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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CHCHD3 Gene

protein-coding   GIFtS: 47
GCID: GC07M132470

coiled-coil-helix-coiled-coil-helix domain containing 3

  Search for CHCHD3
in our new
 Human Malady Compendium 
Biological research products
for CHCHD3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Coiled-Coil-Helix-Coiled-Coil-Helix Domain Containing 31 2     Coiled-Coil-Helix-Coiled-Coil-Helix Domain-Containing Protein 3, Mitochondrial2
MINOS31 2 3     Mitochondrial Inner Membrane Organizing System 32
PPP1R221 2     Protein Phosphatase 1, Regulatory Subunit 222
FLJ204201     

External Ids:    HGNC: 219061   Entrez Gene: 549272   Ensembl: ENSG000001065547   OMIM: 6137485   UniProtKB: Q9NX633   

Export aliases for CHCHD3 gene to outside databases

Previous GC identifers: GC07M131885 GC07M131926 GC07M132120 GC07M126786


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: CHCH3_HUMAN, Q9NX63
Function: Required for maintenance of mitochondrial crista integrity and mitochondrial function. May act as a
scaffolding protein that stabilizes protein complexes involved in crista architecture and protein import. Has also
been shown to function as a transcription factor which binds to the BAG1 promoter and represses BAG1 transcription




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.1  NT_007933.15  NT_079596.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CHCHD3 gene promoter:
         Max1   Lmo2   STAT5A   RORalpha1   FOXO4   POU2F1a   c-Myb   FOXO1a   MRF-2   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCHCHD3 promoter sequence
   Search SABiosciences Chromatin IP Primers for CHCHD3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CHCHD3


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

Entrez Gene cytogenetic band: 7q33   Ensembl cytogenetic band:  7q33   HGNC cytogenetic band: 7q33

CHCHD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CHCHD3 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M132470:  view genomic region     (about GC identifiers)

Start:
132,469,623 bp from pter      End:
132,766,848 bp from pter
Size:
297,226 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 131,809,095-132,106,393     

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CHCH3_HUMAN, Q9NX63 (See protein sequence)
Recommended Name: Coiled-coil-helix-coiled-coil-helix domain-containing protein 3, mitochondrial  
Size: 227 amino acids; 26152 Da
Subunit: Interacts with HSPA1A/HSPA1B and OPA1, preferentially with the soluble OPA1 form (By similarity). Component of
the MINOS/MitOS complex, that includes IMMT, HSPA9 and CHCHD3 and associates with mitochondrial outer membrane
proteins SAMM50, MTX1 and MTX2. Interacts with CHCHD6
Subcellular location: Mitochondrion inner membrane; Lipid-anchor; Intermembrane side (By similarity). Cytoplasm.
Nucleus

Explore the universe of human proteins at neXtProt for CHCHD3: NX_Q9NX63

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NX63

  • CHCHD3 Protein expression data from MOPED and PaxDb:    About this image 
    CHCHD3 Protein Expression
    REFSEQ proteins: NP_060282.1  
    ENSEMBL proteins: 
     ENSP00000262570   ENSP00000389297   ENSP00000410425   ENSP00000403467   ENSP00000440267  

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    Uscn Proteins for CHCHD3

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IDA--
    GO:0005739mitochondrion ISS--
    GO:0005743mitochondrial inner membrane ISS--

    CHCHD3 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    CHCHD3 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR007964 DUF737

    Graphical View of Domain Structure for InterPro Entry Q9NX63

    ProtoNet protein and cluster: Q9NX63

    1 Blocks protein family: IPB010625 CHCH

    UniProtKB/Swiss-Prot: CHCH3_HUMAN, Q9NX63
    Similarity: Contains 1 CHCH domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CHCH3_HUMAN, Q9NX63
    Function: Required for maintenance of mitochondrial crista integrity and mitochondrial function. May act as a
    scaffolding protein that stabilizes protein complexes involved in crista architecture and protein import. Has also
    been shown to function as a transcription factor which binds to the BAG1 promoter and represses BAG1 transcription

