MCM9 (minichromosome maintenance 9 homologous recombination repair factor)

Gene

• Entrez ID: 254394
• Gene name: Minichromosome maintenance 9 homologous recombination repair factor
• Gene symbol: MCM9
• Synonyms: C6orf61, MCMDC1, ODG4, dJ329L24.1, dJ329L24.3
• Chromosome: 6
• Chromosome location: 6q22.31
• 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 recr

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs587777871	A>G	Pathogenic	Genic downstream transcript variant, intron variant, splice donor variant
rs587777872	G>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1060505058	C>A	Pathogenic	Stop gained, genic downstream transcript variant, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT024400	hsa-miR-215-5p	Microarray	19074876
MIRT024400	hsa-miR-215-5p	Microarray	19074876
MIRT026373	hsa-miR-192-5p	Microarray	19074876
MIRT633754	hsa-miR-6895-5p	HITS-CLIP	23824327
MIRT633753	hsa-miR-7160-3p	HITS-CLIP	23824327
MIRT633752	hsa-miR-4512	HITS-CLIP	23824327
MIRT633751	hsa-miR-5693	HITS-CLIP	23824327
MIRT633750	hsa-miR-6499-5p	HITS-CLIP	23824327
MIRT633749	hsa-miR-4284	HITS-CLIP	23824327
MIRT633748	hsa-miR-24-3p	HITS-CLIP	23824327
MIRT633747	hsa-miR-6781-5p	HITS-CLIP	23824327
MIRT633746	hsa-miR-1296-5p	HITS-CLIP	23824327
MIRT633745	hsa-miR-2909	HITS-CLIP	23824327
MIRT446902	hsa-miR-6750-3p	PAR-CLIP	22100165
MIRT446901	hsa-miR-888-5p	PAR-CLIP	22100165
MIRT446900	hsa-miR-4453	PAR-CLIP	22100165
MIRT446899	hsa-miR-4538	PAR-CLIP	22100165
MIRT446898	hsa-miR-3613-3p	PAR-CLIP	22100165
MIRT446897	hsa-miR-371b-5p	PAR-CLIP	22100165
MIRT446896	hsa-miR-373-5p	PAR-CLIP	22100165
MIRT446895	hsa-miR-616-5p	PAR-CLIP	22100165
MIRT446894	hsa-miR-5579-3p	PAR-CLIP	22100165
MIRT446893	hsa-miR-203a-3p	PAR-CLIP	22100165
MIRT633754	hsa-miR-6895-5p	HITS-CLIP	23824327
MIRT633753	hsa-miR-7160-3p	HITS-CLIP	23824327
MIRT633752	hsa-miR-4512	HITS-CLIP	23824327
MIRT633751	hsa-miR-5693	HITS-CLIP	23824327
MIRT633750	hsa-miR-6499-5p	HITS-CLIP	23824327
MIRT633749	hsa-miR-4284	HITS-CLIP	23824327
MIRT633748	hsa-miR-24-3p	HITS-CLIP	23824327
MIRT633747	hsa-miR-6781-5p	HITS-CLIP	23824327
MIRT633746	hsa-miR-1296-5p	HITS-CLIP	23824327
MIRT633745	hsa-miR-2909	HITS-CLIP	23824327
MIRT446902	hsa-miR-6750-3p	PAR-CLIP	22100165
MIRT446901	hsa-miR-888-5p	PAR-CLIP	22100165
