MCM4
protein-codingminichromosome maintenance complex component 4, the group of MCM family|minichromosome maintenance 2-7 complex
Gene summary
The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre_RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. The MCM complex consisting of this protein and MCM2, 6 and 7 proteins possesses DNA helicase activity, and may act as a DNA unwinding enzyme. The phosphorylation of this protein by CDC2 kinase reduces the DNA helicase activity and chromatin binding of the MCM complex. This gene is mapped to a region on the chromosome 8 head-to-head next to the PRKDC/DNA-PK, a DNA-activated protein kinase involved in the repair of DNA double-strand breaks. Alternatively spliced transcript variants encoding the same protein have been reported. [provided by RefSeq, Jul 2008]
- CDC21
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0012383
Submitter: ClinGen
*MCM4* was first reported in relation to autosomal recessive inheritance of primary immunodeficiency with natural-killer cell deficiency and adrenal insufficiency in 2012 (Hughes et al., PMID: 22354170) and (Gineau et al., PMID: 22354167). This condition is characterized by adrenal failure, short stature, and natural killer (NK) cell deficiency. Affected individuals are also typically susceptible to recurrent infections. Evidence supporting this gene-disease relationship includes case-level data, segregation data, and experimental data. The only identified variant (a hypomorphic splice site mutation) in this gene has been reported in 7 probands, segregating with disease in five families from the Irish Traveler community. (PMIDs: 22354170, 22354167, 22499342). This gene-disease relationship is supported by its biochemical function, expression studies, functional assays, rescue studies, and a mouse model (PMIDs: 22354170, 22354167, 10567526, 17143284). In healthy subjects, *MCM4* is part of a complex genetic machinery responsible for genome stability and correct DNA replication with a role in single strand DNA binding (PMID: 10567526). In FGD patients, the specific impact of MCM4 variants is not fully understood but in a functional assay supports the hypothesis that the lack of full length *MCM4* results in selective lack of CD56dim in NK cells (PMID: 22354167). The same author detected no full-length *MCM4* protein in patient 1.2 (P1.2) EBV-B cells as well as P1.3 and P2.1 primary and SV40 fibroblasts, by Western blotting (Gineau et al., PMID: 22354167). In addition, Hughes et al, completed another expression study using immunoblotting in which control subjects were observed to have two main protein species, of approximately 96 and 85 kDa, while predicted full-length 96-kDa product is missing in the patients (Hughes et al., PMID: 22354170). Gineau et al., also addressed the impact of the mutated *MCM4* allele on DNA replication itself by investigating the cell cycle and DNA content in SV40 fibroblasts and identified a rescue. WT *MCM4* or the patients’ *MCM4* allele were expressed in patient fibroblasts and authors assessed the breakage phenotype to demonstrate that the observed genomic instability was due to the absence of the full-length MCM4 in the patients’ cells. Expression of the WT allele greatly decreased the number of DNA breaks per metaphase, whereas expression of the mutant allele did not (PMID: 22354167). Lastly, a mouse model with a hypomorphic *MCM4* allele recapitulated the increased genomic instability observed in patients, though it lacked additional features of the disease (PMID: 17143284). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged.
Inheritance Pattern: AR
Disease ID:MONDO:0012383
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0012383
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012383
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Endocrine; Musculoskeletal; Oncologic
Intervention: Allergy/Immunology/Infectious; Endocrine; Oncologic
Rationale: Individuals are susceptible to recurrent infections, and early and aggressive management may be beneficial related to morbidity and mortality; Adrenal insufficiency has been described, and medical management (with corticosteroids) has been described; Individuals have been suggested to have susceptibility to cancer, and awareness may allow early detection and management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MCM4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_182746.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | 186 | 2 | 193 | ||
| missense | 330 | 12 | 342 | |||
| nonsense | 1 | 3 | 4 | |||
| start loss | 0 | |||||
| frameshift | 1 | 10 | 11 | |||
| splice donor/acceptor (+/-2bp) | 1 | 10 | 11 | |||
| Total | 1 | 2 | 358 | 198 | 2 | 561 |
Highest pathogenic variant AF is 0.0000034296845
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_877423.1 | 16 | MANE Select | |
| Ensembl | ENSP00000496964.1 | 16 | MANE Select | |
| RefSeq | NP_005905.2 | 16 | Standard | |
| Ensembl | ENSP00000262105.2 | 16 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell cycle - Homo sapiens (human)
- DNA replication - Homo sapiens (human)
- Cell Cycle
- Gastric Cancer Network 1
- Retinoblastoma (RB) in Cancer
Biological Process
- G1/S transition of mitotic cell cycle
- DNA replication
- DNA unwinding involved in DNA replication
- DNA replication initiation
Molecular Function
- single-stranded DNA binding
- ATP-dependent DNA helicase activity
- protein binding
- ATP binding
Cellular Component
- nuclear chromosome, telomeric region
- nucleus
- nucleoplasm
- membrane
- MCM complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262105
- Coding exons
- 16
- Length
- 17976
- Individuals with no LoFs
- 125676
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 72
- Defined
- 125748
- p
- 0.000286
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.138 | 498 | 507 | 0.983 | 0.0000292 | 5651 |
| Missense (PolyPhen) | 142 | 185.23 | 0.76661 | 1964 | ||
| Synonymous | -0.918 | 209 | 193 | 1.08 | 0.0000112 | 1712 |
| Loss of Function | 3.78 | 14 | 39.7 | 0.353 | 0.00000200 | 465 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00014 | 0.00012 | rare |
| Latino/Admixed American | 0.00039 | 0.00038 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00098 | 0.00098 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00028 | 0.00027 | rare |
| South Asian | 0.00024 | 0.00023 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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. {ECO:0000269|PubMed:16899510, ECO:0000269|PubMed:9305914}.;
- Disease
- DISEASE: Immunodeficiency 54 (IMD54) [MIM:609981]: An autosomal recessive disorder characterized by severe intra- and extrauterine growth retardation, microcephaly, decreased numbers of natural killer cells, and recurrent viral infections, most often affecting the respiratory tract and leading to respiratory failure. Affected individuals also have adrenal insufficiency requiring corticosteroid replacement therapy and may have an increased susceptibility to cancer. {ECO:0000269|PubMed:22354167, ECO:0000269|PubMed:22354170, ECO:0000269|PubMed:22499342}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.155
Intolerance Scores
- LoFtool
- 0.813
- RVIS EVS
- -1.1
- RVIS percentile EVS
- 6.89
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |