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KLHDC2 Gene

protein-coding   GIFtS: 54
GCID: GC14P050234

Kelch Domain Containing 2

  See KLHDC2-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Kelch Domain Containing 21 2     HCLP12 5
Hepatocellular Carcinoma-Associated Antigen 332 3     LCP2
Host Cell Factor Homolog LCP2 3     Kelch Domain-Containing Protein 22
Host Cell Factor-Like Protein 12 3     HCA333
HCLP-12 3     

External Ids:    HGNC: 202311   Entrez Gene: 235882   Ensembl: ENSG000001655167   OMIM: 6112805   UniProtKB: Q9Y2U93   

Export aliases for KLHDC2 gene to outside databases

Previous GC identifers: GC14P044030 GC14P048224 GC14P049304 GC14P030362


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for KLHDC2 Gene:
KLHDC2 (kelch domain containing 2) is a protein-coding gene. Diseases associated with KLHDC2 include hepatocellular carcinoma. An important paralog of this gene is KLHDC3.

UniProtKB/Swiss-Prot: KLDC2_HUMAN, Q9Y2U9
Function: Represses CREB3-mediated transcription by interfering with CREB3-DNA binding




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000014.8  NT_026437.13  NC_018925.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the KLHDC2 gene promoter:
         USF1   Pax-5   USF2   USF-1:USF-2   PPAR-alpha   Max   FOXO4   FOXJ2 (long isoform)   USF-1   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKLHDC2 promoter sequence
   Search Chromatin IP Primers for KLHDC2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KLHDC2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 14q21.3   Ensembl cytogenetic band:  14q21.3   HGNC cytogenetic band: 14q21.3

KLHDC2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KLHDC2 gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14P050234:  view genomic region     (about GC identifiers)

Start:
50,234,326 bp from pter      End:
50,249,909 bp from pter
Size:
15,584 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: KLDC2_HUMAN, Q9Y2U9 (See protein sequence)
Recommended Name: Kelch domain-containing protein 2  
Size: 406 amino acids; 46099 Da
Subunit: Directly interacts with CREB3, but not with CREB1, ATF4, ATF6, JUN, FOS, CEBPA and herpes simplex virus
transactivator VP16
Secondary accessions: B3KPF9 Q6IAF0 Q86TY9
Alternative splicing: 2 isoforms:  Q9Y2U9-1   Q9Y2U9-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for KLHDC2: NX_Q9Y2U9

Explore proteomics data for KLHDC2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys51, Lys117
  • Modification sites at PhosphoSitePlus

  • See KLHDC2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055130.1  
    ENSEMBL proteins: 
     ENSP00000298307   ENSP00000450539   ENSP00000451439   ENSP00000450944   ENSP00000450658  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR015915 Kelch-typ_b-propeller

    Graphical View of Domain Structure for InterPro Entry Q9Y2U9

    ProtoNet protein and cluster: Q9Y2U9

    1 Blocks protein domain: IPB011498 Kelch

    UniProtKB/Swiss-Prot: KLDC2_HUMAN, Q9Y2U9
    Similarity: Contains 6 Kelch repeats


    Find genes that share domains with KLHDC2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: KLDC2_HUMAN, Q9Y2U9
    Function: Represses CREB3-mediated transcription by interfering with CREB3-DNA binding

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with KLHDC2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for KLHDC2:
     Decreased Tat-dependent transc 

         6 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Klhdc2):
     behavior/neurological  growth/size/body  hematopoietic system  immune system  other 
     vision/eye 

    Find genes that share phenotypes with KLHDC2           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KLHDC2
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    miRNA
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    miRTarBase miRNAs that target KLHDC2:
    hsa-mir-93-5p (MIRT048884), hsa-mir-324-3p (MIRT042902)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    KLDC2_HUMAN, Q9Y2U9: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    extracellular1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    Find genes that share ontologies with KLHDC2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for KLHDC2
    Interactions:

