CCDC13

Summary

CCDC13 (coiled-coil domain containing 13, HGNC:26358) is a protein-coding gene on chromosome 3p22.1, encoding Coiled-coil domain-containing protein 13 (Q8IYE1). Required for primary cilia formation and promotes the localization of the ciliopathy protein BBS4 to both centriolar satellites and cilia.

Acts upstream of or within DNA damage response; cytoplasmic microtubule organization; and non-motile cilium assembly. Located in centriolar satellite.

Source: NCBI Gene 152206 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 136 total
• MANE Select transcript: NM_144719

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26358
Approved symbol	CCDC13
Name	coiled-coil domain containing 13
Location	3p22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25467
Ensembl gene	ENSG00000244607
Ensembl biotype	protein_coding
Entrez	152206

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding_CDS_not_defined, 2 protein_coding, 2 retained_intron

ENST00000310232, ENST00000435327, ENST00000466031, ENST00000472921, ENST00000479576, ENST00000482100, ENST00000492806, ENST00000954780

RefSeq mRNA: 1 — MANE Select: NM_144719 NM_144719

CCDS: CCDS2705

Canonical transcript exons

ENST00000310232 — 16 exons

Exon	Start	End
ENSE00001078199	42773176	42773253
ENSE00001367633	42705756	42709139
ENSE00001372097	42709684	42709798
ENSE00001374653	42739634	42739810
ENSE00001375115	42745923	42746027
ENSE00001377081	42742896	42743057
ENSE00001378910	42730467	42730589
ENSE00001381558	42733470	42733609
ENSE00001389693	42735707	42735913
ENSE00003492336	42752575	42752717
ENSE00003492821	42758125	42758351
ENSE00003517298	42732887	42732970
ENSE00003625847	42747257	42747373
ENSE00003636225	42751936	42752025
ENSE00003665186	42757066	42757214
ENSE00003671791	42713162	42713316

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 91.08.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7842 / max 29.3205, expressed in 321 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41816	0.7014	312
41814	0.0561	39
41813	0.0201	5
41812	0.0066	3

Top tissues by expression

240 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	91.08	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.56	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.04	gold quality
nucleus accumbens	UBERON:0001882	78.09	gold quality
caudate nucleus	UBERON:0001873	77.78	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.69	gold quality
left testis	UBERON:0004533	76.66	gold quality
adenohypophysis	UBERON:0002196	76.12	gold quality
putamen	UBERON:0001874	75.80	gold quality
pituitary gland	UBERON:0000007	75.55	gold quality
right testis	UBERON:0004534	75.39	gold quality
testis	UBERON:0000473	74.77	gold quality
prefrontal cortex	UBERON:0000451	74.74	gold quality
monocyte	CL:0000576	74.72	gold quality
hypothalamus	UBERON:0001898	74.27	gold quality
leukocyte	CL:0000738	73.90	gold quality
amygdala	UBERON:0001876	73.60	gold quality
Brodmann (1909) area 9	UBERON:0013540	73.47	gold quality
right frontal lobe	UBERON:0002810	73.39	gold quality
left lobe of thyroid gland	UBERON:0001120	73.07	gold quality
thyroid gland	UBERON:0002046	72.77	gold quality
metanephros cortex	UBERON:0010533	72.77	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	72.74	gold quality
right lobe of thyroid gland	UBERON:0001119	72.73	gold quality
lower esophagus muscularis layer	UBERON:0035833	72.68	gold quality
lower esophagus	UBERON:0013473	72.63	gold quality
anterior cingulate cortex	UBERON:0009835	72.59	gold quality
corpus callosum	UBERON:0002336	72.56	gold quality
mucosa of transverse colon	UBERON:0004991	72.54	gold quality
forebrain	UBERON:0001890	72.28	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-9388	yes	7.76
E-ANND-3	yes	7.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting CCDC13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-6804-3P	98.72	64.82	852
HSA-MIR-5088-5P	97.97	64.28	487
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-6734-5P	95.70	65.56	950
HSA-MIR-3130-3P	94.98	66.97	574
HSA-MIR-371B-3P	94.48	66.59	345

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc13	ENSDARG00000063451
mus_musculus	Ccdc13	ENSMUSG00000079235
rattus_norvegicus	Ccdc13	ENSRNOG00000025643
drosophila_melanogaster	CG13032	FBGN0036652

Protein

Protein identifiers

Coiled-coil domain-containing protein 13 — Q8IYE1 (reviewed: Q8IYE1)

All UniProt accessions (1): Q8IYE1

UniProt curated annotations — full annotation on UniProt →

Function. Required for primary cilia formation and promotes the localization of the ciliopathy protein BBS4 to both centriolar satellites and cilia.