MIRT446900	hsa-miR-4453	PAR-CLIP	22100165
MIRT446899	hsa-miR-4538	PAR-CLIP	22100165
MIRT446898	hsa-miR-3613-3p	PAR-CLIP	22100165
MIRT446897	hsa-miR-371b-5p	PAR-CLIP	22100165
MIRT446896	hsa-miR-373-5p	PAR-CLIP	22100165
MIRT446895	hsa-miR-616-5p	PAR-CLIP	22100165
MIRT446894	hsa-miR-5579-3p	PAR-CLIP	22100165
MIRT446893	hsa-miR-203a-3p	PAR-CLIP	22100165
MIRT1137845	hsa-miR-1207-3p	CLIP-seq
MIRT1137846	hsa-miR-138	CLIP-seq
MIRT1137847	hsa-miR-224	CLIP-seq
MIRT1137848	hsa-miR-3652	CLIP-seq
MIRT1137849	hsa-miR-3664-5p	CLIP-seq
MIRT1137850	hsa-miR-4282	CLIP-seq
MIRT1137851	hsa-miR-4430	CLIP-seq
MIRT1137852	hsa-miR-4503	CLIP-seq
MIRT1137853	hsa-miR-4699-5p	CLIP-seq
MIRT1137854	hsa-miR-4760-3p	CLIP-seq
MIRT1137855	hsa-miR-4774-5p	CLIP-seq
MIRT1137856	hsa-miR-4803	CLIP-seq
MIRT1137857	hsa-miR-490-3p	CLIP-seq
MIRT1137858	hsa-miR-649	CLIP-seq
MIRT1137859	hsa-miR-3123	CLIP-seq
MIRT1137860	hsa-miR-3159	CLIP-seq
MIRT1137861	hsa-miR-34b	CLIP-seq
MIRT1137862	hsa-miR-34c-3p	CLIP-seq
MIRT1137863	hsa-miR-3647-3p	CLIP-seq
MIRT1137864	hsa-miR-374a	CLIP-seq
MIRT1137865	hsa-miR-374b	CLIP-seq
MIRT1137866	hsa-miR-3925-5p	CLIP-seq
MIRT1137867	hsa-miR-4445	CLIP-seq
MIRT1137868	hsa-miR-4762-5p	CLIP-seq
MIRT1137869	hsa-miR-489	CLIP-seq
MIRT1137870	hsa-miR-539	CLIP-seq
MIRT1137845	hsa-miR-1207-3p	CLIP-seq
MIRT2039124	hsa-miR-140-3p	CLIP-seq
MIRT2039125	hsa-miR-2052	CLIP-seq
MIRT2039126	hsa-miR-3650	CLIP-seq
MIRT1137848	hsa-miR-3652	CLIP-seq
MIRT1137851	hsa-miR-4430	CLIP-seq
MIRT2039127	hsa-miR-496	CLIP-seq
MIRT2039128	hsa-miR-630	CLIP-seq
MIRT2269183	hsa-miR-23a	CLIP-seq
MIRT2269184	hsa-miR-23b	CLIP-seq
MIRT2269185	hsa-miR-23c	CLIP-seq
MIRT2039126	hsa-miR-3650	CLIP-seq
MIRT1137848	hsa-miR-3652	CLIP-seq
MIRT1137849	hsa-miR-3664-5p	CLIP-seq
MIRT1137851	hsa-miR-4430	CLIP-seq
MIRT2269186	hsa-miR-4639-3p	CLIP-seq
MIRT2269187	hsa-miR-4719	CLIP-seq
MIRT1137857	hsa-miR-490-3p	CLIP-seq
MIRT2269188	hsa-miR-587	CLIP-seq
MIRT2269189	hsa-miR-640	CLIP-seq
MIRT1137858	hsa-miR-649	CLIP-seq
MIRT2390737	hsa-miR-1208	CLIP-seq
MIRT2039126	hsa-miR-3650	CLIP-seq
MIRT1137845	hsa-miR-1207-3p	CLIP-seq
MIRT2039124	hsa-miR-140-3p	CLIP-seq
MIRT2269183	hsa-miR-23a	CLIP-seq
MIRT2269184	hsa-miR-23b	CLIP-seq
MIRT2269185	hsa-miR-23c	CLIP-seq
MIRT2039126	hsa-miR-3650	CLIP-seq
