CCDC66

coiled-coil domain containing 66

Basic information

Region (hg38): 3:56557160-56621837

Links

ENSG00000180376 ∙ NCBI:285331 ∙ OMIM:619287 ∙ HGNC:27709 ∙ Uniprot:A2RUB6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC66 gene.

• Inborn genetic diseases (38 variants)
• not provided (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC66 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			34	3		37
nonsense						0
start loss						0
frameshift			1	1		2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	36	5	1

Variants in CCDC66

This is a list of pathogenic ClinVar variants found in the CCDC66 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-56557250-T-TGGGGTAAGCA		not specified	Benign (Mar 28, 2016)
3-56558847-G-T		not specified	Uncertain significance (Feb 06, 2024)
3-56558878-A-T		not specified	Uncertain significance (Jan 09, 2024)
3-56558908-A-G		not specified	Uncertain significance (Mar 28, 2022)
3-56559571-C-T		not specified	Uncertain significance (Jan 29, 2024)
3-56563691-A-G		not specified	Uncertain significance (Feb 28, 2023)
3-56563738-A-T		not specified	Uncertain significance (Sep 16, 2021)
3-56563763-G-A		not specified	Uncertain significance (Jan 18, 2022)
3-56563777-A-G		not specified	Uncertain significance (Jan 31, 2022)
3-56563838-G-T		not specified	Uncertain significance (May 05, 2022)
3-56563846-T-C		not specified	Uncertain significance (Mar 29, 2023)
3-56563853-C-A		not specified	Uncertain significance (Apr 22, 2022)
3-56563855-A-C		not specified	Uncertain significance (Sep 27, 2021)
3-56563889-A-G		not specified	Uncertain significance (Jul 05, 2023)
3-56563922-C-T		not specified	Uncertain significance (Dec 06, 2021)
3-56563961-C-T		not specified	Uncertain significance (Dec 31, 2023)
3-56563983-G-C		not specified	Uncertain significance (Feb 21, 2024)
3-56563990-A-G		not specified	Uncertain significance (Sep 22, 2022)
3-56564006-C-G		not specified	Uncertain significance (Dec 17, 2023)
3-56564021-G-A		not specified	Uncertain significance (Jun 21, 2023)
3-56566615-A-G		not specified	Uncertain significance (Jan 04, 2024)
3-56566628-T-G		not specified	Uncertain significance (Nov 21, 2022)
3-56566681-C-T		not specified	Uncertain significance (Oct 17, 2023)
3-56566701-A-G		not specified	Uncertain significance (Dec 19, 2023)
3-56566707-G-C		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC66	protein_coding	protein_coding	ENST00000394672	18	64658

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.61e-36	0.0000153	123916	10	1822	125748	0.00731

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	524	461	1.14	0.0000218	6257
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00563	0.00562
Ashkenazi Jewish	0.00407	0.00408
East Asian	0.00383	0.00370
Finnish	0.0140	0.0139
European (Non-Finnish)	0.00966	0.00966
Middle Eastern	0.00383	0.00370
South Asian	0.00388	0.00380
Other	0.00897	0.00883

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0698
• hipred: N
• hipred_score: 0.146
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0275

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc66
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: microtubule bundle formation;retina homeostasis;retinal rod cell development;detection of light stimulus involved in visual perception;cilium assembly;regulation of protein localization to cilium
• Cellular component: photoreceptor outer segment;photoreceptor inner segment;centrosome;microtubule;cilium;centriolar satellite;ciliary transition zone;ciliary basal body
• Molecular function: protein binding;microtubule binding;protein homodimerization activity