Subunit / interactions. Interacts with PCM1, CEP290 and PCNT.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriolar satellite. Cilium basal body.

RefSeq proteins (1): NP_653320* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038929	CCDC13	Family

UniProt features (16 total): coiled-coil region 4, region of interest 3, modified residue 3, sequence variant 3, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IYE1-F1	76.77	0.50

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 258, 469, 536

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 54 (showing top): GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, GOCC_MICROTUBULE_ORGANIZING_CENTER, EFC_Q6, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, GOBP_DNA_DAMAGE_RESPONSE, chr3p22, GOBP_ORGANELLE_ASSEMBLY, GOBP_MICROTUBULE_BUNDLE_FORMATION, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_AXONEME_ASSEMBLY, GOCC_CYTOPLASMIC_REGION, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY, GOCC_CENTRIOLAR_SATELLITE

GO Biological Process (4): DNA damage response (GO:0006974), cytoplasmic microtubule organization (GO:0031122), non-motile cilium assembly (GO:1905515), cell projection organization (GO:0030030)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): centrosome (GO:0005813), centriolar satellite (GO:0034451), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cellular response to stress	1
microtubule cytoskeleton organization	1
supramolecular fiber organization	1
cilium assembly	1
cellular component organization	1
binding	1
centriole	1
microtubule organizing center	1
centrosome	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

672 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC13	KRABD3	A5PL33	530
CCDC13	CEP131	Q9UPN4	528
CCDC13	CCDC14	Q49A88	515
CCDC13	KIAA0753	Q2KHM9	505
CCDC13	PIBF1	Q8WXW3	497
CCDC13	CFAP210	Q0VFZ6	491
CCDC13	CCDC18	Q5T9S5	489
CCDC13	CFAP184	Q2M329	476
CCDC13	CCDC160	A6NGH7	463
CCDC13	CEP126	Q9P2H0	454
CCDC13	CEP72	Q9P209	453
CCDC13	SEL1L3	Q68CR1	453
CCDC13	CCDC12	Q8WUD4	448
CCDC13	CCDC81	Q6ZN84	445
CCDC13	PDE6C	P51160	444

IntAct

173 interactions, top by confidence:

A	B	Type	Score
PCM1	PCNT	psi-mi:“MI:0914”(association)	0.710
PCNT	PCM1	psi-mi:“MI:0914”(association)	0.710
CEP131	CEP290	psi-mi:“MI:0914”(association)	0.650
CCDC13	TCHP	psi-mi:“MI:0915”(physical association)	0.600
CCDC13	CCND3	psi-mi:“MI:0915”(physical association)	0.560
CCDC13	CCHCR1	psi-mi:“MI:0915”(physical association)	0.560
TP53BP2	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
USP54	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
CCDC13	TFIP11	psi-mi:“MI:0915”(physical association)	0.560
CCDC13	DISC1	psi-mi:“MI:0915”(physical association)	0.560
CCDC13	ZRANB1	psi-mi:“MI:0915”(physical association)	0.560
NEFL	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
CDR2	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
MYF5	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
EFHC2	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
CCDC13	GMCL1	psi-mi:“MI:0915”(physical association)	0.560
FCHO1	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
KIAA1328	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
RALBP1	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
TRIM23	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
CCDC13	LZTS1	psi-mi:“MI:0915”(physical association)	0.560
ZBED1	CCDC13	psi-mi:“MI:0915”(physical association)	0.560
CCDC13	GOLGA2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (53): CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid), CCDC13 (Two-hybrid)

ESM2 similar proteins: A0JMQ7, A0JMY4, A2AUM9, A2BDR7, A2BGP7, A6NI79, A6PWD2, A6QNP9, B1AJZ9, D3YV10, G9G127, O35550, O35551, O75330, O94986, P0CB05, Q05D60, Q0VFN8, Q0VFX2, Q15276, Q17QT2, Q3UPP8, Q498G2, Q4KLY0, Q4PJT6, Q4R703, Q4V7B0, Q5JU67, Q5NVN6, Q5U3A8, Q5U3Z6, Q5U4W1, Q5ZL12, Q66KE8, Q6DFC2, Q6DIS8, Q6IMY1, Q6NRC9, Q6P402, Q7M6Y5

Diamond homologs: D3YV10, Q8IYE1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 54 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Regulation of PLK1 Activity at G2/M Transition	5	24.4×	3e-04

GO biological processes:

GO term	Partners	Fold	FDR
non-motile cilium assembly	6	35.6×	6e-06
cilium assembly	7	10.5×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

