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.

• not_specified (128 variants)
• not_provided (7 variants)
• Myoepithelial_tumor (1 variants)

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. These statistics are base on transcript: NM_000152562.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	2	4
missense			119	10	2	131
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	119	12	4

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