MCM7

minichromosome maintenance complex component 7, the group of minichromosome maintenance 2-7 complex|Protein phosphatase 1 regulatory subunits|MCM family|MicroRNA protein coding host genes

Basic information

Region (hg38): 7:100092233-100101940

Previous symbols: [ "MCM2" ]

Links

ENSG00000166508 ∙ NCBI:4176 ∙ OMIM:600592 ∙ HGNC:6950 ∙ Uniprot:P33993 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MCM7 gene.

• Meier-Gorlin syndrome (4 variants)
• 9 conditions (2 variants)
• Hereditary spastic paraplegia 50 (2 variants)
• Abnormality of the nervous system (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCM7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	4	5
missense	2		66	2	1	71
nonsense	3					3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding	3	4	14	17	5	43
Total	8	4	80	20	10

Highest pathogenic variant AF is 0.00000662

Variants in MCM7

This is a list of pathogenic ClinVar variants found in the MCM7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-100092988-C-G		not specified	Uncertain significance (Dec 19, 2022)
7-100093021-G-A		not specified	Uncertain significance (Jun 09, 2022)
7-100093033-G-A		not specified	Uncertain significance (Jun 17, 2024)
7-100093051-C-G		not specified	Uncertain significance (Jul 29, 2022)
7-100093055-C-G		not specified	Uncertain significance (Jul 25, 2023)
7-100093099-C-T		not specified	Likely benign (Feb 05, 2024)
7-100093122-G-A		not specified	Uncertain significance (Sep 15, 2021)
7-100093128-T-C		not specified	Uncertain significance (May 11, 2022)
7-100093133-C-T		not specified	Likely benign (Jan 04, 2024)
7-100093353-C-T		not specified	Uncertain significance (Mar 04, 2024)
7-100093358-T-A		not specified	Uncertain significance (Jul 19, 2023)
7-100093380-C-T		not specified	Uncertain significance (Jun 21, 2023)
7-100093384-C-T			Benign (Aug 18, 2018)
7-100094229-C-T		not specified	Uncertain significance (Dec 13, 2023)
7-100094248-C-G		MCM7-related disorder	Likely benign (May 11, 2018)
7-100094322-G-C		not specified	Uncertain significance (Sep 12, 2023)
7-100094334-T-C		not specified	Uncertain significance (Sep 27, 2022)
7-100094340-G-A		not specified	Uncertain significance (Nov 29, 2023)
7-100095391-T-G		not specified	Uncertain significance (Jan 26, 2023)
7-100095423-G-C		not specified	Uncertain significance (Feb 05, 2024)
7-100095433-G-A		not specified	Uncertain significance (Jul 14, 2021)
7-100095450-T-C		Meier-Gorlin syndrome	Pathogenic (-)
7-100095457-T-C		not specified	Uncertain significance (Jan 29, 2024)
7-100095783-T-C		not specified	Uncertain significance (Jun 07, 2023)
7-100095789-C-T		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCM7	protein_coding	protein_coding	ENST00000303887	15	9213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.94e-24	0.000721	125597	0	151	125748	0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.723	498	455	1.10	0.0000301	4647
Missense in Polyphen		136	167.6	0.81144		1706
Synonymous	-3.41	222	166	1.34	0.00000973	1465
Loss of Function	0.158	37	38.1	0.972	0.00000211	406

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000866	0.000865
Ashkenazi Jewish	0.00218	0.00218
East Asian	0.000272	0.000272
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000584	0.000580
Middle Eastern	0.000272	0.000272
South Asian	0.000850	0.000850
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Required for S-phase checkpoint activation upon UV-induced damage. {ECO:0000269|PubMed:15210935, ECO:0000269|PubMed:15538388, ECO:0000269|PubMed:9305914}.
• Pathway: Cell cycle - Homo sapiens (human);DNA replication - Homo sapiens (human);Cell Cycle;miRNA Regulation of DNA Damage Response;Retinoblastoma (RB) in Cancer;G1 to S cell cycle control;DNA Replication;cdk regulation of dna replication;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Activation of the pre-replicative complex;Unwinding of DNA;Mitotic G1-G1/S phases;Orc1 removal from chromatin;DNA Replication;Switching of origins to a post-replicative state;DNA strand elongation;Synthesis of DNA;S Phase;G1/S Transition;Assembly of the pre-replicative complex;DNA Replication Pre-Initiation;M/G1 Transition;Cell Cycle;TNFalpha;Cell Cycle, Mitotic;ATR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.414

Intolerance Scores

• loftool: 0.980
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.31

Haploinsufficiency Scores

• pHI: 0.936
• hipred: Y
• hipred_score: 0.779
• ghis: 0.698

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Mcm7
• Phenotype: cellular phenotype; growth/size/body region phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: mcm7
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;DNA replication;DNA unwinding involved in DNA replication;DNA replication initiation;cellular response to DNA damage stimulus;cell population proliferation;regulation of phosphorylation;response to drug;cellular response to epidermal growth factor stimulus;cellular response to xenobiotic stimulus
• Cellular component: nuclear chromosome, telomeric region;chromatin;nucleus;nucleoplasm;nucleolus;cytosol;membrane;MCM complex
• Molecular function: DNA binding;single-stranded DNA binding;ATP-dependent DNA helicase activity;protein binding;ATP binding