136 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	107
Likely benign	13
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3320 predictions. Top by Δscore:

Variant	Effect	Δscore
3:42709653:AC:A	donor_gain	1.0000
3:42709654:CC:C	donor_gain	1.0000
3:42709699:T:TA	donor_gain	1.0000
3:42713156:CCCTA:C	donor_loss	1.0000
3:42713157:CCTA:C	donor_loss	1.0000
3:42713158:CTAC:C	donor_loss	1.0000
3:42713159:TACCT:T	donor_loss	1.0000
3:42713160:A:T	donor_loss	1.0000
3:42713161:C:CG	donor_loss	1.0000
3:42713205:C:A	donor_gain	1.0000
3:42734280:A:AC	donor_gain	1.0000
3:42734280:AAGT:A	donor_gain	1.0000
3:42734281:A:C	donor_gain	1.0000
3:42735700:TAC:T	donor_loss	1.0000
3:42735701:ACT:A	donor_loss	1.0000
3:42735702:CTC:C	donor_loss	1.0000
3:42735705:A:AC	donor_gain	1.0000
3:42735705:ACG:A	donor_loss	1.0000
3:42735705:ACGTG:A	donor_gain	1.0000
3:42735706:C:A	donor_loss	1.0000
3:42735706:C:CA	donor_gain	1.0000
3:42735706:CGTG:C	donor_gain	1.0000
3:42735706:CGTGC:C	donor_gain	1.0000
3:42735923:C:CT	acceptor_gain	1.0000
3:42735924:A:T	acceptor_gain	1.0000
3:42739628:CCATA:C	donor_loss	1.0000
3:42739629:CATAC:C	donor_loss	1.0000
3:42739630:ATACC:A	donor_loss	1.0000
3:42739631:TACC:T	donor_loss	1.0000
3:42739632:A:AC	donor_gain	1.0000

AlphaMissense

4661 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:42739650:A:G	L383P	0.988
3:42752669:A:G	L140P	0.985
3:42739734:C:G	R355P	0.984
3:42739638:A:G	L387P	0.983
3:42757104:A:G	L111P	0.983
3:42730506:C:G	R560P	0.982
3:42757137:A:G	L100P	0.982
3:42757149:C:G	R96P	0.982
3:42735780:A:G	L433P	0.981
3:42745942:A:G	I269T	0.978
3:42747306:A:G	L224P	0.978
3:42730497:A:G	L563P	0.976
3:42735906:A:G	L391P	0.976
3:42745964:A:G	W262R	0.976
3:42745964:A:T	W262R	0.976
3:42757134:A:G	L101P	0.976
3:42709019:G:C	F703L	0.974
3:42709019:G:T	F703L	0.974
3:42709021:A:G	F703L	0.974
3:42743047:A:G	L279P	0.974
3:42747273:A:G	L235P	0.974
3:42735759:C:G	R440P	0.973
3:42739642:C:G	A386P	0.972
3:42752654:C:G	R145P	0.972
3:42747303:C:G	R225P	0.971
3:42730476:A:G	L570P	0.970
3:42735897:A:G	L394P	0.970
3:42745958:C:G	G264R	0.968
3:42757176:A:G	L87P	0.967
3:42730500:C:G	R562P	0.963

dbSNP variants (sampled 300 via entrez): RS1000022688 (3:42713388 C>T), RS1000043507 (3:42770634 A>G,T), RS1000117738 (3:42716757 C>A,T), RS1000127617 (3:42732241 G>A), RS1000191977 (3:42716278 A>G), RS1000365267 (3:42756312 A>G), RS1000375234 (3:42756008 C>G,T), RS1000459528 (3:42730645 C>T), RS1000495342 (3:42731055 G>A), RS1000553105 (3:42749754 GT>G), RS1000555669 (3:42743449 G>C,T), RS1000631058 (3:42774597 A>G), RS1000718982 (3:42726025 A>G), RS1000740998 (3:42737072 C>A), RS1000825785 (3:42736136 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001762_774	Obesity-related traits	2.000000e-07
GCST001762_789	Obesity-related traits	2.000000e-07
GCST002129_6	Periodontitis (DPAL)	6.000000e-06
GCST002595_14	Clozapine-induced agranulocytosis	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005188	CCL11 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	increases expression, affects cotreatment	2
Air Pollutants	increases expression, affects expression, increases abundance	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
dicrotophos	decreases expression	1
bisphenol A	affects cotreatment, increases methylation	1
tris(2-butoxyethyl) phosphate	affects expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
licochalcone B	increases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	1
Ozone	affects expression, increases abundance	1
Phthalic Acids	increases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.