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    MCM9 minichromosome maintenance 9 homologous recombination repair factor [ Homo sapiens (human) ]

    Gene ID: 254394, updated on 5-Mar-2024

    Summary

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    Official Symbol
    MCM9provided by HGNC
    Official Full Name
    minichromosome maintenance 9 homologous recombination repair factorprovided by HGNC
    Primary source
    HGNC:HGNC:21484
    See related
    Ensembl:ENSG00000111877 MIM:610098; AllianceGenome:HGNC:21484
    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
    ODG4; MCMDC1; C6orf61; dJ329L24.1; dJ329L24.3
    Summary
    The protein encoded by this gene is a member of the mini-chromosome maintenance (MCM) protein family that are essential for the initiation of eukaryotic genome replication. Binding of this protein to chromatin has been shown to be a pre-requisite for recruiting the MCM2-7 helicase to DNA replication origins. This protein also binds, and is a positive regulator of, the chromatin licensing and DNA replication factor 1, CDT1. [provided by RefSeq, Nov 2010]
    Expression
    Ubiquitous expression in thyroid (RPKM 3.1), lymph node (RPKM 3.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6q22.31
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (118813455..118935159, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (119999276..120121020, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (119134618..119256324, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene centrosomal protein 85 like Neighboring gene uncharacterized LOC124901388 Neighboring gene Sharpr-MPRA regulatory region 6198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25013 Neighboring gene selenoprotein K pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25015 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17507 Neighboring gene uncharacterized LOC124901389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17506 Neighboring gene anti-silencing function 1A histone chaperone Neighboring gene family with sequence similarity 184 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:119361669-119362560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17508 Neighboring gene MPRA-validated peak6067 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:119411357-119411858 Neighboring gene microRNA 548b Neighboring gene Sharpr-MPRA regulatory region 12550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17509 Neighboring gene mannosidase alpha class 1A member 1 Neighboring gene ribosomal protein L13a pseudogene 15

    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. The etiology of Down syndrome: Maternal MCM9 polymorphisms increase risk of reduced recombination and nondisjunction of chromosome 21 during meiosis I within oocyte. Pal U, et al. PLoS Genet, 2021 Mar. PMID 33750944, Free PMC Article
    2. Novel pathogenic mutations in minichromosome maintenance complex component 9 (MCM9) responsible for premature ovarian insufficiency. Guo T, et al. Fertil Steril, 2020 Apr. PMID 32145932
    3. Pathogenic germline MCM9 variants are rare in Australian Lynch-like syndrome patients. Liu Q, et al. Cancer Genet, 2016 Nov. PMID 27886675
    4. A non-sense MCM9 mutation in a familial case of primary ovarian insufficiency. Fauchereau F, et al. Clin Genet, 2016 May. PMID 26771056
    5. MCM9 mutations are associated with ovarian failure, short stature, and chromosomal instability. Wood-Trageser MA, et al. Am J Hum Genet, 2014 Dec 4. PMID 25480036, Free PMC Article

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Activity, substrate preference and structure of the HsMCM8/9 helicase.
      Title: Activity, substrate preference and structure of the HsMCM8/9 helicase.
    2. Structural study of the N-terminal domain of human MCM8/9 complex.
      Title: Structural study of the N-terminal domain of human MCM8/9 complex.
    3. The etiology of Down syndrome: Maternal MCM9 polymorphisms increase risk of reduced recombination and nondisjunction of chromosome 21 during meiosis I within oocyte.
      Title: The etiology of Down syndrome: Maternal MCM9 polymorphisms increase risk of reduced recombination and nondisjunction of chromosome 21 during meiosis I within oocyte.
    4. An exome-wide exploration of cases of primary ovarian insufficiency uncovers novel sequence variants and candidate genes.
      Title: An exome-wide exploration of cases of primary ovarian insufficiency uncovers novel sequence variants and candidate genes.
    5. Novel pathogenic mutations in minichromosome maintenance complex component 9 (MCM9) responsible for premature ovarian insufficiency.
      Title: Novel pathogenic mutations in minichromosome maintenance complex component 9 (MCM9) responsible for premature ovarian insufficiency.
    6. MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage.
      Title: MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage.
    7. Pathogenic variant in MCM9 gene is associated with premature ovarian insufficiency.
      Title: Gene variants identified by whole-exome sequencing in 33 French women with premature ovarian insufficiency.
    8. Conceptual MCM8-9 inhibitors will be powerful cancer-specific chemosensitizers for platinum compounds.
      Title: Inhibiting the MCM8-9 complex selectively sensitizes cancer cells to cisplatin and olaparib.
    9. stalled replication forks can be restarted in S phase via homologous recombination using MCM8-9 as an alternative replicative helicase.
      Title: Acute inactivation of the replicative helicase in human cells triggers MCM8-9-dependent DNA synthesis.
    10. Significant number of potentially damaging and novel variants in MCM9 in primary ovarian insufficiency; multiallelic association with variants in DDR and MCM8-MCM9 interactome genes.
      Title: MCM8 and MCM9 Nucleotide Variants in Women With Primary Ovarian Insufficiency.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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

