ANAPC4

anaphase promoting complex subunit 4, the group of Anaphase promoting complex

Basic information

Region (hg38): 4:25377262-25418498

Links

ENSG00000053900 ∙ NCBI:29945 ∙ OMIM:606947 ∙ HGNC:19990 ∙ Uniprot:Q9UJX5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANAPC4 gene.

• Inborn genetic diseases (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANAPC4 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in ANAPC4

This is a list of pathogenic ClinVar variants found in the ANAPC4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-25383279-C-T		not specified	Uncertain significance (Dec 21, 2022)
4-25383333-C-T		not specified	Uncertain significance (Mar 01, 2023)
4-25388852-A-G		not specified	Uncertain significance (Oct 24, 2023)
4-25390990-G-A		not specified	Uncertain significance (Jan 24, 2024)
4-25391010-T-A		not specified	Uncertain significance (Apr 11, 2023)
4-25392380-C-T		not specified	Uncertain significance (Aug 02, 2023)
4-25392381-G-A		not specified	Uncertain significance (Jan 04, 2022)
4-25393823-A-T		not specified	Uncertain significance (Jan 24, 2024)
4-25394860-C-T		not specified	Uncertain significance (Jul 26, 2021)
4-25394869-C-A		not specified	Uncertain significance (Dec 19, 2022)
4-25396747-A-G		not specified	Uncertain significance (Dec 21, 2022)
4-25396857-C-T		not specified	Uncertain significance (Jun 29, 2023)
4-25402972-G-A		not specified	Uncertain significance (Sep 14, 2023)
4-25405617-A-G		not specified	Uncertain significance (Nov 06, 2023)
4-25406881-A-G		not specified	Uncertain significance (Dec 08, 2023)
4-25407222-G-A		not specified	Uncertain significance (Feb 21, 2024)
4-25409763-C-G		not specified	Uncertain significance (May 28, 2023)
4-25413711-A-G		not specified	Uncertain significance (Mar 24, 2023)
4-25414480-G-T		not specified	Uncertain significance (May 30, 2023)
4-25414690-G-C		not specified	Uncertain significance (Nov 30, 2021)
4-25415513-A-G		not specified	Uncertain significance (Oct 27, 2022)
4-25415515-G-A		not specified	Uncertain significance (Jun 27, 2023)
4-25416499-G-A		not specified	Uncertain significance (Aug 02, 2023)
4-25417647-C-T		not specified	Uncertain significance (May 30, 2023)
4-25418176-G-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANAPC4	protein_coding	protein_coding	ENST00000315368	28	41286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000695	0.999	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	263	405	0.650	0.0000199	5288
Missense in Polyphen		49	115.8	0.42314		1547
Synonymous	-0.0829	141	140	1.01	0.00000677	1455
Loss of Function	4.68	16	52.7	0.304	0.00000272	666

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00166	0.00159
East Asian	0.000614	0.000598
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000614	0.000598
South Asian	0.000147	0.000131
Other	0.000342	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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. {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);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: 0.125

Intolerance Scores

• loftool: 0.578
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.649
• hipred: Y
• hipred_score: 0.635
• ghis: 0.636

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.672

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Anapc4
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; embryo 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)

Gene ontology

• Biological process: cell cycle;anaphase-promoting complex-dependent catabolic process;positive regulation of mitotic metaphase/anaphase transition;cell division;protein K11-linked ubiquitination;regulation of mitotic cell cycle phase transition
• Cellular component: nucleus;nucleoplasm;anaphase-promoting complex;cytosol;nuclear periphery
• Molecular function: ubiquitin-protein transferase activity;protein binding;protein phosphatase binding