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    CHCHD3 coiled-coil-helix-coiled-coil-helix domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 54927, updated on 3-Nov-2024

    Summary

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    Official Symbol
    CHCHD3provided by HGNC
    Official Full Name
    coiled-coil-helix-coiled-coil-helix domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:21906
    See related
    Ensembl:ENSG00000106554 MIM:613748; AllianceGenome:HGNC:21906
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Mic19; MINOS3; MICOS19; PPP1R22
    Summary
    The protein encoded by this gene is an inner mitochondrial membrane scaffold protein. Absence of the encoded protein affects the structural integrity of mitochondrial cristae and leads to reductions in ATP production, cell growth, and oxygen consumption. This protein is part of the mitochondrial contact site and cristae organizing system (MICOS). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
    Expression
    Ubiquitous expression in heart (RPKM 24.9), duodenum (RPKM 14.8) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See CHCHD3 in Genome Data Viewer
    Location:
    7q32.3-q33
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (132784870..133082090, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (134106386..134403617, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (132469631..132766850, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD46 Neighboring gene uncharacterized LOC100506937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:132443779-132444332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:132455865-132456366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:132456367-132456866 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:132558086-132558347 Neighboring gene Sharpr-MPRA regulatory region 15449 Neighboring gene Sharpr-MPRA regulatory region 5703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26681 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:132728273-132728435 Neighboring gene eukaryotic translation elongation factor 1 gamma pseudogene Neighboring gene microRNA 3654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:132766583-132767217 Neighboring gene uncharacterized LOC105375512 Neighboring gene RNA, U6 small nuclear 92, pseudogene

    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 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. Sam50-Mic19-Mic60 axis determines mitochondrial cristae architecture by mediating mitochondrial outer and inner membrane contact. Tang J, et al. Cell Death Differ, 2020 Jan. PMID 31097788, Free PMC Article
    2. STED super-resolution microscopy reveals an array of MINOS clusters along human mitochondria. Jans DC, et al. Proc Natl Acad Sci U S A, 2013 May 28. PMID 23676277, Free PMC Article
    3. Cloning and functional analysis of FLJ20420: a novel transcription factor for the BAG-1 promoter. Liu H, et al. PLoS One, 2012. PMID 22567091, Free PMC Article
    4. Mic60/Mitofilin determines MICOS assembly essential for mitochondrial dynamics and mtDNA nucleoid organization. Li H, et al. Cell Death Differ, 2016 Mar. PMID 26250910, Free PMC Article
    5. Targeting and import mechanism of coiled-coil helix coiled-coil helix domain-containing protein 3 (ChChd3) into the mitochondrial intermembrane space. Darshi M, et al. J Biol Chem, 2012 Nov 16. PMID 23019327, Free PMC Article

    See all (157) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sam50-Mic19-Mic60 axis determines mitochondrial cristae architecture by mediating mitochondrial outer and inner membrane contact.
      Title: Sam50-Mic19-Mic60 axis determines mitochondrial cristae architecture by mediating mitochondrial outer and inner membrane contact.
    2. Multicolor 3D MINFLUX nanoscopy of mitochondrial MICOS proteins.
      Title: Multicolor 3D MINFLUX nanoscopy of mitochondrial MICOS proteins.
    3. Sub-mitochondrial localization of the genetic-tagged mitochondrial intermembrane space-bridging components Mic19, Mic60 and Sam50.
      Title: Sub-mitochondrial localization of the genetic-tagged mitochondrial intermembrane space-bridging components Mic19, Mic60 and Sam50.
    4. The findings suggest that Mic19 is a redox-dependent regulator of mitochondrial contact site and crista organizing system complex function.
      Title: The Oxidation Status of Mic19 Regulates MICOS Assembly.
    5. both the myristoylation and the CHCH domain are essential for the import and mitochondrial localization of ChChd3. Once imported, ChChd3 binds to Mia40 for further folding and assembly into macromolecular complexes.
      Title: Targeting and import mechanism of coiled-coil helix coiled-coil helix domain-containing protein 3 (ChChd3) into the mitochondrial intermembrane space.
    6. ChChd3 is a scaffolding protein that stabilizes protein complexes involved in maintaining crista architecture and protein import and is thus essential for maintaining mitochondrial structure and function.
      Title: ChChd3, an inner mitochondrial membrane protein, is essential for maintaining crista integrity and mitochondrial function.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    9. mitofilin helps regulate mitochondrial morphology and at least four of the associated proteins (metaxins 1 and 2, SAM50 and CHCHD3) have been implicated in protein import
      Title: 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.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20420

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular adaptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables phosphatase binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cristae formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cristae formation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in inner mitochondrial membrane organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in inner mitochondrial membrane organization IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in inner mitochondrial membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrial fusion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of MIB complex HDA PubMed 
    part_of MICOS complex HDA PubMed 
    part_of MICOS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of MICOS complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of MICOS complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of SAM complex HDA PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in mitochondrial crista junction NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrial inner membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrial inner membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrion HDA PubMed 
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    MICOS complex subunit MIC19
    Names
    coiled-coil-helix-coiled-coil-helix domain-containing protein 3, mitochondrial
    mitochondrial contact site and cristae organizing system subunit 19
    mitochondrial inner membrane organizing system 3
    protein phosphatase 1, regulatory subunit 22

    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_001317177.2 → NP_001304106.1  MICOS complex subunit MIC19 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK000427, AL516679, DC385940
      Consensus CDS
      CCDS87549.1
      UniProtKB/TrEMBL
      C9JRZ6
      Related
      ENSP00000389297.2, ENST00000448878.6
      Conserved Domains (2) summary
      pfam05300
      Location:15 → 180
      DUF737; Protein of unknown function (DUF737)
      pfam06747
      Location:188 → 220
      CHCH; CHCH domain

    2. NM_001317178.2 → NP_001304107.1  MICOS complex subunit MIC19 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus and lacks an internal segment compared to isoform 1.
      Source sequence(s)
      AC008038, AK294071, DC385940
      UniProtKB/TrEMBL
      B7Z1X9
      Conserved Domains (1) summary
      pfam05300
      Location:15 → 125
      DUF737; Protein of unknown function (DUF737)

    3. NM_017812.4 → NP_060282.1  MICOS complex subunit MIC19 isoform 2

      See identical proteins and their annotated locations for NP_060282.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      BC014839, DC385940
      Consensus CDS
      CCDS5828.1
      UniProtKB/Swiss-Prot
      Q9NX63
      UniProtKB/TrEMBL
      A4D1N4
      Related
      ENSP00000262570.5, ENST00000262570.10
      Conserved Domains (1) summary
      pfam05300
      Location:15 → 175
      DUF737; Protein of unknown function (DUF737)

    RNA

    1. NR_133671.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon but contains three additional alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK000427, AK310236, DC385940

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      132784870..133082090 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420549.1 → XP_047276505.1  MICOS complex subunit MIC19 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      134106386..134403617 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358537.1 → XP_054214512.1  MICOS complex subunit MIC19 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NX63.1 GenPept UniProtKB/Swiss-Prot:Q9NX63

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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