    Associated conditions

    Description Tests
    46,XX ovarian dysgenesis-short stature syndrome
    MedGen: C4015409 OMIM: 616185 GeneReviews: Not available
    		Compare labs

    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

    • FLJ13942, FLJ20170, FLJ56845, MGC35304

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA helicase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables MutLbeta complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables MutSalpha complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables MutSbeta complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to single-stranded DNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA duplex unwinding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA duplex unwinding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    NOT involved_in DNA replication IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in double-strand break repair via homologous recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair via homologous recombination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in double-strand break repair via homologous recombination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in double-strand break repair via homologous recombination NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in female gamete generation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein localization to chromatin IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in recombinational interstrand cross-link repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of MCM complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of MCM8-MCM9 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of MCM8-MCM9 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    DNA helicase MCM9
    Names
    DNA replication licensing factor MCM9
    mini-chromosome maintenance deficient domain-containing protein 1
    minichromosome maintenance complex component 9
    NP_001365285.1
    NP_001365286.1
    NP_001365287.1
    NP_001365288.1
    NP_001365289.1
    NP_001365290.1
    NP_001365291.1
    NP_001365292.1
    NP_001365293.1
    NP_001365294.1
    NP_001365295.1
    NP_001365296.1
    NP_001365297.1
    NP_001365298.1
    NP_001365299.1
    NP_001365300.1
    NP_001365301.1
    NP_060166.2
    NP_694987.1

    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_041822.1 RefSeqGene

      Range
      5004..126708
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001378356.1 → NP_001365285.1  DNA helicase MCM9 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3), as well as variants 1 and 4, encodes isoform 1.
      Source sequence(s)
      AL132874, AL359634
      Consensus CDS
      CCDS56447.1
      UniProtKB/Swiss-Prot
      B4DR30, B9DI77, Q2KHJ0, Q8N5S5, Q9HCV5, Q9NXL9
      Related
      ENSP00000314505.5, ENST00000316316.10
      Conserved Domains (3) summary
      PTZ00449
      Location:751 → 1113
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd17760
      Location:305 → 603
      MCM9; DNA helicase Mcm9
      pfam17207
      Location:116 → 243
      MCM_OB; MCM OB domain

    2. NM_001378357.1 → NP_001365286.1  DNA helicase MCM9 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4), as well as variants 1 and 3, encodes isoform 1.
      Source sequence(s)
      AL132874, AL359634
      Consensus CDS
      CCDS56447.1
      UniProtKB/Swiss-Prot
      B4DR30, B9DI77, Q2KHJ0, Q8N5S5, Q9HCV5, Q9NXL9
      Conserved Domains (3) summary
      PTZ00449
      Location:751 → 1113
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd17760
      Location:305 → 603
      MCM9; DNA helicase Mcm9
      pfam17207
      Location:116 → 243
      MCM_OB; MCM OB domain

    3. NM_001378358.1 → NP_001365287.1  DNA helicase MCM9 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5), as well as variant 2, encodes isoform 2.
      Source sequence(s)
      AL132874
      Consensus CDS
      CCDS5121.1
      UniProtKB/TrEMBL
      A0A0S2Z662, B3KV41
      Conserved Domains (1) summary
      COG1241
      Location:10 → 385
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    4. NM_001378359.1 → NP_001365288.1  DNA helicase MCM9 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variant 7, encodes isoform 3.
      Source sequence(s)
      AL132874, AL359634
      Conserved Domains (2) summary
      cd17760
      Location:305 → 603
      MCM9; DNA helicase Mcm9
      pfam17207
      Location:116 → 243
      MCM_OB; MCM OB domain

    5. NM_001378360.1 → NP_001365289.1  DNA helicase MCM9 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7), as well as variant 6, encodes isoform 3.
      Source sequence(s)
      AL132874, AL359634
      Conserved Domains (2) summary
      cd17760
      Location:305 → 603
      MCM9; DNA helicase Mcm9
      pfam17207
      Location:116 → 243
      MCM_OB; MCM OB domain

