ANAPC1

anaphase promoting complex subunit 1, the group of Anaphase promoting complex |MicroRNA protein coding host genes

Basic information

Region (hg38): 2:111611638-111884690

Links

ENSG00000153107 ∙ NCBI:64682 ∙ OMIM:608473 ∙ HGNC:19988 ∙ Uniprot:Q9H1A4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Rothmund-Thomson syndrome type 1 (Limited), mode of inheritance: AR
• Rothmund-Thomson syndrome type 1 (Strong), mode of inheritance: AR
• Rothmund-Thomson syndrome type 1 (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Rothmund-Thomson syndrome, type 1	AR	Endocrine	Awareness of endocrine manifestations, including growth hormone deficiency, may allow early recognition and treatment	Craniofacial; Dental; Endocrine; Dermatologic; Genitourinary; Musculoskeletal; Ophthalmologic	31303264

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANAPC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANAPC1 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				7	5	12
missense			86	5	1	92
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding				1	3	4
Total	0	0	86	13	10

Variants in ANAPC1

This is a list of pathogenic ClinVar variants found in the ANAPC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-111769289-G-A		Rothmund-Thomson syndrome type 1	Benign (Jul 14, 2021)
2-111772392-C-T		not specified	Uncertain significance (Dec 20, 2023)
2-111772451-G-A		not specified	Uncertain significance (Mar 20, 2024)
2-111772467-C-T		not specified	Uncertain significance (Jan 05, 2022)
2-111772473-C-T		not specified	Uncertain significance (Jul 08, 2022)
2-111778687-G-T		Rothmund-Thomson syndrome type 1	Benign (Jul 14, 2021)
2-111778702-C-T		not specified	Uncertain significance (May 03, 2023)
2-111778736-A-G		not specified	Uncertain significance (Jan 03, 2024)
2-111782370-T-C		not specified	Uncertain significance (May 18, 2023)
2-111782456-C-G		not specified	Uncertain significance (Sep 13, 2023)
2-111782488-C-G		not specified	Uncertain significance (Nov 23, 2021)
2-111784348-A-G		not specified	Uncertain significance (Aug 08, 2023)
2-111784358-G-C		not specified	Uncertain significance (Apr 05, 2023)
2-111784385-C-T		not specified	Uncertain significance (Dec 12, 2023)
2-111784391-A-G		not specified	Uncertain significance (Jun 02, 2023)
2-111785393-CGT-C		-	no classification for the single variant (-)
2-111785394-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-111785448-T-C		not specified	Uncertain significance (Oct 03, 2023)
2-111785475-T-C		not specified	Uncertain significance (Nov 08, 2022)
2-111788250-G-C		not specified	Uncertain significance (Aug 16, 2022)
2-111788298-A-G		not specified	Uncertain significance (Oct 06, 2021)
2-111788301-T-G		not specified	Uncertain significance (Apr 06, 2023)
2-111792437-G-A		not specified	Uncertain significance (Jun 02, 2024)
2-111792471-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-111792510-A-C		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANAPC1	protein_coding	protein_coding	ENST00000341068	47	118420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.945	0.0547	125608	0	53	125661	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.987	681	757	0.899	0.0000379	12564
Missense in Polyphen		167	231.91	0.72011		4315
Synonymous	-0.343	277	270	1.03	0.0000140	3690
Loss of Function	6.61	16	79.7	0.201	0.00000395	1327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000887	0.000881
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000166	0.000150
Middle Eastern	0.000109	0.000109
South Asian	0.000135	0.0000980
Other	0.000167	0.000163

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);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;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: 0.0958

Haploinsufficiency Scores

• pHI: 0.556
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.600

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Anapc1

Gene ontology

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