        Search GeneGlobe Interaction Network for KLHDC2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 18)

    Selected Interacting proteins for KLHDC2 (Q9Y2U92, 3 ENSP000002983074) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EZH2Q159102, 3MINT-64282 I2D: score=5 
    STRN4Q9NRL32, 3MINT-65612 I2D: score=5 
    SFNP319472, 3MINT-3976182 I2D: score=2 
    DDX19BQ9UMR23, ENSP000002880714I2D: score=2 STRING: ENSP00000288071
    UBXN7O948883, ENSP000002963284I2D: score=1 STRING: ENSP00000296328
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for KLHDC2 (KLDC2)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for KLHDC2 gene: 
    NM_014315.2  

    Unigene Cluster for KLHDC2:

    Kelch domain containing 2
    Hs.509264  [show with all ESTs]
    Unigene Representative Sequence: AK056298
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000298307(uc001wwx.3) ENST00000555739 ENST00000554589 ENST00000555443
    ENST00000557247 ENST00000553538 ENST00000553703 ENST00000557063 ENST00000556559
    ENST00000554115 ENST00000553579
    miRNA
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    Block miRNA regulation of human, mouse, rat KLHDC2 using miScript Target Protectors
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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat KLHDC2
      QuantiFast Probe-based Assays in human, mouse, rat KLHDC2

    Additional mRNA sequence: 

    AF113131.1 AF244137.1 AK001771.1 AK021961.1 AK056298.1 BC002335.2 BC024192.1 BX161429.1 
    CR457205.1 

    20 DOTS entries:

    DT.95208911  DT.117673  DT.101983220  DT.91978839  DT.95208922  DT.100825536  DT.100758340  DT.120747991 
    DT.100825540  DT.100825541  DT.120747986  DT.120748048  DT.40109376  DT.91757056  DT.95283668  DT.100825534 
    DT.120747999  DT.70103737  DT.75193817  DT.80101474 

    Selected AceView cDNA sequences (see all 353):

    CD673664 AI801584 CR625292 AA604549 AA628906 AI277272 AI189937 BU686438 
    AA740182 AA857535 BM982140 AL135359 NM_014315 BQ017386 AA488367 CR591808 
    AI919241 BX161429 AI564557 AL580468 AA704095 CB163204 BM695764 AA083986 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for KLHDC2 (see all 6)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b
    SP1:        -                 -                                         -           -     -                                 
    SP2:                                                                    -           -     -                                 
    SP3:                          -                                                                                             
    SP4:                                                                                                                        
    SP5:                                                                                                                        


    ECgene alternative splicing isoforms for KLHDC2

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    KLHDC2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGAATGGCCT
    KLHDC2 Expression
    About this image

    KLHDC2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KLHDC2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.509264

    UniProtKB/Swiss-Prot: KLDC2_HUMAN, Q9Y2U9
    Tissue specificity: Widely expressed, with high levels in skeletal muscle, heart, pancreas and liver. Undetectable
    in peripheral blood leukocytes

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for KLHDC2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Klhdc21 , 5 kelch domain containing 21, 5 91.46(n)1
    96.8(a)1
      12 (28.77 cM)5
    695541  NM_027117.31  NP_081393.21 
     692966815 
    chicken
    (Gallus gallus)
    Aves KLHDC21 kelch domain containing 2 79.06(n)
    84.98(a)
      423569  NM_001012590.1  NP_001012608.1 
    lizard
    (Anolis carolinensis)
    Reptilia KLHDC26
    kelch domain containing 2
    73(a)
    1 ↔ 1
    GL343627.1(380397-395822)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.192102 Xenopus laevis transcribed sequence with weak similarity to protein refNP_055130.1 (H.sapiens) host cell factor homolog [Homo sapiens] less 76.89(n)    BX855021.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.155882 Transcribed sequence with weak similarity to protein refNP_055130.1 (H.sapiens) host cell factor homolog [Homo sapiens] less 74.28(n)    CK147102.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes KEL16
    KEL26
    Protein required for proper cell fusion and cell m...
    Protein that functions in a complex with Kel1p to ...
    8(a)
    10(a)
    many ↔ many
    many ↔ many
    VIII(413685-417179) YHR158C
    VII(966039-968687) YGR238C


