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HDDC2 HD domain containing 2 [ Homo sapiens (human) ]

Gene ID: 51020, updated on 5-Mar-2024

Summary

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Official Symbol
HDDC2provided by HGNC
Official Full Name
HD domain containing 2provided by HGNC
Primary source
HGNC:HGNC:21078
See related
Ensembl:ENSG00000111906 AllianceGenome:HGNC:21078
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C6orf74; CGI-130; NS5ATP2; dJ167O5.2
Summary
Predicted to enable 5'-deoxynucleotidase activity. Predicted to be involved in dephosphorylation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in adrenal (RPKM 20.8), brain (RPKM 17.5) and 25 other tissues See more
Orthologs
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Genomic context

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See HDDC2 in Genome Data Viewer
Location:
6q22.31
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (125275350..125301967, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (126463762..126490399, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (125596496..125623113, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901394 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:125444775-125445974 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:125475715-125476302 Neighboring gene TPD52 like 1 Neighboring gene uncharacterized LOC100126584 Neighboring gene MPRA-validated peak6105 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:125583541-125584054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:125584055-125584568 Neighboring gene uncharacterized LOC124901395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17517 Neighboring gene CRISPRi-validated cis-regulatory element chr6.4553 Neighboring gene CRISPRi-validated cis-regulatory element chr6.4554 Neighboring gene uncharacterized LOC107986640 Neighboring gene uncharacterized LOC102723341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:125711176-125711724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:125765831-125766344

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. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. Lai CH, et al. Genome Res, 2000 May. PMID 10810093, Free PMC Article
  2. MAP4K Interactome Reveals STRN4 as a Key STRIPAK Complex Component in Hippo Pathway Regulation. Seo G, et al. Cell Rep, 2020 Jul 7. PMID 32640226, Free PMC Article
  3. Alterations in the brain interactome of the intrinsically disordered N-terminal domain of the cellular prion protein (PrPC) in Alzheimer's disease. Ulbrich S, et al. PLoS One, 2018. PMID 29791485, Free PMC Article
  4. Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling. Zhai Y, et al. Nat Commun, 2022 Aug 20. PMID 35987950, Free PMC Article
  5. Global landscape of HIV-human protein complexes. Jäger S, et al. Nature, 2011 Dec 21. PMID 22190034, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
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

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
integrase gag-pol HIV-1 IN is identified to have a physical interaction with HD domain containing 2 (HDDC2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC87330

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-deoxynucleotidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
5'-deoxynucleotidase HDDC2
Names
HCV NS5A-transactivated protein 2
HD domain-containing protein 2
hepatitis C virus NS5A-transactivated protein 2
testicular tissue protein Li 83
NP_057147.2
XP_024302218.1
XP_047274806.1
XP_054211526.1

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_016063.3 → NP_057147.2  5'-deoxynucleotidase HDDC2

    See identical proteins and their annotated locations for NP_057147.2

    Status: VALIDATED

    Source sequence(s)
    AL121938, BE743302, BP257644, DB447428
    Consensus CDS
    CCDS43503.1
    UniProtKB/Swiss-Prot
    Q5TDQ4, Q6NZ49, Q7Z4H3, Q9BTT2, Q9BV31, Q9Y3D1
    UniProtKB/TrEMBL
    A0A140VJK7
    Related
    ENSP00000381220.1, ENST00000398153.7
    Conserved Domains (1) summary
    pfam13023
    Location:24 → 183
    HD_3; HD 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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    125275350..125301967 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446450.2 → XP_024302218.1  5'-deoxynucleotidase HDDC2 isoform X1

    Conserved Domains (1) summary
    cl21469
    Location:1 → 131
    HDc; Metal dependent phosphohydrolases with conserved 'HD' motif

  2. XM_047418850.1 → XP_047274806.1  5'-deoxynucleotidase HDDC2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    126463762..126490399 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355551.1 → XP_054211526.1  5'-deoxynucleotidase HDDC2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z4H3.1 GenPept UniProtKB/Swiss-Prot:Q7Z4H3

Gene LinkOut

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