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Gene

MCM9

minichromosome maintenance 9 homologous recombination repair factor

Summary

Cytogenetic location
6q22.31
Coordinates
Chromosome 6: 118,813,455–118,935,159 (GRCh38)
Exons
14 exons across 121.7 kb
Protein
1,143 amino acids
Inheritance
Autosomal recessive
Also known as
MGC35304, dJ329L24.3, FLJ20170
Previous symbols
MCMDC1, C6orf61
MANE Select transcript
ENST00000619706.5NM_017696.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Female Infertility

    • MCM9-related gametogenic failureAutosomal recessive

      A recessive condition caused by biallelic MCM9 variants that causes primary ovarian insufficiency or impaired sperm production, and also predisposes to colorectal polyposis and early-onset colorectal and gastric cancer.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Diagnosis warrants bowel and stomach cancer surveillance in addition to fertility care.

    • Diminished or absent ability of a female to achieve conception.

      • 2 GenCC submitters rate it definitive or strong

  • Male Infertility

    • MCM9-related gametogenic failureAutosomal recessive

      A recessive condition caused by biallelic MCM9 variants that causes primary ovarian insufficiency or impaired sperm production, and also predisposes to colorectal polyposis and early-onset colorectal and gastric cancer.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Diagnosis warrants bowel and stomach cancer surveillance in addition to fertility care.

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How MCM9 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where MCM9 sits. MCM9 and 5 genes near it on chromosome 6, from 118,374,307 to 119,374,306.Chromosome 66q22.31p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q27118.4 Mb118.6 Mb118.8 Mb119 Mb119.2 MbCEP85L: 118,460,760–118,710,098, reverse strandCEP85LPLN: 118,506,292–118,562,853, forward strandPLNMCM9: 118,813,455–118,935,159, reverse strandMCM9ASF1A: 118,894,020–118,909,264, forward strandASF1AFAM184A: 118,957,707–119,149,387, reverse strandFAM184AMAN1A1: 119,177,116–119,349,798, reverse strandMAN1A1Diagram of MCM9: 14 exons on the reverse strand of chromosome 6Exon 11: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 14: 118,813,455–118,816,294, 2,840 basesExon 13: 118,826,147–118,826,292, 146 basesExon 12: 118,826,782–118,826,864, 83 basesExon 11: 118,827,927–118,828,130, 204 basesExon 10: 118,829,048–118,829,250, 203 basesExon 9: 118,856,371–118,856,545, 175 basesExon 8: 118,911,650–118,911,769, 120 basesExon 7: 118,913,295–118,913,420, 126 basesExon 6: 118,917,561–118,917,761, 201 basesExon 5: 118,922,005–118,922,086, 82 basesExon 4: 118,923,811–118,924,127, 317 basesExon 3: 118,931,420–118,931,738, 319 basesExon 2: 118,932,607–118,932,740, 134 basesExon 1: 118,934,891–118,935,159, 269 bases1410515′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 5.2 kb of the gene's 121.7 kb; 3,432 of those bases code for the protein.

How a genome test reads MCM9

9

positions in MCM9 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 121.7 kb of MCM9, introns included, not only the 5.2 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). MCM9 gene: minichromosome maintenance 9 homologous recombination repair factor. Retrieved 17 October 2026, from https://dantelabs.com/genes/mcm9

Vancouver

Dante Labs. MCM9 gene: minichromosome maintenance 9 homologous recombination repair factor [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/mcm9

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