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001227RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription IDA--
    GO:0005515protein binding IPI19389623
    GO:0019902phosphatase binding IDA19389623
    GO:0032947protein complex scaffold ISS--
         
    CHCHD3 for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Chchd3):
     mortality/aging 

    CHCHD3 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for CHCHD3 

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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CHCHD3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    5/16 Interacting proteins for CHCHD3 (Q9NX631, 2, 3 ENSP000002625704) via UniProtKB, MINT, STRING, and/or I2D (see all 16)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCDC85BQ158341, 2, 3, ENSP000003116954EBI-743375,EBI-739674 MINT-66631 I2D: score=6 STRING: ENSP00000311695
    SAMM50Q9Y5122, 3MINT-5007196 I2D: score=1 
    KRTAP4-12Q9BQ662, 3, ENSP000003775824MINT-66335 I2D: score=5 STRING: ENSP00000377582
    NUDT3O959892, 3, ENSP000003516504MINT-8264700 I2D: score=2 STRING: ENSP00000351650
    MYCP011063, ENSP000003672074I2D: score=1 STRING: ENSP00000367207
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IDA--
    GO:0007007inner mitochondrial membrane organization IMP--
    GO:0008053mitochondrial fusion IMP--

    CHCHD3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CHCHD3
    Search CenterWatch for drugs/clinical trials and news about CHCHD3 / CHCH3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for CHCHD3 gene: 
    NM_017812.2  

    Unigene Cluster for CHCHD3:

    Coiled-coil-helix-coiled-coil-helix domain containing 3
    Hs.655010  [show with all ESTs]
    Unigene Representative Sequence: BC011596
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000262570(uc003vre.3 uc010lmi.3 uc022alw.1) ENST00000448878
    ENST00000476546 ENST00000496427 ENST00000423635 ENST00000466644 ENST00000481152
    ENST00000457942 ENST00000542753(uc011kpn.1)

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    Additional cDNA sequence: 

    AK000427.1 AK129533.1 AK294071.1 AK310236.1 BC011596.2 BC014839.1 

    22 DOTS entries:

    DT.418327  DT.92447275  DT.92447264  DT.100027907  DT.100793380  DT.121098384  DT.121098513  DT.91638969 
    DT.100714450  DT.121417369  DT.100793378  DT.100793379  DT.108488  DT.100793383  DT.100793382  DT.121098314 
    DT.40213419  DT.75141800  DT.92447263  DT.95139015  DT.121098316  DT.91925398 

    24/350 AceView cDNA sequences (see all 350):

    AA879072 BG193548 BM794131 BM846708 CB136478 BG826486 CA443157 BM480102 
    BF982246 AI591034 BX096283 BQ231086 BM845315 AA812550 BM015192 BG219998 
    BM853046 BM711268 BM824098 CA443292 BI858573 T16615 CB242069 AA612824 

    GeneLoc Exon Structure


    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CHCHD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTGGTTTTGT
    CHCHD3 Expression
    About this image
    See CHCHD3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CHCHD3

    SOURCE GeneReport for Unigene cluster: Hs.655010

    UniProtKB/Swiss-Prot: CHCH3_HUMAN, Q9NX63
    Tissue specificity: Detected at low levels in brain, placenta, lung, liver, kidney and pancreas with increased levels
    in heart and skeletal muscle. Higher expression in primary lung cancers than in normal lung tissue

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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for CHCHD3 gene from 4/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves CHCHD31 coiled-coil-helix-coiled-coil-helix domain containing more 76.49(n)
    74.11(a)
      418435  XM_416646.3  XP_416646.3 
    African clawed frog
    (Xenopus laevis)
    Amphibia CD328491.12   -- 73.44(n)    CD328491.1 
    zebrafish
    (Danio rerio)
    Actinopterygii AY391426.12   -- 76.16(n)    AY391426.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta l(3)036706
    lethal (3) 03670
    20(a)
    1 → many
    3R(26878338-26879637)


