CDCA2

cell division cycle associated 2, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 8:25459199-25507911

Links

ENSG00000184661 ∙ NCBI:157313 ∙ OMIM:618785 ∙ HGNC:14623 ∙ Uniprot:Q69YH5 ∙ 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 CDCA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDCA2 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	2	3
missense			77	8	2	87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	77	9	4

Variants in CDCA2

This is a list of pathogenic ClinVar variants found in the CDCA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-25460264-C-T		not specified	Uncertain significance (Jan 21, 2025)
8-25460288-A-G		not specified	Likely benign (Jul 13, 2021)
8-25460389-G-A		not specified	Likely benign (Jan 30, 2024)
8-25460425-C-T		not specified	Uncertain significance (Mar 07, 2025)
8-25460446-C-T		not specified	Uncertain significance (Jun 16, 2023)
8-25460450-C-T			Likely benign (Jun 01, 2022)
8-25460471-C-T			Benign (Feb 25, 2018)
8-25460498-C-T		not specified	Uncertain significance (Sep 16, 2021)
8-25460525-C-T		not specified	Uncertain significance (Sep 01, 2021)
8-25462080-T-C		not specified	Uncertain significance (Dec 20, 2023)
8-25462138-G-A		not specified	Uncertain significance (May 09, 2024)
8-25466194-G-A		not specified	Uncertain significance (Oct 22, 2021)
8-25466218-G-A		not specified	Uncertain significance (Nov 20, 2023)
8-25466252-A-G		not specified	Uncertain significance (Jul 14, 2021)
8-25466256-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-25466307-T-C		not specified	Uncertain significance (Apr 09, 2024)
8-25468228-G-T		not specified	Uncertain significance (Dec 13, 2021)
8-25468295-A-C		not specified	Likely benign (Aug 12, 2021)
8-25468328-C-T		not specified	Uncertain significance (Nov 16, 2021)
8-25468343-T-C		not specified	Likely benign (Dec 08, 2023)
8-25468361-A-G		not specified	Likely benign (Jun 26, 2024)
8-25468374-C-G		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
8-25468397-C-A		not specified	Uncertain significance (Oct 06, 2024)
8-25469957-C-T		not specified	Uncertain significance (Nov 08, 2022)
8-25469971-A-T		not specified	Uncertain significance (Feb 07, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDCA2	protein_coding	protein_coding	ENST00000330560	14	48924

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-11	0.565	125688	0	60	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.434	566	538	1.05	0.0000277	6704
Missense in Polyphen		130	129.63	1.0029		1790
Synonymous	0.228	188	192	0.979	0.0000101	1970
Loss of Function	1.39	21	29.1	0.723	0.00000142	406

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000452
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000268	0.000264
Middle Eastern	0.000381	0.000381
South Asian	0.000432	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of chromosome structure during mitosis required for condensin-depleted chromosomes to retain their compact architecture through anaphase. Acts by mediating the recruitment of phopsphatase PP1-gamma subunit (PPP1CC) to chromatin at anaphase and into the following interphase. At anaphase onset, its association with chromatin targets a pool of PPP1CC to dephosphorylate substrates. {ECO:0000269|PubMed:16492807, ECO:0000269|PubMed:16998479}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.907
• rvis_EVS: 1.03
• rvis_percentile_EVS: 91.12

Haploinsufficiency Scores

• pHI: 0.0467
• hipred: N
• hipred_score: 0.233
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdca2

Gene ontology

• Biological process: cell cycle;positive regulation of protein dephosphorylation;cell division
• Cellular component: nucleoplasm;chromosome;cytosol