CCDC25

protein-coding

coiled-coil domain containing 25

Gene summary

Enables DNA binding activity. Involved in positive regulation of cell motility. Located in endomembrane system and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018246.3

Inheritance

—

ClinVar variants

U:35

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr8:27,733,316-27,772,653

External References & Databases

Ensembl (ENSG00000147419)

Transcript & Mutation Effects

hg38 • Region Span ~39.3 kb

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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 CCDC25 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 30

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018246.3. 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			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	35	0	0	35

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018246.3	RefSeq	NP_060716.2	9	MANE Select
ENST00000356537.9	Ensembl	ENSP00000348933.4	9	MANE Select
NM_001304529.2	RefSeq	NP_001291458.1	6	Standard
NM_001304530.2	RefSeq	NP_001291459.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356537
Coding exons: 9
Length: 39336
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125729
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.55	65	111	0.585	0.00000559	1402
Missense (PolyPhen)		11	27.525	0.39964		386
Synonymous	0.725	32	37.7	0.850	0.00000207	322
Loss of Function	2.24	6	15.5	0.387	8.07e-7	189

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0719

Intolerance Scores

LoFtool: 0.498
RVIS EVS: 0.01
RVIS percentile EVS: 54.95

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.692

Gene Damage Prediction

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