CDCA5

cell division cycle associated 5

Basic information

Region (hg38): 11:65066300-65084164

Links

ENSG00000146670 ∙ NCBI:113130 ∙ OMIM:609374 ∙ HGNC:14626 ∙ Uniprot:Q96FF9 ∙ 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 CDCA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDCA5 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	3	4
missense			12		2	14
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	12	2	5

Variants in CDCA5

This is a list of pathogenic ClinVar variants found in the CDCA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65079153-T-A		not specified	Uncertain significance (Oct 19, 2024)
11-65079156-A-G		not specified	Uncertain significance (Feb 01, 2025)
11-65079179-C-G		not specified	Uncertain significance (Mar 01, 2023)
11-65079183-G-A		not specified	Uncertain significance (Nov 23, 2021)
11-65079364-G-A		not specified	Uncertain significance (May 17, 2023)
11-65079377-C-T			Likely benign (Dec 31, 2019)
11-65079475-A-C		not specified	Uncertain significance (Jun 26, 2024)
11-65079477-C-G		not specified	Uncertain significance (Jul 14, 2024)
11-65079496-C-T			Benign (Oct 17, 2018)
11-65079512-C-T			Benign (Dec 31, 2019)
11-65079523-C-T		not specified	Uncertain significance (Jul 06, 2021)
11-65079526-C-T		not specified	Uncertain significance (Sep 17, 2021)
11-65079664-C-T			Benign (Dec 31, 2019)
11-65079671-A-T			Benign (Jun 05, 2018)
11-65079672-G-C		not specified	Uncertain significance (Jun 03, 2024)
11-65079706-G-A		not specified	Uncertain significance (Aug 02, 2022)
11-65079714-T-C		not specified	Uncertain significance (Jan 16, 2025)
11-65079716-T-C			Benign (Aug 17, 2018)
11-65083354-G-A			Likely benign (Jan 11, 2019)
11-65083390-C-A		not specified	Uncertain significance (Aug 13, 2021)
11-65083956-G-T		not specified	Uncertain significance (Feb 04, 2025)
11-65083969-T-C		not specified	Uncertain significance (Jul 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDCA5	protein_coding	protein_coding	ENST00000275517	6	17865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00116	0.853	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	105	142	0.741	0.00000774	1597
Missense in Polyphen		39	50.235	0.77636		598
Synonymous	1.16	46	57.1	0.805	0.00000327	525
Loss of Function	1.25	6	10.4	0.579	4.37e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000736	0.0000703
Middle Eastern	0.000326	0.000326
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of sister chromatid cohesion in mitosis stabilizing cohesin complex association with chromatin. May antagonize the action of WAPL which stimulates cohesin dissociation from chromatin. Cohesion ensures that chromosome partitioning is accurate in both meiotic and mitotic cells and plays an important role in DNA repair. Required for efficient DNA double-stranded break repair. {ECO:0000269|PubMed:15837422, ECO:0000269|PubMed:17349791, ECO:0000269|PubMed:21111234}.
• Pathway: MicroRNAs in cancer - Homo sapiens (human);Establishment of Sister Chromatid Cohesion;S Phase;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Intolerance Scores

• loftool: 0.673
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.649
• hipred: Y
• hipred_score: 0.549
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.659

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdca5
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; growth/size/body region phenotype; hearing/vestibular/ear phenotype; embryo phenotype

Gene ontology

• Biological process: mitotic cell cycle;double-strand break repair;mitotic sister chromatid cohesion;mitotic chromosome condensation;mitotic metaphase plate congression;positive regulation of exit from mitosis;cell division;regulation of cohesin loading
• Cellular component: chromosome, centromeric region;nuclear chromatin;nucleus;nucleoplasm;chromosome;cytoplasm;cytosol;cohesin complex
• Molecular function: chromatin binding;protein binding;protein-containing complex binding