MCM4

protein-coding

minichromosome 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]

Previous symbols:
  • CDC21

MANE transcript

NM_182746.3

Inheritance

AR

ClinVar variants

P:3U:358B:200

Top phenotype

Immunodeficiency 54

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr8:47,960,185-47,978,160

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~18.0 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

primary immunodeficiency with natural-killer cell deficiency and adrenal insufficiencyMODERATE

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.

primary immunodeficiency with natural-killer cell deficiency and adrenal insufficiencyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012383

Submitter: PanelApp Australia

primary immunodeficiency with natural-killer cell deficiency and adrenal insufficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012383

Submitter: Orphanet

primary immunodeficiency with natural-killer cell deficiency and adrenal insufficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012383

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Immunodeficiency 54AR

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

Refs: 14702466; 17142786; 22354167; 22354170Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MCM4 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 623
not specifiedTotal: 158
Primary immunodeficiency with natural-killer cell deficiency and adrenal insufficiencyTotal: 78
MCM4-related disorderTotal: 16
Inborn errors of metabolismTotal: 1
MicrocephalyTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
186
clinvar
2
clinvar
193
missense
330
clinvar
12
clinvar
342
nonsense
1
clinvar
3
clinvar
4
start loss
0
frameshift
1
clinvar
10
clinvar
11
splice donor/acceptor (+/-2bp)
1
clinvar
10
clinvar
11
Total123581982561

Highest pathogenic variant AF is 0.0000034296845

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_182746.3RefSeqNP_877423.116MANE Select
ENST00000649973.1EnsemblENSP00000496964.116MANE Select
NM_005914.4RefSeqNP_005905.216Standard
ENST00000262105.6EnsemblENSP00000262105.216Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.1384985070.9830.00002925651
Missense (PolyPhen)142185.230.766611964
Synonymous-0.9182091931.080.00001121712
Loss of Function3.781439.70.3530.00000200465

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000140.00012rare
Latino/Admixed American0.000390.00038rare
Ashkenazi Jewish00.0absent
East Asian0.000980.00098rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000280.00027rare
South Asian0.000240.00023rare
Other00.0absent

dbNSFP Gene Annotations

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. {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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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