MIRT1137848	hsa-miR-3652	CLIP-seq
MIRT2568425	hsa-miR-3672	CLIP-seq
MIRT1137851	hsa-miR-4430	CLIP-seq
MIRT2269188	hsa-miR-587	CLIP-seq
MIRT2390737	hsa-miR-1208	CLIP-seq
MIRT2684739	hsa-miR-1236	CLIP-seq
MIRT2039124	hsa-miR-140-3p	CLIP-seq
MIRT2039126	hsa-miR-3650	CLIP-seq
MIRT1137848	hsa-miR-3652	CLIP-seq
MIRT1137849	hsa-miR-3664-5p	CLIP-seq
MIRT2568425	hsa-miR-3672	CLIP-seq
MIRT1137851	hsa-miR-4430	CLIP-seq
MIRT2684740	hsa-miR-4474-5p	CLIP-seq
MIRT2269186	hsa-miR-4639-3p	CLIP-seq
MIRT2684741	hsa-miR-4695-3p	CLIP-seq
MIRT2684742	hsa-miR-4729	CLIP-seq
MIRT2684743	hsa-miR-4778-3p	CLIP-seq
MIRT2684744	hsa-miR-579	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000724	Process	Double-strand break repair via homologous recombination	IBA	21873635
GO:0000724	Process	Double-strand break repair via homologous recombination	IDA	22771115
GO:0000724	Process	Double-strand break repair via homologous recombination	IMP	23401855
GO:0003678	Function	DNA helicase activity	IMP	26300262
GO:0003682	Function	Chromatin binding	IDA	23401855, 26300262
GO:0003688	Function	DNA replication origin binding	IBA	21873635
GO:0003697	Function	Single-stranded DNA binding	IBA	21873635
GO:0005515	Function	Protein binding	IPI	23401855, 26215093, 26300262
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA	23401855, 26300262
GO:0005694	Component	Chromosome	IEA
GO:0006260	Process	DNA replication	IGI	23401855
GO:0006974	Process	Cellular response to DNA damage stimulus	IDA	22771115
GO:0007292	Process	Female gamete generation	ISS
GO:0019899	Function	Enzyme binding	IPI	23401855, 26300262
GO:0032406	Function	MutLbeta complex binding	IDA	26300262
GO:0032407	Function	MutSalpha complex binding	IDA	26300262
GO:0032408	Function	MutSbeta complex binding	IDA	26300262
GO:0032508	Process	DNA duplex unwinding	IMP	26300262
GO:0036298	Process	Recombinational interstrand cross-link repair	IMP	23401855
GO:0042555	Component	MCM complex	IBA	21873635
GO:0044877	Function	Protein-containing complex binding	IDA	26215093
GO:0070716	Process	Mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication	IMP	26300262
GO:0071168	Process	Protein localization to chromatin	IMP	23401855, 26300262
GO:0097362	Component	MCM8-MCM9 complex	IDA	22771115, 23401855, 26215093, 26300262

