CCDC9B

Summary

CCDC9B (coiled-coil domain containing 9B, HGNC:33488) is a protein-coding gene on chromosome 15q15.1, encoding Coiled-coil domain-containing protein 9B (Q6ZUT6).

Enables RNA binding activity.

Source: NCBI Gene 388115 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_207380

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33488
Approved symbol	CCDC9B
Name	coiled-coil domain containing 9B
Location	15q15.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ43339
Ensembl gene	ENSG00000188549
Ensembl biotype	protein_coding
Entrez	388115

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000382688, ENST00000397536, ENST00000557973, ENST00000558858, ENST00000558912, ENST00000559313, ENST00000560922, ENST00000906859, ENST00000967943

RefSeq mRNA: 1 — MANE Select: NM_207380 NM_207380

CCDS: CCDS10055

Canonical transcript exons

ENST00000397536 — 11 exons

Exon	Start	End
ENSE00001493019	40338748	40338903
ENSE00001493020	40339512	40339619
ENSE00001493022	40340808	40340939
ENSE00003479416	40336760	40336813
ENSE00003484628	40339905	40340015
ENSE00003490865	40335784	40335826
ENSE00003498948	40336574	40336664
ENSE00003552820	40337724	40337893
ENSE00003584429	40331452	40335700
ENSE00003625319	40337388	40337446
ENSE00003653101	40338535	40338660

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 96.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.8513 / max 114.2915, expressed in 1204 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
149493	6.7631	1190
149489	0.5852	256
149492	0.2473	138
149491	0.1516	55
149490	0.1040	47

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	96.66	gold quality
muscle layer of sigmoid colon	UBERON:0035805	96.50	gold quality
right lobe of thyroid gland	UBERON:0001119	95.71	gold quality
lower esophagus	UBERON:0013473	95.28	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.28	gold quality
lower esophagus mucosa	UBERON:0035834	95.09	gold quality
left lobe of thyroid gland	UBERON:0001120	95.08	gold quality
gastrocnemius	UBERON:0001388	94.84	gold quality
mucosa of stomach	UBERON:0001199	94.62	gold quality
thyroid gland	UBERON:0002046	94.59	gold quality
skeletal muscle tissue	UBERON:0001134	94.58	gold quality
heart left ventricle	UBERON:0002084	94.56	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.15	gold quality
muscle of leg	UBERON:0001383	93.89	gold quality
sural nerve	UBERON:0015488	93.36	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.07	gold quality
esophagus	UBERON:0001043	92.91	gold quality
right atrium auricular region	UBERON:0006631	92.77	gold quality
heart	UBERON:0000948	92.62	gold quality
muscle tissue	UBERON:0002385	91.76	gold quality
stromal cell of endometrium	CL:0002255	91.50	gold quality
minor salivary gland	UBERON:0001830	91.48	gold quality
colon	UBERON:0001155	91.42	gold quality
myometrium	UBERON:0001296	91.39	gold quality
descending thoracic aorta	UBERON:0002345	91.39	gold quality
thoracic aorta	UBERON:0001515	91.13	gold quality
ascending aorta	UBERON:0001496	91.05	gold quality
esophagus mucosa	UBERON:0002469	90.88	gold quality
saliva-secreting gland	UBERON:0001044	90.85	gold quality
right coronary artery	UBERON:0001625	90.62	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

108 targeting CCDC9B, 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-5193	100.00	67.26	1744
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-5093	99.67	69.26	2291

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc9b	ENSDARG00000090013
mus_musculus	Ccdc9b	ENSMUSG00000045838
rattus_norvegicus	Ccdc9b	ENSRNOG00000028910
caenorhabditis_elegans		WBGENE00015684

Paralogs (1): CCDC9 (ENSG00000105321)

Protein

Protein identifiers

Coiled-coil domain-containing protein 9B — Q6ZUT6 (reviewed: Q6ZUT6)

All UniProt accessions (2): H0YM82, Q6ZUT6

UniProt curated annotations — full annotation on UniProt →

Isoforms (5)

UniProt ID	Names	Canonical?
Q6ZUT6-1	1	yes
Q6ZUT6-2	2
Q6ZUT6-3	3
Q6ZUT6-4	4
Q6ZUT6-5	5

RefSeq proteins (1): NP_997263* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029336	DUF4594	Family

Pfam: PF15266

UniProt features (23 total): compositionally biased region 7, splice variant 7, region of interest 2, modified residue 2, sequence conflict 2, chain 1, sequence variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZUT6-F1	54.65	0.07

