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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
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Genomic context

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See MCM9 in Genome Data Viewer
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
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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

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