Other IDs

• MIM: 610098
• HGNC: 21484
• e!Ensembl: ENSG00000111877

Protein

• UniProt ID: Q9NXL9
• Protein name: DNA helicase MCM9 (hMCM9) (EC 3.6.4.12) (Mini-chromosome maintenance deficient domain-containing protein 1) (Minichromosome maintenance 9)
• Protein function: Component of the MCM8-MCM9 complex, a complex involved in the repair of double-stranded DNA breaks (DBSs) and DNA interstrand cross-links (ICLs) by homologous recombination (HR) (PubMed:23401855). Required for DNA resection by the MRE11-RAD50-NB
• PDB: 7DPD, 7WI7, 7YOX, 8S91, 8S92, 8S94
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF17207	MCM_OB	114 → 247	MCM OB domain	Domain
  PF00493	MCM	294 → 509	MCM P-loop domain	Domain
  PF17855	MCM_lid	522 → 604	MCM AAA-lid domain	Domain

• Sequence:

  MNSDQVTLVGQVFESYVSEYHKNDILLILKERDEDAHYPVVVNAMTLFETNMEIGEYFNM
  FPSEVLTIFDSALRRSALTILQSLSQPEAVSMKQNLHARISGLPVCPELVREHIPKTKDV
  GHFLSVTGTVIRTSLVKVLEFERDYMCNKCKHVFVIKADFEQYYTFCRPSSCPSLESCDS
  SKFTCLSGLSSSPTRCRDYQEIKIQEQVQRLSVGSIPRSMKVILEDDLVDSCKSGDDLTI
  YGIVMQRWKPFQQDVRCEVEIVLKANYIQVNNEQSSGIIMDEEVQKEFEDFWEYYKSDPF
  AGRNVILASLCPQVFGMYLVKLAVAMVLAGGIQRTDATGTRVRGESHLLLVGDPGTGKSQ
  FLKYAAKITPRSVLTTGIGSTSAGLTVTAVKDSGEWNLEAGALVLADAGLCCIDEFNSLK
  EHDRTSIHEAMEQQTISVAKAGLVCKLNTRTTILAATNPKGQYDPQESVSVNIALGSPLL
  SRFDLILVLLDTKNEDWDRIISSFILENKGYPSKSEKLWSMEKMKTYFCLIRNLQPTLSD
  VGNQVLLRYYQMQRQSDCRNAARTTIRLLESLIRLAEAHARLMFRDTVTLEDAITVVSVM
  ESSMQGGALLGGVNALHTSFPENPGEQYQRQCELILEKLELQSLLSEELRRLERLQNQSV
  HQSQPRVLEVETTPGSLRNGPGEESNFRTSSQQEINYSTHIFSPGGSPEGSPVLDPPPHL
  EPNRSTSRKHSAQHKNNRDDSLDWFDFMATHQSEPKNTVVVSPHPKTSGENMASKISNST
  SQGKEKSEPGQRSKVDIGLLPSPGETGVPWRADNVESNKKKRLALDSEAAVSADKPDSVL
  THHVPRNLQKLCKERAQKLCRNSTRVPAQCTVPSHPQSTPVHSPDRMLDSPKRKRPKSLA
  QVEEPAIENVKPPGSPVAKLAKFTFKQKSKLIHSFEDHSHVSPGATKIAVHSPKISQRRT
  RRDAALPVKRPGKLTSTPGNQISSQPQGETKEVSQQPPEKHGPREKVMCAPEKRIIQPEL
  ELGNETGCAHLTCEGDKKEEVSGSNKSGKVHACTLARLANFCFTPPSESKSKSPPPERKN
  RGERGPSSPPTTTAPMRVSKRKSFQLRGSTEKLIVSKESLFTLPELGDEAFDCDWDEEMR
  KKS

• Sequence length: 1143

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
46, xx ovarian dysgenesis-short stature syndrome	46,XX ovarian dysgenesis-short stature syndrome	rs587777871, rs587777872, rs1060505058
Ovarian dysgenesis	OVARIAN DYSGENESIS 4	rs104894765, rs121909658, rs121909660, rs121909661, rs121909662, rs386833512, rs2093045125, rs386833510, rs386833511, rs386833513, rs386833514, rs386833515, rs864309645, rs864309646, rs1555178358, rs1567753148, rs1597722169	25480036, 2771120
Premature ovarian failure	Premature Ovarian Failure 1	rs587776535, rs71647804, rs137853320, rs606231206, rs121918655, rs121918656, rs606231207, rs606231208, rs80359775, rs397507719, rs200503569, rs587777267, rs730880018, rs587777268, rs587777269, rs587777270, rs201840174, rs587778428, rs41293513, rs200928781, rs587777871, rs587777872, rs606231343, rs672601359, rs193303102, rs193303103, rs193303104, rs138761187, rs869320753, rs869320765, rs878854403, rs875989810, rs875989885, rs876657679, rs1057517779, rs764841861, rs1057519602, rs147021911, rs1060505055, rs376787666, rs1554721235, rs1553752779, rs1553752894, rs144567652, rs1216260561, rs900140738, rs1560311010, rs1060502376, rs1001164504, rs1031011371, rs1596591051, rs1218620893, rs201115244, rs377712900, rs1800917478

Unknown
Disease name	Disease term	dbSNP ID	References
Dwarfism	Dwarfism
Hypogonadism	Primary hypogonadism
Mental depression	Major Depressive Disorder	rs587778876, rs587778877	30219690
Physiologic amenorrhea	Primary physiologic amenorrhea