CCDC17

protein-coding

coiled-coil domain containing 17

Gene summary

Located in axoneme. Implicated in colorectal adenocarcinoma. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001114938.3

Inheritance

—

ClinVar variants

U:126B:5

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr1:45,620,044-45,624,057

External References & Databases

Ensembl (ENSG00000159588)

Transcript & Mutation Effects

hg38 • Region Span ~4.0 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 CCDC17 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 115

not providedTotal: 1

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001114938.3. 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
missense			118 clinvar	4 clinvar	1 clinvar	123
nonsense			5 clinvar			5
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	126	4	1	131

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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_001114938.3	RefSeq	NP_001108410.2	13	MANE Select
ENST00000528266.6	Ensembl	ENSP00000432172.1	13	MANE Select
NM_001190182.2	RefSeq	NP_001177111.1	13	Standard
ENST00000372044.7	Ensembl	ENSP00000361114.3	2	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: ENST00000528266
Coding exons: 13
Length: 4014
Individuals with no LoFs: 125366
Homozygous LoFs: 0
Heterozygous LoFs: 225
Defined: 125591
p: 0.000896

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.14	315	377	0.835	0.0000246	3818
Missense (PolyPhen)		92	119.34	0.77092		1335
Synonymous	0.582	150	159	0.941	0.0000101	1377
Loss of Function	-0.234	32	30.6	1.05	0.00000165	306

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00037	rare
Latino/Admixed American	0.0040	0.0037	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00055	0.00054	rare
Finnish	0.0010	0.00097	rare
European (Non-Finnish)	0.00051	0.00046	rare
South Asian	0.00027	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0783

Intolerance Scores

LoFtool: 0.975
RVIS EVS: 0.4
RVIS percentile EVS: 76.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.646

Gene Damage Prediction

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