CDC16

cell division cycle 16, the group of MicroRNA protein coding host genes|Anaphase promoting complex |Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 13:114234886-114272723

Links

ENSG00000130177 ∙ NCBI:8881 ∙ OMIM:603461 ∙ HGNC:1720 ∙ Uniprot:Q13042 ∙ 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 CDC16 gene.

• Inborn genetic diseases (27 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC16 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					1	1
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	27	1	1

Variants in CDC16

This is a list of pathogenic ClinVar variants found in the CDC16 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-114235094-G-A		not specified	Uncertain significance (Mar 12, 2024)
13-114236696-C-G		not specified	Uncertain significance (Apr 22, 2022)
13-114236808-A-G			Likely benign (Apr 16, 2018)
13-114236826-C-G		not specified	Uncertain significance (Oct 12, 2021)
13-114236846-G-A		not specified	Uncertain significance (Sep 14, 2023)
13-114236864-G-A		not specified	Uncertain significance (Dec 27, 2022)
13-114239364-G-T		not specified	Uncertain significance (Oct 26, 2021)
13-114239405-T-C		not specified	Uncertain significance (Oct 25, 2023)
13-114242131-C-G		not specified	Uncertain significance (Jun 02, 2023)
13-114242133-A-G		not specified	Uncertain significance (Jun 28, 2022)
13-114242135-C-T			Benign (Apr 16, 2018)
13-114242152-A-G		not specified	Uncertain significance (Dec 13, 2022)
13-114242163-G-A		not specified	Uncertain significance (Apr 04, 2023)
13-114243289-A-G		not specified	Uncertain significance (Nov 29, 2023)
13-114243290-A-G		not specified	Uncertain significance (Mar 29, 2023)
13-114243309-G-T		not specified	Uncertain significance (May 04, 2023)
13-114243907-G-A		not specified	Uncertain significance (Jun 06, 2022)
13-114243922-G-A		not specified	Uncertain significance (Aug 10, 2021)
13-114243950-A-G		not specified	Uncertain significance (Apr 27, 2023)
13-114244895-T-C		not specified	Uncertain significance (Aug 21, 2023)
13-114244957-A-C		not specified	Uncertain significance (Nov 30, 2021)
13-114246975-T-G		not specified	Uncertain significance (Jun 18, 2021)
13-114250575-A-G		not specified	Uncertain significance (Aug 17, 2022)
13-114250589-A-G		not specified	Uncertain significance (Dec 19, 2023)
13-114250647-A-T		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC16	protein_coding	protein_coding	ENST00000360383	18	37837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.614	0.386	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	243	332	0.733	0.0000171	4089
Missense in Polyphen		50	100.76	0.49625		1238
Synonymous	0.0130	122	122	0.999	0.00000717	1087
Loss of Function	4.52	8	38.1	0.210	0.00000188	498

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000608	0.0000544
Finnish	0.000233	0.000231
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.0000608	0.0000544
South Asian	0.0000687	0.0000653
Other	0.000163	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);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: 0.151

Intolerance Scores

• loftool: 0.371
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.753
• hipred: Y
• hipred_score: 0.792
• ghis: 0.629

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.838

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc16

Zebrafish Information Network

• Gene name: cdc16
• Affected structure: ceratobranchial 5 cartilage
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: mitotic cell cycle;regulation of mitotic nuclear division;cell population proliferation;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;cytoplasm;centrosome;spindle;cytosol;spindle microtubule
• Molecular function: protein binding