GeneBe

MCM10

minichromosome maintenance 10 replication initiation factor

Basic information

Region (hg38): 10:13161558-13211110

Links

ENSG00000065328 ∙ NCBI:55388 ∙ OMIM:609357 ∙ HGNC:18043 ∙ Uniprot:Q7L590 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • immunodeficiency 80 with or without congenital cardiomyopathy (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Immunodeficiency 80 with or without congenital cardiomyopathyARAllergy/Immunology/Infectious; CardiovascularIndividuals are susceptible to severe infections, and early and aggressive management may be beneficial related to morbidity and mortality; BMT has been described; Individuals have been described with cardiomyopathy, and early diagnosis may allow managementAllergy/Immunology/Infectious; Cardiovascular32865517; 33712616

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MCM10 gene.

  • not_specified (110 variants)
  • not_provided (16 variants)
  • Immunodeficiency_80_with_or_without_congenital_cardiomyopathy (7 variants)
  • Fetal_Cardiomyopathy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCM10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018518.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
1
clinvar
 9
missense
1
clinvar
101
clinvar
12
clinvar
2
clinvar
 116
nonsense
1
clinvar
1
clinvar
 2
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total 3 0 102 20 3

Highest pathogenic variant AF is 0.00005927391

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MCM10protein_codingprotein_codingENST00000484800 1949551
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
4.38e-150.9771256790691257480.000274
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1674964861.020.00002805674
Missense in Polyphen150138.791.08081657
Synonymous0.7311711840.9310.00001111672
Loss of Function2.483149.90.6210.00000269602

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006950.000693
Ashkenazi Jewish0.000.00
East Asian0.0005500.000544
Finnish0.0003260.000323
European (Non-Finnish)0.0002300.000229
Middle Eastern0.0005500.000544
South Asian0.0002620.000261
Other0.0003370.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication. Additionally, plays a role in preventing DNA damage during replication. Key effector of the RBBP6 and ZBTB38-mediated regulation of DNA-replication and common fragile sites stability; acts as a direct target of transcriptional repression by ZBTB38 (PubMed:24726359). {ECO:0000269|PubMed:11095689, ECO:0000269|PubMed:15136575, ECO:0000269|PubMed:17699597, ECO:0000269|PubMed:19608746, ECO:0000269|PubMed:24726359}.;
Pathway
Cell Cycle;DNA Replication;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Activation of the pre-replicative complex;Mitotic G1-G1/S phases;DNA Replication;G1/S Transition;DNA Replication Pre-Initiation;M/G1 Transition;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

pRec
0.137

Intolerance Scores

loftool
0.937
rvis_EVS
-0.03
rvis_percentile_EVS
50.54

Haploinsufficiency Scores

pHI
0.264
hipred
N
hipred_score
0.277
ghis
0.636

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.648

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mcm10
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); embryo phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
G1/S transition of mitotic cell cycle;DNA replication;DNA replication initiation;cellular response to DNA damage stimulus;cell population proliferation
Cellular component
nucleus;nucleoplasm;nucleolus;replication fork protection complex
Molecular function
DNA replication origin binding;double-stranded DNA binding;single-stranded DNA binding;protein binding;enzyme binding;identical protein binding;metal ion binding