CCDC15

protein-coding

coiled-coil domain containing 15

Gene summary

Involved in cilium assembly and positive regulation of centriole elongation. Located in centriole and centrosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_025004.3

Inheritance

—

ClinVar variants

U:133B:11

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr11:124,954,121-125,041,489

External References & Databases

Ensembl (ENSG00000149548)

Transcript & Mutation Effects

hg38 • Region Span ~87.4 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 CCDC15 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 134

not providedTotal: 4

Neurodevelopmental disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025004.3. 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			1 clinvar	1 clinvar	1 clinvar	3
missense			125 clinvar	9 clinvar		134
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	133	10	1	144

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025004.3	RefSeq	NP_079280.2	15	MANE Select
ENST00000344762.6	Ensembl	ENSP00000341684.5	15	MANE Select
ENST00000529051.5	Ensembl	ENSP00000435403.1	15	Standard
ENST00000529051.6	Ensembl	ENSP00000435403.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

centrosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344762
Coding exons: 15
Length: 87369
Individuals with no LoFs: 124596
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 124638
p: 0.000169

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.131	420	428	0.982	0.0000201	6251
Missense (PolyPhen)		106	116.48	0.91002		1941
Synonymous	2.25	119	155	0.769	0.00000741	1669
Loss of Function	1.24	35	43.9	0.797	0.00000221	612

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00065	rare
Latino/Admixed American	0.00028	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.00014	0.00013	rare
Other	0.00069	0.00066	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.964
RVIS EVS: -0.66
RVIS percentile EVS: 16.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.141

Gene Damage Prediction

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