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    MGME1 mitochondrial genome maintenance exonuclease 1 [ Homo sapiens (human) ]

    Gene ID: 92667, updated on 10-Dec-2024

    Summary

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    Official Symbol
    MGME1provided by HGNC
    Official Full Name
    mitochondrial genome maintenance exonuclease 1provided by HGNC
    Primary source
    HGNC:HGNC:16205
    See related
    Ensembl:ENSG00000125871 MIM:615076; AllianceGenome:HGNC:16205
    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
    DDK1; MTDPS11; C20orf72; bA504H3.4
    Summary
    The protein encoded by this gene is a nuclear-encoded mitochondrial protein necessary for the maintenance of mitochondrial genome synthesis. The encoded protein is a RecB-type exonuclease and primarily cleaves single-stranded DNA. Defects in this gene have been associated with mitochondrial DNA depletion syndrome-11. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]
    Expression
    Ubiquitous expression in skin (RPKM 10.5), lymph node (RPKM 7.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MGME1 in Genome Data Viewer
    Location:
    20p11.23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (17968590..17991122)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (18019713..18042263)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (17949661..17971765)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17568 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:17887704-17887865 Neighboring gene RNA, U6 small nuclear 192, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17909901-17910427 Neighboring gene MPRA-validated peak4160 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17919356-17919949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17921137-17921728 Neighboring gene sorting nexin 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17573 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948150-17948904 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948905-17949659 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:17950167-17951366 Neighboring gene small nucleolar RNA, C/D box 17 Neighboring gene NANOG hESC enhancer GRCh37_chr20:17964055-17965008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17579 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:17980569-17981070 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17985803-17986364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17988051-17988612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17988613-17989173 Neighboring gene prothymosin alpha pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:18017759-18018259 Neighboring gene ovo like zinc finger 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:18034137-18034637 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:18036965-18037752

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. MGME1 associates with poor prognosis and is vital for cell proliferation in lower-grade glioma. Xiao F, et al. Aging (Albany NY), 2023 May 8. PMID 37166417, Free PMC Article
    2. Structural insights into DNA degradation by human mitochondrial nuclease MGME1. Yang C, et al. Nucleic Acids Res, 2018 Nov 16. PMID 30247721, Free PMC Article
    3. Homozygous c.359del variant in MGME1 is associated with early onset cerebellar ataxia. Hebbar M, et al. Eur J Med Genet, 2017 Oct. PMID 28711739, Free PMC Article
    4. Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels. Szczesny RJ, et al. Nucleic Acids Res, 2013 Mar 1. PMID 23358826, Free PMC Article
    5. Mitochondrial pathology in inclusion body myositis. Lindgren U, et al. Neuromuscul Disord, 2015 Apr. PMID 25638290

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MGME1 associates with poor prognosis and is vital for cell proliferation in lower-grade glioma.
      Title: MGME1 associates with poor prognosis and is vital for cell proliferation in lower-grade glioma.
    2. Besides the conserved two-cation-assisted catalytic mechanism, structural analysis of HsMGME1 and comparison with homologous proteins also clarified substrate binding and cleavage directionalities of the DNA double-strand break repair complexes RecBCD and AddAB.
      Title: Structural insights into DNA degradation by human mitochondrial nuclease MGME1.
    3. MGME1 is part of a termination complex acting at the end of the D-loop region where it modulates mtDNA replication and H-strand transcription termination
      Title: Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria.
    4. A novel frameshift deletion in MGME1 causes early onset cerebellar ataxia.
      Title: Homozygous c.359del variant in MGME1 is associated with early onset cerebellar ataxia.
    5. MGME1 processes flaps into ligatable nicks in concert with DNA polymerase gamma during mtDNA replication.
      Title: MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication.
    6. MGME1-mediated mtDNA processing is essential for faithful mitochondrial genome replication and might be required for intramolecular recombination of mtDNA.
      Title: Linear mtDNA fragments and unusual mtDNA rearrangements associated with pathological deficiency of MGME1 exonuclease.
    7. Overexperssion of Ddk1 decreases the levels of 7S DNA, suggesting an important role of the protein in 7S DNA regulation.
      Title: Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels.
    8. Loss-of-function mutations in MGME1 impair mtDNA replication and cause multisystemic mitochondrial disease.
      Title: Loss-of-function mutations in MGME1 impair mtDNA replication and cause multisystemic mitochondrial disease.
    9. 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14597

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded DNA 5'-3' DNA exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded DNA exodeoxyribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in mitochondrial DNA repair TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in mitochondrial DNA replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial DNA replication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrial genome maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    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 

    General protein information

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    Preferred Names
    mitochondrial genome maintenance exonuclease 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.

