CDC20B

cell division cycle 20B, the group of MicroRNA protein coding host genes|WD repeat domain containing

Basic information

Region (hg38): 5:55112970-55173177

Links

ENSG00000164287 ∙ NCBI:166979 ∙ ∙ HGNC:24222 ∙ Uniprot:Q86Y33 ∙ 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 CDC20B gene.

• Inborn genetic diseases (28 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC20B 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7		1	8
Total	0	0	26	3	1

Variants in CDC20B

This is a list of pathogenic ClinVar variants found in the CDC20B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-55114222-T-C		not specified	Likely benign (Mar 27, 2023)
5-55114232-A-C		not specified	Uncertain significance (Oct 03, 2022)
5-55119821-G-A		not specified	Uncertain significance (Nov 17, 2022)
5-55119836-G-A		not specified	Uncertain significance (Mar 22, 2023)
5-55119856-C-A		not specified	Uncertain significance (Jan 18, 2022)
5-55120544-C-A		not specified	Uncertain significance (Aug 12, 2021)
5-55124837-G-A		not specified	Uncertain significance (Oct 05, 2022)
5-55124912-A-G		not specified	Uncertain significance (Mar 20, 2023)
5-55124924-G-A		not specified	Uncertain significance (Mar 07, 2024)
5-55124960-C-T		not specified	Likely benign (Jan 16, 2024)
5-55124964-G-C		not specified	Uncertain significance (Dec 06, 2022)
5-55124997-C-T		not specified	Uncertain significance (Jun 06, 2022)
5-55127274-A-T		not specified	Uncertain significance (Aug 02, 2023)
5-55128425-A-T		not specified	Uncertain significance (Mar 14, 2023)
5-55128432-C-T		not specified	Uncertain significance (Dec 15, 2022)
5-55128468-T-C		not specified	Uncertain significance (Nov 13, 2023)
5-55128615-G-C		not specified	Uncertain significance (Aug 02, 2021)
5-55133454-G-A		not specified	Uncertain significance (Dec 14, 2022)
5-55133459-A-G		not specified	Uncertain significance (Oct 18, 2021)
5-55133466-A-G		not specified	Uncertain significance (Jan 17, 2024)
5-55133485-A-C		not specified	Likely benign (Feb 07, 2023)
5-55143536-C-G		not specified	Uncertain significance (Sep 29, 2023)
5-55143566-C-A		not specified	Uncertain significance (Jun 17, 2022)
5-55143567-C-G		not specified	Uncertain significance (Jul 09, 2021)
5-55146644-T-C			Likely benign (May 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC20B	protein_coding	protein_coding	ENST00000381375	12	60207

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.12e-12	0.351	125023	12	713	125748	0.00289

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.544	257	283	0.909	0.0000141	3373
Missense in Polyphen		52	63.789	0.81519		776
Synonymous	-0.579	115	107	1.07	0.00000560	1017
Loss of Function	1.14	21	27.4	0.765	0.00000124	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0376	0.0376
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000218	0.000217
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.000453	0.000440
Middle Eastern	0.000218	0.000217
South Asian	0.000499	0.000490
Other	0.00212	0.00212

dbNSFP

Source: dbNSFP

• Pathway: miRNA Regulation of DNA Damage Response (Consensus)

Recessive Scores

• pRec: 0.0813

Intolerance Scores

• loftool: 0.983
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.83

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0733

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc20b

Gene ontology

• Biological process: positive regulation of ubiquitin protein ligase activity
• Molecular function: protein binding;anaphase-promoting complex binding;ubiquitin-protein transferase activator activity