CDCA3

protein-coding

cell division cycle associated 3

Gene summary

Predicted to be involved in cell division and protein ubiquitination. Located in adherens junction. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_031299.7

Inheritance

—

ClinVar variants

U:34B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr12:6,844,793-6,851,292

External References & Databases

Ensembl (ENSG00000111665)

Transcript & Mutation Effects

hg38 • Region Span ~6.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDCA3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 34

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031299.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			34 clinvar	1 clinvar		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	1	0	35

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031299.7	RefSeq	NP_112589.1	5	MANE Select
ENST00000538862.7	Ensembl	ENSP00000442068.1	5	MANE Select
NM_001297602.3	RefSeq	NP_001284531.1	5	Standard
NM_001297603.3	RefSeq	NP_001284532.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell cycle
biological_process
protein ubiquitination
cell division

Molecular Function

protein binding

Cellular Component

cytosol
cell-cell adherens junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000538862
Coding exons: 5
Length: 7274
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125745
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.657	127	150	0.849	0.00000783	1703
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0.000068	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.995

Gene Damage Prediction

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