MCM3
minichromosome maintenance complex component 3, the group of minichromosome maintenance 2-7 complex|MCM family
Basic information
Region (hg38): 6:52264014-52284881
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCM3 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 | 0 | |||||
| missense | 47 | 48 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 47 | 1 | 1 |
Variants in MCM3
This is a list of pathogenic ClinVar variants found in the MCM3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-52264602-T-C | not specified | Likely benign (Nov 30, 2022) | ||
| 6-52264628-T-C | not specified | Uncertain significance (Oct 31, 2023) | ||
| 6-52264644-T-G | not specified | Uncertain significance (Jan 06, 2023) | ||
| 6-52264681-C-A | not specified | Uncertain significance (Jul 12, 2022) | ||
| 6-52264697-T-C | not specified | Uncertain significance (Apr 25, 2023) | ||
| 6-52264722-T-G | not specified | Uncertain significance (Nov 21, 2022) | ||
| 6-52264733-T-A | Meier-Gorlin syndrome | Uncertain significance (-) | ||
| 6-52266649-G-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 6-52266686-G-A | not specified | Uncertain significance (May 01, 2022) | ||
| 6-52267932-C-T | not specified | Uncertain significance (Jun 16, 2023) | ||
| 6-52267947-G-T | not specified | Uncertain significance (Jul 27, 2022) | ||
| 6-52269153-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 6-52269225-G-A | not specified | Uncertain significance (Oct 10, 2023) | ||
| 6-52272306-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
| 6-52272326-T-C | not specified | Uncertain significance (May 01, 2022) | ||
| 6-52272442-C-G | not specified | Uncertain significance (Jun 07, 2023) | ||
| 6-52273783-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
| 6-52273807-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
| 6-52276308-C-T | not specified | Uncertain significance (Oct 10, 2023) | ||
| 6-52276377-A-G | not specified | Uncertain significance (Apr 25, 2023) | ||
| 6-52276384-T-C | not specified | Uncertain significance (Feb 01, 2023) | ||
| 6-52277084-G-C | not specified | Uncertain significance (Dec 13, 2022) | ||
| 6-52277165-C-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 6-52277198-C-A | not specified | Uncertain significance (Nov 21, 2023) | ||
| 6-52278756-T-C | not specified | Uncertain significance (Oct 22, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MCM3 | protein_coding | protein_coding | ENST00000596288 | 17 | 20873 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 6.95e-11 | 0.998 | 125646 | 0 | 102 | 125748 | 0.000406 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.805 | 453 | 504 | 0.899 | 0.0000292 | 5568 |
| Missense in Polyphen | 107 | 153.85 | 0.69547 | 1576 | ||
| Synonymous | -0.0677 | 187 | 186 | 1.01 | 0.00000998 | 1674 |
| Loss of Function | 2.88 | 24 | 44.8 | 0.535 | 0.00000276 | 491 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000760 | 0.000760 |
| Ashkenazi Jewish | 0.000397 | 0.000397 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000302 | 0.000299 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00144 | 0.00144 |
| Other | 0.000491 | 0.000489 |
dbNSFP
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. Required for DNA replication and cell proliferation.;
- Pathway
- Cell cycle - Homo sapiens (human);DNA replication - Homo sapiens (human);Cell Cycle;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;Cell Cycle, Mitotic;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.275
Intolerance Scores
- loftool
- rvis_EVS
- -0.93
- rvis_percentile_EVS
- 9.68
Haploinsufficiency Scores
- pHI
- 0.965
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.707
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.911
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mcm3
- 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); hematopoietic system phenotype; neoplasm; embryo phenotype; liver/biliary system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- mcm3
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;DNA replication;DNA replication initiation
- Cellular component
- nuclear chromosome, telomeric region;nucleus;nucleoplasm;alpha DNA polymerase:primase complex;nucleolus;centrosome;membrane;MCM complex;perinuclear region of cytoplasm
- Molecular function
- DNA binding;helicase activity;protein binding;ATP binding