    ENSEMBL Gene Tree for KLHDC2 (if available)
    TreeFam Gene Tree for KLHDC2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KLHDC2 gene
    KLHDC32  HCFC12  KLHDC12  LZTR12  RABEPK2  KLHDC102  HCFC22  
    1 SIMAP similar gene for KLHDC2 using alignment to 3 protein entries:     KLDC2_HUMAN (see all proteins):
    KLHDC1

    Find genes that share paralogs with KLHDC2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for KLHDC2 (see all 416)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1512396611,2
    --31216074(+) CCTCAC/TGCCTG 1 -- us2k10--------
    rs1860353561,2
    C--31216220(+) TAGTCA/CCAGCT 1 -- us2k10--------
    rs1912121491,2
    --31216291(+) GAGATC/TGAGCC 1 -- us2k10--------
    rs1995344041,2
    C--31216342(+) GAACA-/AACAAAAA 1 -- us2k10--------
    rs2004615521,2
    C--31216352(-) TTTTTG/TTNNNN 1 -- us2k10--------
    rs1404578501,2
    --31216359(+) AAAACA/GATGAT 1 -- us2k10--------
    rs1175800831,2
    F--31216865(+) GGTTGG/TTTCAC 1 -- us2k11Minor allele frequency- T:0.01EA 120
    rs1382260411,2
    --31216911(+) AATTCA/GACTGG 1 -- us2k10--------
    rs1413435791,2
    --31217140(+) AAAAAA/GAAGCC 1 -- us2k10--------
    rs1166192961,2
    F--31217194(+) CAGAAG/TATGAG 1 -- us2k11Minor allele frequency- T:0.03WA 118

    HapMap Linkage Disequilibrium report for KLHDC2 (50234326 - 50249909 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for KLHDC2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509533CNV Insertion20534489
    nsv1269CNV Insertion18451855
    nsv901937CNV Loss21882294
    esv28926CNV Gain+Loss19812545

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 611280    OMIM disorders: --

    1 disease for KLHDC2:    
    About MalaCards
    hepatocellular carcinoma


    Find genes that share disorders with KLHDC2           About GenesLikeMe

    Genetic Association Database (GAD): KLHDC2
    Human Genome Epidemiology (HuGE) Navigator: KLHDC2 (1 document)

    Export disorders for KLHDC2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for KLHDC2 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with KLHDC2)
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    1. Inhibition of LZIP-mediated transcription through direct interaction with a novel host cell factor-like protein. (PubMed id 11384994)1, 2, 3 Zhou H.-J....Jin D.-Y. (J. Biol. Chem. 2001)
    2. Differential subcellular localization and activity of kelch repeat proteins KLHDC1 and KLHDC2. (PubMed id 16964437)1, 2, 9 Chin K.-T.... Jin D.-Y. (Mol. Cell. Biochem. 2007)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. Large scale identification of human hepatocellular carcinoma- associated antigens by autoantibodies. (PubMed id 12097419)1, 2 Wang Y....Chen W.-F. (J. Immunol. 2002)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    7. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    8. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    9. Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection. (PubMed id 21083371)4 Chinn L.W....O'Brien S.J. (J. Infect. Dis. 2010)
    10. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 23588 HGNC: 20231 AceView: KLHDC2 Ensembl:ENSG00000165516 euGenes: HUgn23588
    ECgene: KLHDC2 H-InvDB: KLHDC2

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for KLHDC2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for KLHDC2 gene:
    Search GeneIP for patents involving KLHDC2

    GeneCards and IP:
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