CCDC13

protein-coding

coiled-coil domain containing 13

Gene summary

Predicted to enable microtubule binding activity. Acts upstream of or within DNA damage response; cytoplasmic microtubule organization; and non-motile cilium assembly. Located in centriolar satellite. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_144719.4

Inheritance

—

ClinVar variants

U:113B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr3:42,705,756-42,773,253

External References & Databases

Ensembl (ENSG00000244607)

Transcript & Mutation Effects

hg38 • Region Span ~67.5 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 CCDC13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 121

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144719.4. 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			110 clinvar	12 clinvar	1 clinvar	123
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	113	13	1	127

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144719.4	RefSeq	NP_653320.3	15	MANE Select
ENST00000310232.11	Ensembl	ENSP00000309836.6	15	MANE Select
ENST00000954780.1	Ensembl	ENSP00000624839.1	14	Standard
ENST00000954780.2	Ensembl	ENSP00000624839.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular response to DNA damage stimulus
cytoplasmic microtubule organization
non-motile cilium assembly

Molecular Function

protein binding

Cellular Component

nucleus
centrosome
cytosol
centriolar satellite
cell projection

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310232
Coding exons: 15
Length: 80591
Individuals with no LoFs: 125333
Homozygous LoFs: 2
Heterozygous LoFs: 413
Defined: 125748
p: 0.00165

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.570	387	420	0.922	0.0000252	4628
Missense (PolyPhen)		114	136.15	0.83732		1460
Synonymous	1.55	149	175	0.851	0.0000107	1414
Loss of Function	2.95	20	40.2	0.497	0.00000230	426

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00055	0.00055	rare
Latino/Admixed American	0.00062	0.00061	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.013	0.013	notable
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00049	0.00047	rare
South Asian	0.0024	0.0024	notable
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for primary cilia formation and promotes the localization of the ciliopathy protein BBS4 to both centriolar satellites and cilia. {ECO:0000269|PubMed:24816561}.;

Intolerance Scores

LoFtool: 0.924
RVIS EVS: 0.87
RVIS percentile EVS: 88.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.120

Gene Damage Prediction

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