MCM5

protein-coding

minichromosome maintenance complex component 5, the group of minichromosome maintenance 2-7 complex|MCM family

Gene summary

The protein encoded by this gene is structurally very similar to the CDC46 protein from S. cerevisiae, a protein involved in the initiation of DNA replication. The encoded protein is a member of the MCM family of chromatin-binding proteins and can interact with at least two other members of this family. The encoded protein is upregulated in the transition from the G0 to G1/S phase of the cell cycle and may actively participate in cell cycle regulation. [provided by RefSeq, Jul 2008]

Previous symbols:
  • CDC46

MANE transcript

NM_006739.4

Inheritance

AR

ClinVar variants

P:1U:275B:118

Top phenotype

Meier-Gorlin syndrome 8

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr22:35,400,134-35,425,431

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~25.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Meier-Gorlin syndrome 8LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0033046

Submitter: PanelApp Australia

Meier-Gorlin syndrome 8LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0033046

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Meier-Gorlin syndrome 8AR

Manifestation: Craniofacial; Genitourinary; Musculoskeletal

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 28198391Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MCM5 variants in ClinVar

4 Conditions Cataloged
not providedTotal: 409
not specifiedTotal: 121
MCM5-related disorderTotal: 8
Meier-Gorlin syndrome 8Total: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006739.4. 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
99
clinvar
7
clinvar
106
missense
1
clinvar
260
clinvar
9
clinvar
2
clinvar
272
nonsense
3
clinvar
3
start loss
0
frameshift
5
clinvar
5
splice donor/acceptor (+/-2bp)
7
clinvar
1
clinvar
8
Total102751099394

Highest pathogenic variant AF is 6.842173e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006739.4RefSeqNP_006730.216MANE Select
ENST00000216122.9EnsemblENSP00000216122.316MANE Select
ENST00000382011.10EnsemblENSP00000371441.515Standard
ENST00000382011.9EnsemblENSP00000371441.515Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
mcm5Danio rerio

Structure: whole organism

Quality: dwarf-like

abnormal

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
  • G1 to S cell cycle control
  • DNA Replication

Biological Process

  • G1/S transition of mitotic cell cycle
  • DNA replication
  • DNA replication initiation

Molecular Function

  • DNA replication origin binding
  • helicase activity
  • protein binding
  • ATP binding

Cellular Component

  • nuclear chromosome, telomeric region
  • nucleus
  • nucleoplasm
  • cytosol
  • membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000216122
Coding exons
16
Length
25368
Individuals with no LoFs
125717
Homozygous LoFs
0
Heterozygous LoFs
31
Defined
125748
p
0.000123
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.164094810.8510.00003054806
Missense (PolyPhen)114174.60.652931668
Synonymous-0.7392041911.070.00001221455
Loss of Function3.561234.60.3470.00000189386

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000190.00018rare
Latino/Admixed American0.000200.00020rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000140.00014rare
South Asian0.0000980.000098rare
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 (By similarity). Interacts with MCMBP. {ECO:0000250}.;
Disease
DISEASE: Meier-Gorlin syndrome 8 (MGORS8) [MIM:617564]: A form of Meier-Gorlin syndrome, a syndrome characterized by bilateral microtia, aplasia/hypoplasia of the patellae, and severe intrauterine and postnatal growth retardation with short stature and poor weight gain. Additional clinical findings include anomalies of cranial sutures, microcephaly, apparently low-set and simple ears, microstomia, full lips, highly arched or cleft palate, micrognathia, genitourinary tract anomalies, and various skeletal anomalies. While almost all cases have primordial dwarfism with substantial prenatal and postnatal growth retardation, not all cases have microcephaly, and microtia and absent/hypoplastic patella are absent in some. Despite the presence of microcephaly, intellect is usually normal. MGORS8 inheritance is autosomal recessive. {ECO:0000269|PubMed:28198391}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.190

Intolerance Scores

LoFtool
0.624
RVIS EVS
-0.44
RVIS percentile EVS
24.63

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.987

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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