CCDC9

Summary

CCDC9 (coiled-coil domain containing 9, HGNC:24560) is a protein-coding gene on chromosome 19q13.32, encoding Coiled-coil domain-containing protein 9 (Q9Y3X0). Probable component of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post-transcriptional processes in the cyto….

Enables RNA binding activity. Part of exon-exon junction complex.

Source: NCBI Gene 26093 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 189 total
• MANE Select transcript: NM_015603

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24560
Approved symbol	CCDC9
Name	coiled-coil domain containing 9
Location	19q13.32
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP586M1019
Ensembl gene	ENSG00000105321
Ensembl biotype	protein_coding
Entrez	26093

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000221922, ENST00000595659, ENST00000596938, ENST00000599398, ENST00000600117, ENST00000601154, ENST00000643617, ENST00000851059, ENST00000851060, ENST00000878859, ENST00000878860, ENST00000925672, ENST00000925673, ENST00000925674, ENST00000925675, ENST00000957309

RefSeq mRNA: 1 — MANE Select: NM_015603 NM_015603

CCDS: CCDS12698

Canonical transcript exons

ENST00000221922 — 12 exons

Exon	Start	End
ENSE00000714755	47271274	47271953
ENSE00000714758	47271082	47271187
ENSE00000714761	47270553	47270688
ENSE00000714764	47266611	47266792
ENSE00000714765	47264773	47264946
ENSE00000714766	47264603	47264686
ENSE00000714767	47260588	47260839
ENSE00000714768	47260321	47260422
ENSE00000858320	47258559	47258663
ENSE00001350378	47258330	47258403
ENSE00001350383	47256525	47256609
ENSE00003667010	47270407	47270453

Expression profiles

Bgee: expression breadth ubiquitous, 198 present calls, max score 96.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.9771 / max 315.2002, expressed in 1817 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176639	18.1097	1816
176640	2.1763	1090
176641	1.3341	827
176642	0.3362	164
208877	0.0178	9
176645	0.0030	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	96.97	gold quality
type B pancreatic cell	CL:0000169	94.53	gold quality
olfactory bulb	UBERON:0002264	93.53	gold quality
body of pancreas	UBERON:0001150	92.79	gold quality
left testis	UBERON:0004533	92.34	gold quality
right testis	UBERON:0004534	92.02	gold quality
skin of leg	UBERON:0001511	91.46	gold quality
popliteal artery	UBERON:0002250	91.23	gold quality
tibial artery	UBERON:0007610	91.23	gold quality
skin of abdomen	UBERON:0001416	91.09	gold quality
mucosa of stomach	UBERON:0001199	91.04	gold quality
left ovary	UBERON:0002119	90.82	gold quality
artery	UBERON:0001637	90.68	gold quality
right ovary	UBERON:0002118	90.67	gold quality
left uterine tube	UBERON:0001303	90.59	gold quality
aorta	UBERON:0000947	90.48	gold quality
endocervix	UBERON:0000458	90.39	gold quality
body of uterus	UBERON:0009853	90.39	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	90.26	gold quality
body of stomach	UBERON:0001161	90.07	gold quality
lower esophagus muscularis layer	UBERON:0035833	90.02	gold quality
lower esophagus	UBERON:0013473	89.98	gold quality
pancreatic ductal cell	CL:0002079	89.93	gold quality
muscle layer of sigmoid colon	UBERON:0035805	89.77	gold quality
ascending aorta	UBERON:0001496	89.74	gold quality
tibial nerve	UBERON:0001323	89.72	gold quality
thoracic aorta	UBERON:0001515	89.67	gold quality
descending thoracic aorta	UBERON:0002345	89.58	gold quality
ectocervix	UBERON:0012249	89.58	gold quality
right coronary artery	UBERON:0001625	89.44	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting CCDC9, 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-8485	100.00	77.57	4731
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-4253	97.48	65.11	692

Literature-anchored findings (GeneRIF, showing 1)

• homozygous variant (NC_000019.9: g.47763960C>T, NM_015603.3, NP_056418.1: p. Ser109Leu) associated with severe asthenozoospermia (PMID:31502483)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc9	ENSDARG00000004636
mus_musculus	Ccdc9	ENSMUSG00000041375
rattus_norvegicus	Ccdc9	ENSRNOG00000048848
caenorhabditis_elegans		WBGENE00015684

Paralogs (1): CCDC9B (ENSG00000188549)

Protein

Protein identifiers

Coiled-coil domain-containing protein 9 — Q9Y3X0 (reviewed: Q9Y3X0)

All UniProt accessions (5): Q9Y3X0, A0A2R8Y4Z8, M0QYB4, M0QZR0, M0R2W0

UniProt curated annotations — full annotation on UniProt →

Function. Probable component of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation.

Subunit / interactions. Probable component of the exon junction complex (EJC); the association is RNA-dependent.