    Genomic

    1. NG_042236.1 RefSeqGene

      Range
      5128..27232
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001310338.2 → NP_001297267.1  mitochondrial genome maintenance exonuclease 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001297267.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC016869, BM750186, BX382492, DB014120
      UniProtKB/Swiss-Prot
      Q9BQP7
      Conserved Domains (1) summary
      cl00641
      Location:148 → 291
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4

    2. NM_001310339.2 → NP_001297268.1  mitochondrial genome maintenance exonuclease 1 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks three alternate coding exons compared to variant 1, that causes a frameshift. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC016869, BM750186, CV807140, DB014120
      Consensus CDS
      CCDS82600.1
      UniProtKB/TrEMBL
      Q5QPE7
      Related
      ENSP00000366933.4, ENST00000377704.4

    3. NM_001363738.2 → NP_001350667.1  mitochondrial genome maintenance exonuclease 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AF306686, AK310282, BC016869, BG684257, DB014120
      Consensus CDS
      CCDS86934.1
      UniProtKB/TrEMBL
      Q5QPE8
      Related
      ENSP00000366938.1, ENST00000377709.1
      Conserved Domains (1) summary
      cl00641
      Location:96 → 205
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4

    4. NM_052865.4 → NP_443097.1  mitochondrial genome maintenance exonuclease 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_443097.1

      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)
      BC016869, BM750186, DB014120
      Consensus CDS
      CCDS13131.1
      UniProtKB/Swiss-Prot
      B2RDG5, D3DW29, Q96SW3, Q9BQP7
      Related
      ENSP00000366939.5, ENST00000377710.10
      Conserved Domains (1) summary
      cl00641
      Location:176 → 285
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      17968590..17991122
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017028128.2 → XP_016883617.1  mitochondrial genome maintenance exonuclease 1 isoform X2

      UniProtKB/Swiss-Prot
      B2RDG5, D3DW29, Q96SW3, Q9BQP7
      Conserved Domains (1) summary
      cl00641
      Location:176 → 285
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4

    2. XM_047440586.1 → XP_047296542.1  mitochondrial genome maintenance exonuclease 1 isoform X5

    3. XM_047440584.1 → XP_047296540.1  mitochondrial genome maintenance exonuclease 1 isoform X4

    4. XM_011529394.1 → XP_011527696.1  mitochondrial genome maintenance exonuclease 1 isoform X1

      See identical proteins and their annotated locations for XP_011527696.1

      Conserved Domains (1) summary
      cl00641
      Location:148 → 291
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4

    5. XM_047440582.1 → XP_047296538.1  mitochondrial genome maintenance exonuclease 1 isoform X3

      UniProtKB/TrEMBL
      Q5QPE8

    6. XM_005260867.4 → XP_005260924.1  mitochondrial genome maintenance exonuclease 1 isoform X1

      See identical proteins and their annotated locations for XP_005260924.1

      Conserved Domains (1) summary
      cl00641
      Location:148 → 291
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4

    7. XM_017028127.3 → XP_016883616.1  mitochondrial genome maintenance exonuclease 1 isoform X2

      UniProtKB/Swiss-Prot
      B2RDG5, D3DW29, Q96SW3, Q9BQP7
      Conserved Domains (1) summary
      cl00641
      Location:176 → 285
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4

    8. XM_047440585.1 → XP_047296541.1  mitochondrial genome maintenance exonuclease 1 isoform X5

    9. XM_047440583.1 → XP_047296539.1  mitochondrial genome maintenance exonuclease 1 isoform X3

      UniProtKB/TrEMBL
      Q5QPE8

    10. XM_006723663.5 → XP_006723726.1  mitochondrial genome maintenance exonuclease 1 isoform X4

    11. XM_005260870.5 → XP_005260927.1  mitochondrial genome maintenance exonuclease 1 isoform X5

      See identical proteins and their annotated locations for XP_005260927.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      18019713..18042263
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324216.1 → XP_054180191.1  mitochondrial genome maintenance exonuclease 1 isoform X2

      UniProtKB/Swiss-Prot
      B2RDG5, D3DW29, Q96SW3, Q9BQP7

    2. XM_054324223.1 → XP_054180198.1  mitochondrial genome maintenance exonuclease 1 isoform X5

    3. XM_054324220.1 → XP_054180195.1  mitochondrial genome maintenance exonuclease 1 isoform X4

    4. XM_054324214.1 → XP_054180189.1  mitochondrial genome maintenance exonuclease 1 isoform X1

    5. XM_054324217.1 → XP_054180192.1  mitochondrial genome maintenance exonuclease 1 isoform X3

      UniProtKB/TrEMBL
      Q5QPE8

    6. XM_054324213.1 → XP_054180188.1  mitochondrial genome maintenance exonuclease 1 isoform X1

    7. XM_054324215.1 → XP_054180190.1  mitochondrial genome maintenance exonuclease 1 isoform X2

      UniProtKB/Swiss-Prot
      B2RDG5, D3DW29, Q96SW3, Q9BQP7

    8. XM_054324222.1 → XP_054180197.1  mitochondrial genome maintenance exonuclease 1 isoform X5

    9. XM_054324219.1 → XP_054180194.1  mitochondrial genome maintenance exonuclease 1 isoform X3

      UniProtKB/TrEMBL
      Q5QPE8

    10. XM_054324218.1 → XP_054180193.1  mitochondrial genome maintenance exonuclease 1 isoform X4

    11. XM_054324221.1 → XP_054180196.1  mitochondrial genome maintenance exonuclease 1 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQP7.1 GenPept UniProtKB/Swiss-Prot:Q9BQP7

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