CCDC60

Gene

coiled-coil domain containing 60

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

MANE transcript

NM_178499.5

Inheritance

—

ClinVar variants

P:1U:110B:4

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr12:119,334,712-119,541,040

External References & Databases

Ensembl (ENSG00000183273)

Transcript & Mutation Effects

hg38 • Region Span ~206.3 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 CCDC60 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 109

Primary ciliary dyskinesiaTotal: 3

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178499.5. 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			107 clinvar	3 clinvar		110
nonsense			1 clinvar			1
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	1	110	4	0	115

Highest pathogenic variant AF is 0.00054663594

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178499.5	RefSeq	NP_848594.2	14	MANE Select
ENST00000327554.3	Ensembl	ENSP00000333374.2	14	MANE Select
ENST00000536742.5	Ensembl	ENSP00000445505.1	3	Standard
ENST00000536742.6	Ensembl	ENSP00000445505.1	3	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: ENST00000327554
Coding exons: 14
Length: 206336
Individuals with no LoFs: 125274
Homozygous LoFs: 1
Heterozygous LoFs: 472
Defined: 125747
p: 0.00188

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.142	307	314	0.977	0.0000172	3644
Missense (PolyPhen)		116	118.51	0.97886		1363
Synonymous	1.93	85	111	0.767	0.00000572	1012
Loss of Function	1.80	19	29.5	0.643	0.00000158	348

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00094	0.00092	rare
Latino/Admixed American	0.0017	0.0016	notable
Ashkenazi Jewish	0.00080	0.00079	rare
East Asian	0.00060	0.00060	rare
Finnish	0.0025	0.0025	notable
European (Non-Finnish)	0.0020	0.0020	notable
South Asian	0.0030	0.0027	notable
Other	0.0026	0.0026	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0760

Intolerance Scores

LoFtool: 0.984
RVIS EVS: 0.71
RVIS percentile EVS: 85.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0319

Gene Damage Prediction

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