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 (2): 201, 392

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 64 (showing top): TGACCTY_ERR1_Q2, AP2_Q3, CTCTAGA_MIR526C_MIR518F_MIR526A, KOYAMA_SEMA3B_TARGETS_UP, TGCTGAY_UNKNOWN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, TGGNNNNNNKCCAR_UNKNOWN, RYTTCCTG_ETS2_B, TAATTA_CHX10_01, ER_Q6_02, FIGUEROA_AML_METHYLATION_CLUSTER_1_DN, WIERENGA_STAT5A_TARGETS_DN, KRIEG_HYPOXIA_NOT_VIA_KDM3A

GO Biological Process (0):

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1

Protein interactions and networks

STRING

470 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC9B	FAM86B1	Q8N7N1	507
CCDC9B	IQCC	Q4KMZ1	507
CCDC9B	PROSER3	Q2NL68	480
CCDC9B	TMEM51	Q9NW97	479
CCDC9B	LYSMD4	Q5XG99	471
CCDC9B	KRABD2	Q6ZNG9	447
CCDC9B	KRABD3	A5PL33	431
CCDC9B	DCTN5	Q9BTE1	405
CCDC9B	LEPROT	O15243	401
CCDC9B	SHISAL1	Q3SXP7	397
CCDC9B	VPS18	Q9P253	369
CCDC9B	TBC1D31	Q96DN5	368
CCDC9B	TMEM250	H0YL14	368
CCDC9B	ERLIN2	O94905	348
CCDC9B	UACA	Q9BZF9	344

IntAct

15 interactions, top by confidence:

A	B	Type	Score
PNN	CASC3	psi-mi:“MI:0914”(association)	0.640
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
THOC1	TARS3	psi-mi:“MI:0914”(association)	0.350
THOC7	ALYREF	psi-mi:“MI:0914”(association)	0.350
BMI1	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
CHTOP	C1orf226	psi-mi:“MI:0914”(association)	0.350
ERH	SAP18	psi-mi:“MI:0914”(association)	0.350
LUC7L2	SAP18	psi-mi:“MI:0914”(association)	0.350
SERBP1	ZNF593	psi-mi:“MI:0914”(association)	0.350
SRSF6	PLEKHO1	psi-mi:“MI:0914”(association)	0.350
	NFIB	psi-mi:“MI:0914”(association)	0.350
	SRRM1	psi-mi:“MI:0914”(association)	0.350
	RPS10-NUDT3	psi-mi:“MI:0914”(association)	0.350

BioGRID (20): C15orf52 (Affinity Capture-MS), C15orf52 (Affinity Capture-MS), C15orf52 (Affinity Capture-MS), C15orf52 (Affinity Capture-MS), C15orf52 (Affinity Capture-MS), C15orf52 (Affinity Capture-MS), C15orf52 (Affinity Capture-RNA), C15orf52 (Affinity Capture-MS), C15orf52 (Affinity Capture-MS), C15orf52 (Proximity Label-MS), C15orf52 (Proximity Label-MS), C15orf52 (Proximity Label-MS), C15orf52 (Affinity Capture-MS), C15orf52 (Co-fractionation), C15orf52 (Co-fractionation)

ESM2 similar proteins: A0A096LP49, A0A8V8TNH8, A0A8V8TPE2, A1L443, A2IDD5, A5D7L8, A6NDY2, A6NIJ5, A6NNJ1, A6NNL0, A7E346, A8K0R7, A8MXJ8, A8MXZ1, B1AL46, B1ASB6, C9JSJ3, E9PGG2, O08574, P0C7V4, P0C7W8, P0C7X0, P0CG20, P0DV73, P0DV75, P0DV76, Q0VG99, Q0ZCJ7, Q149B8, Q2M3G4, Q3TQ03, Q3V0C3, Q4KLY2, Q5JXC2, Q5RCJ6, Q5SV97, Q5SW24, Q5VT03, Q5VZR2, Q6ZMY3

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 23 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	5	173.0×	9e-10
mRNA 3’-end processing	7	125.3×	1e-12
RNA Polymerase II Transcription Termination	5	99.8×	1e-08
Transport of Mature mRNA derived from an Intron-Containing Transcript	7	96.9×	4e-12
Processing of Capped Intron-Containing Pre-mRNA	6	44.8×	2e-08
mRNA Splicing - Major Pathway	6	29.8×	2e-07
Metabolism of RNA	6	22.7×	7e-07

GO biological processes:

GO term	Partners	Fold	FDR
mRNA export from nucleus	5	77.8×	4e-07
RNA splicing	5	23.2×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1624 predictions. Top by Δscore:

Variant	Effect	Δscore
15:40336755:CTCA:C	donor_loss	1.0000
15:40336756:TCA:T	donor_loss	1.0000
15:40336757:CA:C	donor_loss	1.0000
15:40336758:A:AT	donor_loss	1.0000
15:40336810:GGAC:G	acceptor_gain	1.0000
15:40336811:GACC:G	acceptor_loss	1.0000
15:40336813:CCT:C	acceptor_loss	1.0000
15:40336815:T:A	acceptor_loss	1.0000
15:40336824:C:CT	acceptor_gain	1.0000
15:40336825:A:T	acceptor_gain	1.0000
15:40337386:ACC:A	donor_gain	1.0000
15:40337387:CCC:C	donor_gain	1.0000
15:40337722:A:AC	donor_gain	1.0000
15:40337723:C:CC	donor_gain	1.0000
15:40337765:AC:A	donor_gain	1.0000
15:40337766:CC:C	donor_gain	1.0000
15:40337892:CC:C	acceptor_gain	1.0000
15:40337893:CC:C	acceptor_gain	1.0000
15:40338747:CCT:C	donor_gain	1.0000
15:40339511:CA:C	donor_gain	1.0000
15:40339900:CTCA:C	donor_loss	1.0000
15:40339902:CA:C	donor_loss	1.0000
15:40340012:TTCC:T	acceptor_gain	1.0000
15:40340014:CC:C	acceptor_gain	1.0000
15:40340015:CC:C	acceptor_gain	1.0000
15:40340806:A:AC	donor_gain	1.0000
15:40340806:ACAG:A	donor_gain	1.0000
15:40340807:C:CC	donor_gain	1.0000
15:40340807:CAG:C	donor_gain	1.0000
15:40340807:CAGC:C	donor_gain	1.0000

AlphaMissense

3180 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:40339939:C:G	R74P	0.995
15:40339942:A:G	L73P	0.994
15:40339921:A:G	L80S	0.993
15:40339931:T:C	N77D	0.992
15:40339940:G:T	R74S	0.992
15:40337825:C:A	W238C	0.991
15:40337825:C:G	W238C	0.991
15:40339951:A:T	I70K	0.991
15:40339929:G:C	N77K	0.990
15:40339929:G:T	N77K	0.990
15:40339932:C:A	K76N	0.990
15:40339932:C:G	K76N	0.990
15:40339911:C:A	R83S	0.989
15:40339911:C:G	R83S	0.989
15:40339615:A:G	I87T	0.988
15:40339951:A:G	I70T	0.988
15:40339963:A:G	L66P	0.987
15:40339912:C:G	R83T	0.986
15:40339925:C:G	A79P	0.986
15:40337827:A:G	W238R	0.984
15:40337827:A:T	W238R	0.984
15:40339930:T:A	N77I	0.984
15:40339942:A:T	L73Q	0.984
15:40339951:A:C	I70R	0.984
15:40339912:C:A	R83M	0.982
15:40339930:T:G	N77T	0.982
15:40339946:C:G	A72P	0.982
15:40339534:A:T	V114D	0.979
15:40339915:C:G	R82P	0.979
15:40339953:C:A	R69S	0.979

dbSNP variants (sampled 300 via entrez): RS1000842084 (15:40342838 G>A,T), RS1000964502 (15:40341530 T>C), RS1000986891 (15:40337513 C>A,G,T), RS1001320870 (15:40333870 G>C), RS1001427366 (15:40331613 G>A), RS1001649533 (15:40331872 C>G,T), RS1002249169 (15:40333371 C>T), RS1002422537 (15:40331902 C>A,T), RS1002642849 (15:40337661 C>T), RS1002832828 (15:40333090 G>A), RS1003309863 (15:40340232 G>T), RS1003423580 (15:40334485 G>A), RS1004196352 (15:40335208 C>G), RS1004359842 (15:40341224 C>T), RS1004481033 (15:40335508 G>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression	3
Benzo(a)pyrene	increases expression	3
Tetrachlorodibenzodioxin	increases expression	3
Cyclosporine	decreases expression, increases expression	3
Tobacco Smoke Pollution	affects expression, decreases expression	2
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
2-butenal	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
dimethylarsinous acid	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Calcitriol	increases expression	1
Cisplatin	increases expression, affects cotreatment	1
Estradiol	affects cotreatment, increases expression	1
Folic Acid	decreases expression	1
Lipopolysaccharides	increases expression, decreases expression, affects response to substance	1
Mustard Gas	increases expression	1
Smoke	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression, increases methylation	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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