CDCA3

cell division cycle associated 3

Basic information

Region (hg38): 12:6844793-6851292

Links

ENSG00000111665 ∙ NCBI:83461 ∙ OMIM:607749 ∙ HGNC:14624 ∙ Uniprot:Q99618 ∙ 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 CDCA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDCA3 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in CDCA3

This is a list of pathogenic ClinVar variants found in the CDCA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6845459-GG-TT			Likely benign (Jul 21, 2023)
12-6845460-G-A			Benign (Jan 31, 2024)
12-6845460-G-T			Likely benign (Jan 01, 2024)
12-6845569-G-A			Likely benign (May 25, 2023)
12-6845575-C-T			Likely benign (Jun 26, 2023)
12-6845576-G-A			Benign (Nov 24, 2023)
12-6845581-C-T			Likely benign (Nov 21, 2020)
12-6845593-CCAATGGAGAGG-C			Uncertain significance (Jul 26, 2021)
12-6845596-A-G		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
12-6845614-C-T		Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
12-6845615-G-A			Benign (Jan 29, 2024)
12-6845617-G-T			Uncertain significance (Nov 29, 2022)
12-6845620-C-T			Uncertain significance (Dec 12, 2023)
12-6845621-G-A			Uncertain significance (Dec 13, 2021)
12-6845627-C-T			Benign (Oct 25, 2023)
12-6845628-G-A		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
12-6845628-G-T			Uncertain significance (Jul 06, 2022)
12-6845634-T-G			Uncertain significance (Oct 01, 2021)
12-6845637-C-T			Uncertain significance (Jul 01, 2022)
12-6845638-G-A			Uncertain significance (Jul 06, 2023)
12-6845642-G-A			Likely benign (Jul 14, 2022)
12-6845648-C-T			Benign (Jan 29, 2024)
12-6845652-C-A			Likely benign (Aug 15, 2022)
12-6845652-C-T			Uncertain significance (Nov 27, 2023)
12-6845653-G-A			Uncertain significance (Jul 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDCA3	protein_coding	protein_coding	ENST00000538862	5	7274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.689	0.311	125730	0	15	125745	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.657	127	150	0.849	0.00000783	1703
Missense in Polyphen		30	42.35	0.70838		513
Synonymous	0.895	48	56.6	0.849	0.00000270	577
Loss of Function	2.75	2	12.5	0.160	7.33e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000303	0.0000303
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000980	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000685	0.0000653
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: F-box-like protein which is required for entry into mitosis. Acts by participating in E3 ligase complexes that mediate the ubiquitination and degradation of WEE1 kinase at G2/M phase (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.276
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.650
• hipred: Y
• hipred_score: 0.545
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdca3

Gene ontology

• Biological process: cell cycle;biological_process;protein ubiquitination;cell division
• Cellular component: cytosol;cell-cell adherens junction
• Molecular function: protein binding