    ENSEMBL Gene Tree for CHCHD3 (if available)
    TreeFam Gene Tree for CHCHD3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CHCHD3 gene
    CHCHD62  
    1 SIMAP similar gene for CHCHD3 using alignment to 6 protein entries:     CHCH3_HUMAN (see all proteins):
    CHCHD6

    CHCHD3 for paralogs           About GeneDecksing


    4 Pseudogenes.org Pseudogenes for CHCHD3
    PGOHUM00000238673 PGOHUM00000239851 PGOHUM00000243946 PGOHUM00000233464


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/4525 NCBI SNPs in CHCHD3 are shown (see all 4525    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs13184621,2
    C--132469144(+) ACCTTC/TTCATT 1 -- int11Minor allele frequency- T:0.00NA 2
    rs1880066701,2
    --132469166(+) TGACTA/GCTTAT 1 -- int10--------
    rs13184601,2
    C,F,A,H--132469174(+) TATTTC/ACAACT 1 -- int135Minor allele frequency- A:0.33NA EA NS CSA WA 3439
    rs13184611,2
    C,F,A--132469266(+) AAAAAT/CTGGAA 1 -- int117Minor allele frequency- C:0.34NA EA WA 1119
    rs11142621,2
    C,F,H--132469331(+) TGCAGG/AGTCAG 1 -- int122Minor allele frequency- A:0.09NA EA NS 1981
    rs1925863291,2
    --132469417(+) GTTCAC/TACAAT 1 -- int10--------
    rs1501893941,2
    --132469431(+) TAAAGA/TTCTTC 1 -- int10--------
    rs1855557661,2
    --132469463(+) GGCAAA/GTTATA 1 -- int10--------
    rs1892125471,2
    --132469822(+) CACCAC/TAATAA 1 -- ut310--------
    rs1478678251,2
    --132469851(+) TTACAC/TAATCA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for CHCHD3 (132469623 - 132719623 bp, first 250kb of CHCHD3)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 5 variations for CHCHD3
         3 CNVs: 94880 82192 3703
         1 Indel: 28452
         1 Inversion: 37280

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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.)
    About This Section

    CHCHD3 for disorders           About MalaCards

    CHCHD3 for disorders           About GeneDecksing

    OMIM gene information: 613748    OMIM disorders: --

    Human Genome Epidemiology (HuGE) Navigator: CHCHD3 (3 documents)

    Export disorders for CHCHD3 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)
    About This Section

    PubMed articles for CHCHD3 gene, integrated from 9 sources (see all 35):
    (articles sorted by number of sources associating them with CHCHD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. ChChd3, an inner mitochondrial membrane protein, is essential for maintaining crista integrity and mitochondrial function. (PubMed id 21081504)1, 2, 3 Darshi M.... Taylor S.S. (2011)
    2. MINOS1 is a conserved component of mitofilin complexe s and required for mitochondrial function and cristae organization. (PubMed id 22114354)1, 2 Alkhaja A.K....Deckers M. (2012)
    3. Targeting and import mechanism of coiled-coil helix co iled-coil helix domain-containing protein 3 (ChChd3) into the mitochondrial inte rmembrane space. (PubMed id 23019327)1, 3 Darshi M....Taylor S.S. (2012)
    4. Sam50 functions in mitochondrial intermembrane space b ridging and biogenesis of respiratory complexes. (PubMed id 22252321)1, 3 Ott C....Kozjak-Pavlovic V. (2012)
    5. The mitochondrial inner membrane protein mitofilin exists as a complex with SAM50, metaxins 1 and 2, coiled-coil-helix coiled-coil-helix domain-containing protein 3 and 6 and DnaJC11. (PubMed id 17624330)1, 3 Xie J....Capaldi R.A. (2007)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. 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. (2004)
    8. Cloning and functional analysis of FLJ20420: a novel transcription factor for the BAG-1 promoter. (PubMed id 22567091)2 Liu H.... Chen J. (2012)
    9. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    10. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)

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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: 54927 HGNC: 21906 AceView: CHCHD3 Ensembl:ENSG00000106554 euGenes: HUgn54927
    ECgene: CHCHD3 H-InvDB: CHCHD3

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for CHCHD3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for CHCHD3 gene:
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