RefSeq proteins (1): NP_056418* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029336	DUF4594	Family

Pfam: PF15266

UniProt features (35 total): modified residue 18, compositionally biased region 11, sequence variant 3, chain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y3X0-F1	59.06	0.08

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 (18): 80, 95, 107, 111, 121, 128, 130, 131, 133, 135, 137, 202, 248, 255, 376, 386, 390, 521

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, MODULE_45, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MODULE_118, MODULE_379, BLALOCK_ALZHEIMERS_DISEASE_UP, MODULE_242, SHEN_SMARCA2_TARGETS_DN, MODULE_104, GOCC_EXON_EXON_JUNCTION_COMPLEX, LAIHO_COLORECTAL_CANCER_SERRATED_DN, MODULE_181, MIKKELSEN_MCV6_LCP_WITH_H3K4ME3, MIKKELSEN_MEF_LCP_WITH_H3K4ME3

GO Biological Process (0):

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (1): exon-exon junction complex (GO:0035145)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
binding	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

792 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC9	PPP1R35	Q8TAP8	494
CCDC9	DALRD3	Q5D0E6	479
CCDC9	ZNF593	O00488	443
CCDC9	PRR15L	Q9BU68	412
CCDC9	NHSL1	Q5SYE7	389
CCDC9	CYB561D1	Q8N8Q1	369
CCDC9	SCAND1	P57086	368
CCDC9	DCAF6	Q58WW2	361
CCDC9	CHMP2A	O43633	359
CCDC9	PPIL2	Q13356	350
CCDC9	CISD3	P0C7P0	348
CCDC9	DLGAP4	Q9Y2H0	340
CCDC9	SSUH2	Q9Y2M2	336
CCDC9	ARFIP2	P53365	335
CCDC9	SNX14	Q9Y5W7	325

IntAct

99 interactions, top by confidence:

A	B	Type	Score
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
RBM8A	CASC3	psi-mi:“MI:0914”(association)	0.900
SARNP	DDX39A	psi-mi:“MI:0914”(association)	0.740
SNIP1	RNPS1	psi-mi:“MI:0914”(association)	0.670
PNN	CASC3	psi-mi:“MI:0914”(association)	0.640
AP3M1	AP3B1	psi-mi:“MI:0914”(association)	0.640
SNRNP70	GEMIN2	psi-mi:“MI:0914”(association)	0.640
SARNP	ZC3H11A	psi-mi:“MI:0914”(association)	0.610
CCDC9	WFS1	psi-mi:“MI:0915”(physical association)	0.560
CCDC9	KIF1B	psi-mi:“MI:0915”(physical association)	0.560
HTT	CCDC9	psi-mi:“MI:0915”(physical association)	0.560
PIP4K2A	AP3B1	psi-mi:“MI:0914”(association)	0.530
SNIP1	CASC3	psi-mi:“MI:0914”(association)	0.530
TMEM184B	INPPL1	psi-mi:“MI:0914”(association)	0.530
RALYL	CDC40	psi-mi:“MI:0914”(association)	0.530
NCBP3	SAP18	psi-mi:“MI:0914”(association)	0.530
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
LUC7L2	CASC3	psi-mi:“MI:0914”(association)	0.530
WSB2	UBB	psi-mi:“MI:0914”(association)	0.530
TADA2B	SUPT3H	psi-mi:“MI:0914”(association)	0.530

BioGRID (126): CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS)

ESM2 similar proteins: A0P8Z5, A2AI08, A2RU30, A5PKK7, B0KYV5, B1H222, F1LR10, O43247, P07516, Q14684, Q14DQ1, Q32LQ1, Q3U132, Q5JXC2, Q5PQN4, Q5PR69, Q5R8C5, Q5SWA1, Q5T7N3, Q5XI03, Q5ZMW6, Q60829, Q66H19, Q6J4I0, Q6P2K3, Q6ZUX3, Q7TNY7, Q80XI1, Q80YS5, Q8BFW3, Q8BRM2, Q8BVV7, Q8IYY4, Q8K124, Q8K3I4, Q8NDD1, Q8NFW9, Q8R0W1, Q8TD55, Q8VC31

Diamond homologs: A3KGF9, Q5RCJ6, Q6ZUT6, Q8VC31, Q9Y3X0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 116 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
Transport of Mature Transcript to Cytoplasm	8	38.5×	2e-09
mRNA 3’-end processing	14	34.9×	4e-16
Transport of Mature mRNA derived from an Intron-Containing Transcript	16	30.8×	2e-17
Polymerase switching on the C-strand of the telomere	5	26.8×	6e-05
RNA Polymerase II Transcription Termination	9	25.0×	7e-09
Processing of Capped Intron-Containing Pre-mRNA	13	13.5×	2e-09
mRNA Splicing	8	11.1×	4e-05
mRNA Splicing - Major Pathway	15	10.4×	2e-09

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of telomere maintenance via telomerase	6	43.1×	6e-07
mRNA export from nucleus	13	37.7×	9e-15
poly(A)+ mRNA export from nucleus	5	33.0×	3e-05
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	5	22.9×	2e-04
regulation of alternative mRNA splicing, via spliceosome	6	14.4×	2e-04
RNA splicing	15	13.0×	2e-10
mRNA splicing, via spliceosome	13	11.7×	2e-08
regulation of RNA splicing	5	10.7×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	162
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1644 predictions. Top by Δscore:

Variant	Effect	Δscore
19:47256527:G:GT	donor_gain	1.0000
19:47256675:G:GT	donor_gain	1.0000
19:47258711:G:GG	donor_gain	1.0000
19:47260308:T:A	acceptor_gain	1.0000
19:47260312:T:TA	acceptor_gain	1.0000
19:47260320:G:A	acceptor_loss	1.0000
19:47260320:GGA:G	acceptor_gain	1.0000
19:47260419:GTCG:G	donor_gain	1.0000
19:47260586:A:AG	acceptor_gain	1.0000
19:47260587:G:GG	acceptor_gain	1.0000
19:47264602:GGA:G	acceptor_gain	1.0000
19:47264668:G:GG	donor_gain	1.0000
19:47264683:GCGG:G	donor_gain	1.0000
19:47266660:C:CA	acceptor_gain	1.0000
19:47266793:G:GG	donor_gain	1.0000
19:47270551:A:AG	acceptor_gain	1.0000
19:47270552:G:GG	acceptor_gain	1.0000
19:47270680:GGCC:G	donor_gain	1.0000
19:47271078:CTAG:C	acceptor_loss	1.0000
19:47271079:TAGT:T	acceptor_loss	1.0000
19:47271080:A:AG	acceptor_gain	1.0000
19:47271080:AGT:A	acceptor_gain	1.0000
19:47271080:AGTG:A	acceptor_loss	1.0000
19:47271081:G:GG	acceptor_gain	1.0000
19:47271081:GT:G	acceptor_gain	1.0000
19:47271081:GTG:G	acceptor_gain	1.0000
19:47271081:GTGA:G	acceptor_gain	1.0000
19:47271081:GTGAC:G	acceptor_gain	1.0000
19:47271184:GCAG:G	donor_gain	1.0000
19:47271187:GGT:G	donor_loss	1.0000

AlphaMissense

3446 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:47266689:T:A	W267R	1.000
19:47266689:T:C	W267R	1.000
19:47266691:G:C	W267C	1.000
19:47266691:G:T	W267C	1.000
19:47266755:T:A	W289R	1.000
19:47266755:T:C	W289R	1.000
19:47266757:G:C	W289C	1.000
19:47266757:G:T	W289C	1.000
19:47266767:T:A	W293R	1.000
19:47266767:T:C	W293R	1.000
19:47266769:G:C	W293C	1.000
19:47266769:G:T	W293C	1.000
19:47258626:T:C	L24P	0.999
19:47258629:G:C	R25P	0.999
19:47258636:G:C	K27N	0.999
19:47258636:G:T	K27N	0.999
19:47258647:T:C	L31P	0.999
19:47258655:C:A	R34S	0.999
19:47258656:G:C	R34P	0.999
19:47260337:G:C	R42P	0.999
19:47266690:G:C	W267S	0.999
19:47266761:C:A	R291S	0.999
19:47258605:T:C	L17S	0.998
19:47258622:G:C	A23P	0.998
19:47258626:T:A	L24H	0.998
19:47258637:A:G	N28D	0.998
19:47258638:A:T	N28I	0.998
19:47258643:G:C	A30P	0.998
19:47258647:T:A	L31H	0.998
19:47264608:G:C	W156C	0.998

dbSNP variants (sampled 300 via entrez): RS1000027685 (19:47264076 TC>T), RS1000051605 (19:47266490 T>C), RS1000114306 (19:47254771 C>A,T), RS1000171253 (19:47261936 G>C,T), RS1000181939 (19:47255361 C>G,T), RS1000302262 (19:47270816 G>A), RS1000463159 (19:47260345 G>A,C), RS1000514708 (19:47256602 C>T), RS1000613004 (19:47258819 T>G), RS1000820712 (19:47275085 G>A), RS1000916473 (19:47262981 T>C,G), RS1000936321 (19:47275179 C>A,T), RS1001177094 (19:47269874 C>A,T), RS1001227480 (19:47264747 C>T), RS1001289609 (19:47256761 C>T)

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

2 associations (top):

Study	Trait	p-value
GCST010002_57	Refractive error	1.000000e-27
GCST90002381_352	Eosinophil count	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004842	eosinophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, increases abundance, decreases expression	2
Tobacco Smoke Pollution	increases expression, decreases expression	2
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
sodium arsenite	affects binding, increases reaction, increases activity	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
licochalcone B	increases expression	1
Amiodarone	increases expression	1
Benzo(a)pyrene	affects methylation	1
Caffeine	decreases phosphorylation	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Ivermectin	decreases expression	1
Ozone	increases abundance, affects expression	1
Ribonucleotides	affects binding, increases reaction	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Thiram	increases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	increases expression	1
Cadmium Chloride	increases expression	1
Palmitic Acid	decreases phosphorylation	1
Okadaic Acid	increases expression	1
Acrylamide	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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