CDCA4

cell division cycle associated 4

Basic information

Region (hg38): 14:105009573-105021083

Links

ENSG00000170779 ∙ NCBI:55038 ∙ OMIM:612270 ∙ HGNC:14625 ∙ Uniprot:Q9BXL8 ∙ 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 CDCA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDCA4 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in CDCA4

This is a list of pathogenic ClinVar variants found in the CDCA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-105011245-C-G		not specified	Uncertain significance (Dec 20, 2021)
14-105011298-T-C		not specified	Uncertain significance (Jul 21, 2022)
14-105011304-C-T		not specified	Uncertain significance (Jan 09, 2024)
14-105011308-C-T		not specified	Uncertain significance (Jan 30, 2024)
14-105011333-C-A		not specified	Uncertain significance (Mar 28, 2024)
14-105011497-C-G		not specified	Uncertain significance (Oct 07, 2022)
14-105011526-G-A		not specified	Uncertain significance (May 09, 2022)
14-105011596-G-A		not specified	Uncertain significance (Dec 19, 2023)
14-105011622-C-T		not specified	Uncertain significance (Oct 16, 2023)
14-105011632-T-A		not specified	Uncertain significance (May 31, 2023)
14-105011665-G-A		not specified	Uncertain significance (Aug 14, 2023)
14-105011691-C-A		not specified	Uncertain significance (Jan 29, 2024)
14-105011692-G-A		not specified	Uncertain significance (Aug 03, 2022)
14-105011697-G-A		not specified	Uncertain significance (Aug 02, 2022)
14-105011709-G-A		not specified	Uncertain significance (Mar 07, 2024)
14-105011812-T-A		not specified	Uncertain significance (Oct 24, 2023)
14-105011821-G-C		not specified	Uncertain significance (Feb 28, 2024)
14-105011825-C-G		not specified	Uncertain significance (Jan 10, 2023)
14-105011829-C-T		not specified	Uncertain significance (Jun 14, 2023)
14-105011863-C-T		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDCA4	protein_coding	protein_coding	ENST00000336219	1	11576

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0835	0.770	124936	0	3	124939	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.296	147	157	0.934	0.0000100	1550
Missense in Polyphen		32	41.383	0.77327		418
Synonymous	0.0601	71	71.6	0.991	0.00000523	517
Loss of Function	1.07	2	4.43	0.452	3.54e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000616
Ashkenazi Jewish	0.0000996	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000341	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in the regulation of cell proliferation through the E2F/RB pathway. May be involved in molecular regulation of hematopoietic stem cells and progenitor cell lineage commitment and differentiation (By similarity). {ECO:0000250, ECO:0000269|PubMed:16984923}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.404
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.267
• hipred: Y
• hipred_score: 0.630
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.867

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdca4

Gene ontology

• Cellular component: nucleoplasm;cytosol;plasma membrane
• Molecular function: protein binding