MAD2L1
mitotic arrest deficient 2 like 1
Basic information
Region (hg38): 4:120055623-120066858
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 MAD2L1 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 | 4 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 4 | 1 |
Variants in MAD2L1
This is a list of pathogenic ClinVar variants found in the MAD2L1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-120060123-C-T | not specified | Uncertain significance (Apr 20, 2023) | ||
| 4-120060168-T-C | Benign (Aug 08, 2018) | |||
| 4-120060943-C-T | not specified | Uncertain significance (Oct 10, 2023) | ||
| 4-120060960-G-C | not specified | Uncertain significance (Sep 14, 2023) | ||
| 4-120062048-T-C | not specified | Uncertain significance (Nov 21, 2023) | ||
| 4-120065761-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 4-120065779-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 4-120066681-T-C | Likely benign (Nov 01, 2022) | |||
| 4-120066698-G-A | Likely benign (Nov 01, 2022) | |||
| 4-120066704-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
| 4-120066705-T-G | Likely benign (Nov 01, 2022) | |||
| 4-120066707-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
| 4-120066708-C-T | Likely benign (Nov 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MAD2L1 | protein_coding | protein_coding | ENST00000296509 | 5 | 11467 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00930 | 0.944 | 125735 | 0 | 10 | 125745 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.06 | 79 | 110 | 0.717 | 0.00000571 | 1317 |
| Missense in Polyphen | 12 | 29.84 | 0.40215 | 379 | ||
| Synonymous | 0.569 | 37 | 41.7 | 0.888 | 0.00000213 | 399 |
| Loss of Function | 1.73 | 5 | 11.2 | 0.445 | 5.20e-7 | 135 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000619 | 0.0000615 |
| Ashkenazi Jewish | 0.000201 | 0.000198 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000166 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the spindle-assembly checkpoint that prevents the onset of anaphase until all chromosomes are properly aligned at the metaphase plate. Required for the execution of the mitotic checkpoint which monitors the process of kinetochore- spindle attachment and inhibits the activity of the anaphase promoting complex by sequestering CDC20 until all chromosomes are aligned at the metaphase plate. {ECO:0000269|PubMed:10700282, ECO:0000269|PubMed:11804586, ECO:0000269|PubMed:15024386}.;
- Pathway
- Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Cell Cycle;Regulation of sister chromatid separation at the metaphase-anaphase transition;Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Inactivation of APC/C via direct inhibition of the APC/C complex;Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;KitReceptor;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Regulation of APC/C activators between G1/S and early anaphase;Cdc20:Phospho-APC/C mediated degradation of Cyclin A;APC-Cdc20 mediated degradation of Nek2A;APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint;APC/C:Cdc20 mediated degradation of mitotic proteins;Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins;APC/C-mediated degradation of cell cycle proteins;Regulation of mitotic cell cycle;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.304
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.992
- hipred
- Y
- hipred_score
- 0.842
- ghis
- 0.691
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mad2l1
- Phenotype
- immune system phenotype; neoplasm; 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; embryo phenotype; cellular 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;
Gene ontology
- Biological process
- mitotic sister chromatid segregation;mitotic cell cycle checkpoint;mitotic spindle assembly checkpoint;anaphase-promoting complex-dependent catabolic process;negative regulation of protein catabolic process;negative regulation of apoptotic process;negative regulation of mitotic cell cycle;cell division;positive regulation of mitotic cell cycle spindle assembly checkpoint;regulation of mitotic cell cycle phase transition;negative regulation of ubiquitin protein ligase activity
- Cellular component
- kinetochore;condensed chromosome kinetochore;spindle pole;nucleus;nucleoplasm;chromosome;cytosol;nuclear pore nuclear basket;perinuclear region of cytoplasm;mitotic spindle
- Molecular function
- protein binding;protein C-terminus binding;identical protein binding;protein homodimerization activity