CCDC66

protein-coding

coiled-coil domain containing 66

Gene summary

Enables identical protein binding activity and microtubule binding activity. Involved in several processes, including ciliary transition zone assembly; microtubule cytoskeleton organization; and mitotic metaphase chromosome alignment. Located in cytoskeleton; midbody; and photoreceptor inner segment. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001141947.3

Inheritance

—

ClinVar variants

U:156B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr3:56,557,161-56,621,837

External References & Databases

Ensembl (ENSG00000180376)

Transcript & Mutation Effects

hg38 • Region Span ~64.7 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 CCDC66 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 150

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001141947.3. 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		2
missense			147 clinvar	9 clinvar		156
nonsense			2 clinvar	1 clinvar		3
start loss						0
frameshift			4 clinvar	1 clinvar		5
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	156	12	0	168

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001141947.3	RefSeq	NP_001135419.1	18	MANE Select
ENST00000394672.8	Ensembl	ENSP00000378167.3	18	MANE Select
NM_001012506.5	RefSeq	NP_001012524.4	15	Standard
NM_001353147.1	RefSeq	NP_001340076.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule bundle formation
retina homeostasis
retinal rod cell development
detection of light stimulus involved in visual perception
cilium assembly

Molecular Function

protein binding
microtubule binding
protein homodimerization activity

Cellular Component

photoreceptor outer segment
photoreceptor inner segment
centrosome
microtubule
cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394672
Coding exons: 18
Length: 64658
Individuals with no LoFs: 123916
Homozygous LoFs: 10
Heterozygous LoFs: 1822
Defined: 125748
p: 0.00731

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.04	524	461	1.14	0.0000218	6257
Missense (PolyPhen)		128	132.2	0.9682		1900
Synonymous	-0.506	168	160	1.05	0.00000763	1638
Loss of Function	0.207	55	56.7	0.970	0.00000299	701

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0018	0.0018	notable
Latino/Admixed American	0.0038	0.0038	notable
Ashkenazi Jewish	0.0041	0.0041	notable
East Asian	0.0038	0.0037	notable
Finnish	0.014	0.014	notable
European (Non-Finnish)	0.0097	0.0097	notable
South Asian	0.0039	0.0038	notable
Other	0.0090	0.0088	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Microtubule-binding protein required for ciliogenesis (PubMed:28235840). May function in ciliogenesis by mediating the transport of proteins like BBS4 to the cilium, but also through the organization of the centriolar satellites (PubMed:28235840). Plays a role in retina morphogenesis and/or homeostasis (By similarity). {ECO:0000250|UniProtKB:Q6NS45, ECO:0000269|PubMed:28235840}.;

Intolerance Scores

LoFtool: 0.631
RVIS EVS: 0.81
RVIS percentile EVS: 87.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0275

Gene Damage Prediction

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