ANAPC2
anaphase promoting complex subunit 2, the group of Anaphase promoting complex
Basic information
Region (hg38): 9:137174783-137188560
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 ANAPC2 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 | 3 | |||||
| missense | 33 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 33 | 3 | 1 |
Variants in ANAPC2
This is a list of pathogenic ClinVar variants found in the ANAPC2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-137175136-G-T | not specified | Uncertain significance (Oct 27, 2023) | ||
| 9-137175144-G-A | not specified | Uncertain significance (May 29, 2024) | ||
| 9-137175247-T-C | not specified | Uncertain significance (Aug 02, 2021) | ||
| 9-137175305-T-C | not specified | Uncertain significance (Dec 13, 2023) | ||
| 9-137175307-A-G | not specified | Uncertain significance (Oct 14, 2023) | ||
| 9-137175359-T-C | not specified | Uncertain significance (Sep 06, 2022) | ||
| 9-137175362-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 9-137175369-C-A | not specified | Uncertain significance (Jan 08, 2024) | ||
| 9-137175402-G-A | Likely benign (Mar 01, 2022) | |||
| 9-137175458-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
| 9-137175710-T-C | not specified | Uncertain significance (Jul 26, 2022) | ||
| 9-137175736-C-T | Benign/Likely benign (Aug 01, 2022) | |||
| 9-137180318-C-G | not specified | Uncertain significance (Apr 04, 2024) | ||
| 9-137180327-G-A | not specified | Uncertain significance (Feb 27, 2023) | ||
| 9-137180341-T-C | not specified | Uncertain significance (Aug 30, 2021) | ||
| 9-137180347-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
| 9-137180871-G-A | Benign (Dec 31, 2019) | |||
| 9-137181684-G-C | not specified | Uncertain significance (Aug 12, 2021) | ||
| 9-137181761-C-G | not specified | Uncertain significance (Aug 21, 2023) | ||
| 9-137183134-C-T | not specified | Uncertain significance (Jun 06, 2022) | ||
| 9-137183218-G-C | not specified | Uncertain significance (Mar 04, 2024) | ||
| 9-137183242-C-G | not specified | Uncertain significance (Feb 28, 2023) | ||
| 9-137183696-G-C | not specified | Uncertain significance (Dec 20, 2023) | ||
| 9-137184993-C-T | not specified | Uncertain significance (Aug 08, 2022) | ||
| 9-137184994-G-A | not specified | Uncertain significance (Jan 05, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ANAPC2 | protein_coding | protein_coding | ENST00000323927 | 13 | 13754 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000676 | 125702 | 0 | 5 | 125707 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.41 | 371 | 527 | 0.704 | 0.0000357 | 5281 |
| Missense in Polyphen | 59 | 144.33 | 0.40879 | 1495 | ||
| Synonymous | -2.39 | 274 | 228 | 1.20 | 0.0000147 | 1686 |
| Loss of Function | 5.25 | 2 | 36.0 | 0.0555 | 0.00000172 | 395 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000994 | 0.0000993 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000275 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Together with the RING-H2 protein ANAPC11, constitutes the catalytic component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. The CDC20-APC/C complex positively regulates the formation of synaptic vesicle clustering at active zone to the presynaptic membrane in postmitotic neurons. CDC20-APC/C-induced degradation of NEUROD2 drives presynaptic differentiation. {ECO:0000269|PubMed:11739784, ECO:0000269|PubMed:18485873}.;
- Pathway
- Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Ubiquitin mediated proteolysis - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Regulation of sister chromatid separation at the metaphase-anaphase transition;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;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;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;DNA Replication;Switching of origins to a post-replicative state;Class I MHC mediated antigen processing & presentation;Synthesis of DNA;S Phase;Cellular responses to external stimuli;TGF_beta_Receptor;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Regulation of APC/C activators between G1/S and early anaphase;Phosphorylation of the APC/C;CDK-mediated phosphorylation and removal of Cdc6;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 Cyclin B;APC/C:Cdc20 mediated degradation of Securin;APC/C:Cdc20 mediated degradation of mitotic proteins;Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins;Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase;APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1;Autodegradation of Cdh1 by Cdh1:APC/C;APC/C-mediated degradation of cell cycle proteins;Regulation of mitotic cell cycle;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- loftool
- 0.157
- rvis_EVS
- -1.66
- rvis_percentile_EVS
- 2.72
Haploinsufficiency Scores
- pHI
- 0.161
- hipred
- Y
- hipred_score
- 0.714
- ghis
- 0.640
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.957
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Anapc2
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; skeleton 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); hematopoietic system phenotype; liver/biliary system phenotype;
Gene ontology
- Biological process
- cell cycle;anaphase-promoting complex-dependent catabolic process;positive regulation of synaptic plasticity;positive regulation of axon extension;positive regulation of dendrite morphogenesis;cell division;protein K11-linked ubiquitination;positive regulation of synapse maturation;regulation of mitotic cell cycle phase transition
- Cellular component
- nucleoplasm;anaphase-promoting complex;cytosol
- Molecular function
- protein binding;ubiquitin protein ligase binding