    6. NM_001378361.1 → NP_001365290.1  DNA helicase MCM9 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8), as well as variants 9 and 10, encodes isoform 4.
      Source sequence(s)
      AL132874
      Conserved Domains (1) summary
      COG1241
      Location:34 → 319
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    7. NM_001378362.1 → NP_001365291.1  DNA helicase MCM9 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9), as well as variants 8 and 10, encodes isoform 4.
      Source sequence(s)
      AL132874
      Conserved Domains (1) summary
      COG1241
      Location:34 → 319
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    8. NM_001378363.1 → NP_001365292.1  DNA helicase MCM9 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10), as well as variants 8 and 9, encodes isoform 4.
      Source sequence(s)
      AL132874
      Conserved Domains (1) summary
      COG1241
      Location:34 → 319
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    9. NM_001378364.1 → NP_001365293.1  DNA helicase MCM9 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL132874, AL359634
      Conserved Domains (3) summary
      PTZ00449
      Location:683 → 1045
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      COG1241
      Location:10 → 511
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]
      cl28901
      Location:305 → 535
      MCM; MCM helicase family

    10. NM_001378365.1 → NP_001365294.1  DNA helicase MCM9 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL132874, FP885910
      Conserved Domains (2) summary
      PHA03307
      Location:365 → 631
      PHA03307; transcriptional regulator ICP4; Provisional
      COG1241
      Location:10 → 384
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    11. NM_001378366.1 → NP_001365295.1  DNA helicase MCM9 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL132874, AL359634
      Conserved Domains (2) summary
      COG1241
      Location:10 → 563
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]
      cd17760
      Location:302 → 561
      MCM9; DNA helicase Mcm9

    12. NM_001378367.1 → NP_001365296.1  DNA helicase MCM9 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AL132874, AL359634
      Conserved Domains (2) summary
      cd17760
      Location:239 → 537
      MCM9; DNA helicase Mcm9
      pfam17207
      Location:50 → 177
      MCM_OB; MCM OB domain

    13. NM_001378368.1 → NP_001365297.1  DNA helicase MCM9 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AL132874
      UniProtKB/TrEMBL
      B3KV41
      Conserved Domains (1) summary
      COG1241
      Location:10 → 343
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    14. NM_001378369.1 → NP_001365298.1  DNA helicase MCM9 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AL132874
      Conserved Domains (1) summary
      COG1241
      Location:10 → 286
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    15. NM_001378370.1 → NP_001365299.1  DNA helicase MCM9 isoform 11

      Status: REVIEWED

      Source sequence(s)
      AL132874
      Conserved Domains (1) summary
      COG1241
      Location:34 → 277
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    16. NM_001378371.1 → NP_001365300.1  DNA helicase MCM9 isoform 12

      Status: REVIEWED

      Source sequence(s)
      AL132874
      Conserved Domains (1) summary
      COG1241
      Location:10 → 233
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    17. NM_001378372.1 → NP_001365301.1  DNA helicase MCM9 isoform 13

      Status: REVIEWED

      Source sequence(s)
      AL132874
      Conserved Domains (1) summary
      COG1241
      Location:34 → 220
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    18. NM_017696.3 → NP_060166.2  DNA helicase MCM9 isoform 1

      See identical proteins and their annotated locations for NP_060166.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1, 3, and 4 all encode the same isoform (1).
      Source sequence(s)
      AL132874, AL359634
      Consensus CDS
      CCDS56447.1
      UniProtKB/Swiss-Prot
      B4DR30, B9DI77, Q2KHJ0, Q8N5S5, Q9HCV5, Q9NXL9
      Related
      ENSP00000480469.1, ENST00000619706.5
      Conserved Domains (3) summary
      PTZ00449
      Location:751 → 1113
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd17760
      Location:305 → 603
      MCM9; DNA helicase Mcm9
      pfam17207
      Location:116 → 243
      MCM_OB; MCM OB domain

    19. NM_153255.5 → NP_694987.1  DNA helicase MCM9 isoform 2

      See identical proteins and their annotated locations for NP_694987.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate 3' terminal exon and lacks 6 exons in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 2 and 5 both encode the same isoform (2).
      Source sequence(s)
      AL132874
      Consensus CDS
      CCDS5121.1
      UniProtKB/TrEMBL
      A0A0S2Z662, B3KV41
      Related
      ENSP00000312870.3, ENST00000316068.7
      Conserved Domains (1) summary
      COG1241
      Location:10 → 385
      Mcm2; DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]

    RNA

    1. NR_165493.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL132874, AL359634

    2. NR_165494.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL132874

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      118813455..118935159 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      119999276..120121020 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NXL9.4 GenPept UniProtKB/Swiss-Prot:Q9NXL9

    Gene LinkOut

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

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