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

Gene ID: 92667, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (17968590..17991122)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (18019713..18042263)
105.20220307 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: 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. 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. Mitochondrial pathology in inclusion body myositis. Lindgren U, et al. Neuromuscul Disord, 2015 Apr. PMID 25638290
  5. Linear mtDNA fragments and unusual mtDNA rearrangements associated with pathological deficiency of MGME1 exonuclease. Nicholls TJ, et al. Hum Mol Genet, 2014 Dec 1. PMID 24986917, Free PMC Article

See all (43) 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)

Genotypes

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
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_2023_10

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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