miscellaneous discrepancy; Note=Correction of a non-canonical splice junction.; Evidence={ECO:0000305}; Sequence=AAH03357.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 3]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Three dimensional structures from OCA and Proteopedia for HDDC2 Gene

    Alternative splice isoforms for HDDC2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HDDC2 Gene

Post-translational modifications for HDDC2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HDDC2 Gene

No data available for DME Specific Peptides for HDDC2 Gene

Domains & Families for HDDC2 Gene

Gene Families for HDDC2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HDDC2 Gene

InterPro:
Blocks:
  • Metal-dependent phosphohydrolase, HD region
ProtoNet:

Suggested Antigen Peptide Sequences for HDDC2 Gene

GenScript: Design optimal peptide antigens:
  • HD domain containing 2, isoform CRA_b (E1P566_HUMAN)
  • HD domain containing 2, isoform CRA_a (E1P567_HUMAN)
  • Hepatitis C virus NS5A-transactivated protein 2 (HDDC2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q7Z4H3

UniProtKB/Swiss-Prot:

HDDC2_HUMAN :
  • Belongs to the HDDC2 family.
Family:
  • Belongs to the HDDC2 family.
genes like me logo Genes that share domains with HDDC2: view

Function for HDDC2 Gene

Molecular function for HDDC2 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the dephosphorylation of the nucleoside 5'-monophosphates deoxyadenosine monophosphate (dAMP), deoxycytidine monophosphate (dCMP), deoxyguanosine monophosphate (dGMP) and deoxythymidine monophosphate (dTMP).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate; Xref=Rhea:RHEA:36167, ChEBI:CHEBI:15377, ChEBI:CHEBI:18274, ChEBI:CHEBI:43474, ChEBI:CHEBI:65317; EC=3.1.3.89; Evidence={ECO:0000250|UniProtKB:P53144};.

Enzyme Numbers (IUBMB) for HDDC2 Gene

Phenotypes From GWAS Catalog for HDDC2 Gene

Gene Ontology (GO) - Molecular Function for HDDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002953 5'-deoxynucleotidase activity IEA,IBA 21873635
GO:0005515 protein binding IPI 22190034
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with HDDC2: view
genes like me logo Genes that share phenotypes with HDDC2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDDC2

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HDDC2 Gene

Localization for HDDC2 Gene

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 HDDC2 gene
Compartment Confidence
mitochondrion 3
peroxisome 2
nucleus 2
cytosol 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HDDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with HDDC2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for HDDC2 Gene

Pathways & Interactions for HDDC2 Gene

PathCards logo

SuperPathways for HDDC2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HDDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016311 dephosphorylation IEA --
genes like me logo Genes that share ontologies with HDDC2: view

No data available for Pathways by source and SIGNOR curated interactions for HDDC2 Gene

Drugs & Compounds for HDDC2 Gene

No Compound Related Data Available

Transcripts for HDDC2 Gene

mRNA/cDNA for HDDC2 Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
10 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 HDDC2

Alternative Splicing Database (ASD) splice patterns (SP) for HDDC2 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b · 9c · 9d · 9e · 9f
SP1: - - - - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - -
SP4: - - - - - - - - - - - -
SP5: - - - - - - - - -
SP6: - - - - - - - - -
SP7: - - - - - - -
SP8: - - - -
SP9: - - - - - - -
SP10: - -
SP11: - -
SP12: -

Relevant External Links for HDDC2 Gene

GeneLoc Exon Structure for
HDDC2

Expression for HDDC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HDDC2 Gene

Protein differential expression in normal tissues from HIPED for HDDC2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (10.1) and Skin (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HDDC2 Gene



Protein tissue co-expression partners for HDDC2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HDDC2

SOURCE GeneReport for Unigene cluster for HDDC2 Gene:

Hs.32826

Evidence on tissue expression from TISSUES for HDDC2 Gene

  • Nervous system(4.5)
  • Lung(4.3)
genes like me logo Genes that share expression patterns with HDDC2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HDDC2 Gene

Orthologs for HDDC2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HDDC2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia HDDC2 30 31
  • 99.18 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia HDDC2 30 31
  • 91.01 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia HDDC2 30 31
  • 86.93 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Hddc2 30 17 31
  • 85.4 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Hddc2 30
  • 83.58 (n)
Oppossum
(Monodelphis domestica)
Mammalia HDDC2 31
  • 80 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia HDDC2 31
  • 75 (a)
OneToOne
Chicken
(Gallus gallus)
Aves HDDC2 30 31
  • 74.91 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia HDDC2 31
  • 81 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hddc2 30
  • 69.05 (n)
Str.10992 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.23921 30
Zebrafish
(Danio rerio)
Actinopterygii hddc2 30 31
  • 64.13 (n)
OneToOne
wufb71h08 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.14203 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012582 30
  • 50.45 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG11050 30 31
  • 48.85 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea F45F2.9 30 31
  • 49.53 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YBR242W 30
  • 51.02 (n)
-- 31
  • 34 (a)
OneToMany
-- 31
  • 33 (a)
OneToMany
-- 33
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AFL036C 30
  • 50.67 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F06798g 30
  • 45.93 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G23820 30
  • 59.3 (n)
Rice
(Oryza sativa)
Liliopsida Os02g0179100 30
  • 53.56 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 60 (a)
OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC4G3.17 30
  • 52.85 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU04470 30
  • 46.71 (n)
Species where no ortholog for HDDC2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • 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 HDDC2 Gene

ENSEMBL:
Gene Tree for HDDC2 (if available)
TreeFam:
Gene Tree for HDDC2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HDDC2: view image

Paralogs for HDDC2 Gene

No data available for Paralogs for HDDC2 Gene

Variants for HDDC2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HDDC2 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs12213371 - p.Arg64Cys

Additional dbSNP identifiers (rs#s) for HDDC2 Gene

Structural Variations from Database of Genomic Variants (DGV) for HDDC2 Gene

Variant ID Type Subtype PubMed ID
nsv604601 CNV loss 21841781
nsv820070 CNV gain 19587683

Variation tolerance for HDDC2 Gene

Residual Variation Intolerance Score: 64.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.04; 21.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HDDC2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HDDC2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HDDC2 Gene

Disorders for HDDC2 Gene

Additional Disease Information for HDDC2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

No disorders were found for HDDC2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HDDC2 Gene

Publications for HDDC2 Gene

  1. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. (PMID: 31091453) Shami Shah A … Baskin JM (Cell reports 2019) 3
  5. Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family. (PMID: 27432908) Li X … Wang W (Molecular & cellular proteomics : MCP 2016) 3

Products for HDDC2 Gene

Sources for HDDC2 Gene