MCM2
Basic information
Region (hg38): 3:127598223-127622436
Previous symbols: [ "CCNL1", "CDCL1" ]
Links
Phenotypes
GenCC
Source:
- autosomal dominant nonsyndromic hearing loss 70 (Limited), mode of inheritance: AD
- autosomal dominant nonsyndromic hearing loss (Supportive), mode of inheritance: AD
- autosomal dominant nonsyndromic hearing loss 70 (Strong), mode of inheritance: AD
- nonsyndromic genetic hearing loss (Limited), mode of inheritance: AD
- autosomal dominant nonsyndromic hearing loss 70 (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Deafness, autosomal dominant 70 | AD | General | 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 | Audiologic/Otolaryngologic | 26196677 |
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 MCM2 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 | 55 | 12 | 67 | |||
missense | 138 | 14 | 157 | |||
nonsense | 1 | |||||
start loss | 1 | |||||
frameshift | 0 | |||||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 4 | 4 | 2 | 10 | ||
non coding | 28 | 39 | ||||
Total | 0 | 2 | 147 | 97 | 24 |
Variants in MCM2
This is a list of pathogenic ClinVar variants found in the MCM2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-127598469-G-A | Uncertain significance (May 29, 2023) | |||
3-127598471-C-A | Uncertain significance (Mar 10, 2022) | |||
3-127599299-A-G | Likely benign (Dec 16, 2022) | |||
3-127599302-G-A | Likely benign (Oct 04, 2022) | |||
3-127599326-G-A | Likely benign (Jan 03, 2024) | |||
3-127599344-A-C | Likely benign (Oct 15, 2022) | |||
3-127599350-C-G | Uncertain significance (Nov 15, 2022) | |||
3-127599351-C-G | Uncertain significance (Jun 13, 2024) | |||
3-127599359-G-T | Uncertain significance (Apr 17, 2021) | |||
3-127599363-C-T | Uncertain significance (Dec 31, 2023) | |||
3-127599364-G-C | not specified | Benign/Likely benign (May 12, 2023) | ||
3-127599379-C-T | Uncertain significance (Feb 03, 2023) | |||
3-127599409-G-A | Benign/Likely benign (Jul 31, 2023) | |||
3-127599412-G-C | not specified | Uncertain significance (May 21, 2024) | ||
3-127599427-C-T | not specified | Uncertain significance (Nov 17, 2023) | ||
3-127599437-T-C | MCM2-related disorder | Benign (Jan 02, 2024) | ||
3-127599441-C-T | Autosomal dominant nonsyndromic hearing loss 70 | no classifications from unflagged records (Apr 30, 2024) | ||
3-127599442-G-A | not specified | Uncertain significance (Dec 16, 2022) | ||
3-127599455-A-G | Likely benign (May 23, 2018) | |||
3-127599470-C-T | MCM2-related disorder | Likely benign (Dec 01, 2023) | ||
3-127599471-G-A | Uncertain significance (Nov 20, 2022) | |||
3-127599494-G-A | Likely benign (Oct 24, 2023) | |||
3-127599515-T-G | MCM2-related disorder | Benign (Jan 15, 2024) | ||
3-127599518-A-G | Likely benign (Sep 21, 2023) | |||
3-127599524-G-C | Uncertain significance (Dec 22, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MCM2 | protein_coding | protein_coding | ENST00000265056 | 16 | 24211 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000263 | 1.00 | 125705 | 0 | 43 | 125748 | 0.000171 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.68 | 490 | 606 | 0.808 | 0.0000418 | 5984 |
Missense in Polyphen | 151 | 225.96 | 0.66827 | 2235 | ||
Synonymous | -1.36 | 268 | 241 | 1.11 | 0.0000169 | 1786 |
Loss of Function | 3.61 | 15 | 39.5 | 0.380 | 0.00000213 | 440 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000387 | 0.000387 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000327 | 0.000326 |
Finnish | 0.000185 | 0.000185 |
European (Non-Finnish) | 0.000160 | 0.000158 |
Middle Eastern | 0.000327 | 0.000326 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.000493 | 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 the entry in S phase and for cell division. Plays a role in terminally differentiated hair cells development of the cochlea and induces cells apoptosis. {ECO:0000269|PubMed:26196677, ECO:0000269|PubMed:8175912}.;
- Disease
- DISEASE: Deafness, autosomal dominant, 70 (DFNA70) [MIM:616968]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA70 is characterized by slowly progressive, postlingual hearing impairment. {ECO:0000269|PubMed:26196677}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Cell cycle - Homo sapiens (human);DNA replication - Homo sapiens (human);Cell Cycle;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;ATR signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.129
Intolerance Scores
- loftool
- 0.429
- rvis_EVS
- -0.95
- rvis_percentile_EVS
- 9.38
Haploinsufficiency Scores
- pHI
- 0.994
- hipred
- Y
- hipred_score
- 0.661
- ghis
- 0.679
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.991
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mcm2
- Phenotype
- growth/size/body region 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; muscle phenotype; cellular phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; hematopoietic system phenotype; normal 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); pigmentation phenotype; neoplasm; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype;
Zebrafish Information Network
- Gene name
- mcm2
- Affected structure
- pharyngeal arch 3-7
- Phenotype tag
- abnormal
- Phenotype quality
- aplastic
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;DNA replication;DNA unwinding involved in DNA replication;DNA replication initiation;nucleosome assembly;apoptotic process;cellular response to interleukin-4;cochlea development;negative regulation of DNA helicase activity
- Cellular component
- nuclear chromosome, telomeric region;chromatin;nucleus;nucleoplasm;nuclear origin of replication recognition complex;nucleolus;cytoplasm;microtubule cytoskeleton;MCM complex
- Molecular function
- DNA binding;DNA replication origin binding;helicase activity;protein binding;ATP binding;enzyme binding;histone binding;metal ion binding