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    CHCHD6 coiled-coil-helix-coiled-coil-helix domain containing 6 [ Homo sapiens (human) ]

    Gene ID: 84303, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CHCHD6provided by HGNC
    Official Full Name
    coiled-coil-helix-coiled-coil-helix domain containing 6provided by HGNC
    Primary source
    HGNC:HGNC:28184
    See related
    Ensembl:ENSG00000159685 MIM:615634; AllianceGenome:HGNC:28184
    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
    CHCM1; Mic25; MICOS25; PPP1R23
    Summary
    Involved in DNA damage response and cristae formation. Located in cytosol and mitochondrial inner membrane. Part of MICOS complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 1.6), brain (RPKM 0.9) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See CHCHD6 in Genome Data Viewer
    Location:
    3q21.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (126704240..126960420)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (129436700..129692602)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (126423083..126679263)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14679 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126397718-126398324 Neighboring gene nucleoporin 210 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126423783-126424334 Neighboring gene SF3A2 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126465189-126465888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126469383-126470020 Neighboring gene Sharpr-MPRA regulatory regions 1012 and 11425 Neighboring gene regulator of chromosome condensation 2 pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:126549126-126549983 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:126549984-126550840 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126570363-126570924 Neighboring gene Sharpr-MPRA regulatory region 387 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:126627623-126627935 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:126629966-126631165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126678753-126679300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126680398-126680946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126680947-126681493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20447 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126713795-126714428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126716329-126716962 Neighboring gene Sharpr-MPRA regulatory region 11201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126719495-126720128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20449 Neighboring gene Sharpr-MPRA regulatory region 421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20450 Neighboring gene plexin A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126762997-126763640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126772262-126772762 Neighboring gene MPRA-validated peak4817 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126783715-126784214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126789374-126789874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126789875-126790375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126807100-126807726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126807727-126808352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126811845-126812457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126815371-126816008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126826424-126826924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126857595-126858095 Neighboring gene MPRA-validated peak4818 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126903541-126904408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126915318-126916262 Neighboring gene PRR23 family member E

    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. Mitofilin and CHCHD6 physically interact with Sam50 to sustain cristae structure. Ding C, et al. Sci Rep, 2015 Nov 4. PMID 26530328, Free PMC Article
    2. A CHCHD6-APP axis connects amyloid and mitochondrial pathology in Alzheimer's disease. Shang Y, et al. Acta Neuropathol, 2022 Nov. PMID 36104602, Free PMC Article
    3. CHCHD10 mutations promote loss of mitochondrial cristae junctions with impaired mitochondrial genome maintenance and inhibition of apoptosis. Genin EC, et al. EMBO Mol Med, 2016 Jan 1. PMID 26666268, Free PMC Article
    4. CHCM1/CHCHD6, novel mitochondrial protein linked to regulation of mitofilin and mitochondrial cristae morphology. An J, et al. J Biol Chem, 2012 Mar 2. PMID 22228767, Free PMC Article
    5. PKA Regulates PINK1 Stability and Parkin Recruitment to Damaged Mitochondria through Phosphorylation of MIC60. Akabane S, et al. Mol Cell, 2016 May 5. PMID 27153535

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A CHCHD6-APP axis connects amyloid and mitochondrial pathology in Alzheimer's disease.
      Title: A CHCHD6-APP axis connects amyloid and mitochondrial pathology in Alzheimer's disease.
    2. mitochondria exhibited lower cristae density in CHCHD6-knockout cells. CHCHD6 directly interacted with Sam50.
      Title: Mitofilin and CHCHD6 physically interact with Sam50 to sustain cristae structure.
    3. CHCM1/CHCHD6, novel mitochondrial protein linked to regulation of mitofilin and mitochondrial cristae morphology.
      Title: CHCM1/CHCHD6, novel mitochondrial protein linked to regulation of mitofilin and mitochondrial cristae morphology.
    4. 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.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    6. anti-mitofilin mAb immunocaptures its target protein in association with six other proteins, metaxins 1 and 2, SAM50, CHCHD3, CHCHD6 and DnaJC11, respectively
      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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    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

    • MGC13016

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cristae formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 IC
    Inferred by Curator
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of MIB complex HDA PubMed 
    part_of MICOS complex HDA PubMed 
    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 cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrial crista junction NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial inner membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    MICOS complex subunit MIC25
    Names
    coiled coil helix cristae morphology 1
    coiled-coil-helix cristae morphology protein 1
    coiled-coil-helix-coiled-coil-helix domain-containing protein 6, mitochondrial
    mitochondrial contact site and cristae organizing system subunit 25
    protein phosphatase 1, regulatory subunit 23

    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_001320610.2 → NP_001307539.1  MICOS complex subunit MIC25 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC117450, AK310910, BC006123, BG192698, DN992600
      UniProtKB/TrEMBL
      J3QTA6
      Related
      ENSP00000422912.1, ENST00000508789.5
      Conserved Domains (1) summary
      pfam05300
      Location:17 → 190
      DUF737; Protein of unknown function (DUF737)

    2. NM_032343.3 → NP_115719.1  MICOS complex subunit MIC25 isoform 2

      See identical proteins and their annotated locations for NP_115719.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC117450, BC006123, DN992600
      Consensus CDS
      CCDS3041.1
      UniProtKB/Swiss-Prot
      D6R9U0, D6RIB4, H8Y0Y7, Q9BRQ6
      UniProtKB/TrEMBL
      J3QTA6
      Related
      ENSP00000290913.3, ENST00000290913.8
      Conserved Domains (1) summary
      pfam05300
      Location:17 → 189
      DUF737; Protein of unknown function (DUF737)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      126704240..126960420
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      129436700..129692602
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRQ6.1 GenPept UniProtKB/Swiss-Prot:Q9BRQ6

    Gene LinkOut

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

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