CCDC106

Summary

CCDC106 (coiled-coil domain containing 106, HGNC:30181) is a protein-coding gene on chromosome 19q13.42, encoding Coiled-coil domain-containing protein 106 (Q9BWC9). Promotes the degradation of p53/TP53 protein and inhibits its transactivity.

Located in cytosol and nucleoplasm.

Source: NCBI Gene 29903 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 54 total — 1 likely-pathogenic
• MANE Select transcript: NM_001370470

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30181
Approved symbol	CCDC106
Name	coiled-coil domain containing 106
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Aliases	HSU79303
Ensembl gene	ENSG00000173581
Ensembl biotype	protein_coding
OMIM	613478
Entrez	29903

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 retained_intron

ENST00000308964, ENST00000586790, ENST00000586864, ENST00000587213, ENST00000588740, ENST00000591241, ENST00000591578, ENST00000592996, ENST00000593069, ENST00000895045, ENST00000895047, ENST00000912480, ENST00000912481

RefSeq mRNA: 6 — MANE Select: NM_001370470 NM_001370467, NM_001370468, NM_001370469, NM_001370470, NM_001370471, NM_013301

CCDS: CCDS33118, CCDS92692

Canonical transcript exons

ENST00000586790 — 5 exons

Exon	Start	End
ENSE00001178846	55651283	55651495
ENSE00001178851	55649408	55649584
ENSE00001178873	55652430	55653161
ENSE00002933146	55648212	55649077
ENSE00003790363	55649205	55649309

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 94.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.6307 / max 93.0395, expressed in 1724 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177657	28.1466	1807
177664	7.2231	1674
177662	4.1207	1480
177665	1.5128	776
177663	0.3493	192
177666	0.3073	122
177667	0.1175	40

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
nucleus accumbens	UBERON:0001882	94.17	gold quality
caudate nucleus	UBERON:0001873	93.46	gold quality
putamen	UBERON:0001874	93.45	gold quality
anterior cingulate cortex	UBERON:0009835	93.11	gold quality
right frontal lobe	UBERON:0002810	93.06	gold quality
cingulate cortex	UBERON:0003027	93.02	gold quality
prefrontal cortex	UBERON:0000451	92.26	gold quality
right hemisphere of cerebellum	UBERON:0014890	91.96	gold quality
amygdala	UBERON:0001876	91.86	gold quality
cerebellar hemisphere	UBERON:0002245	91.21	gold quality
cerebellar cortex	UBERON:0002129	91.18	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.74	gold quality
apex of heart	UBERON:0002098	90.72	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.34	gold quality
cerebellum	UBERON:0002037	89.94	gold quality
neocortex	UBERON:0001950	89.22	gold quality
metanephros cortex	UBERON:0010533	89.10	gold quality
frontal cortex	UBERON:0001870	89.07	gold quality
frontal lobe	UBERON:0016525	89.06	gold quality
adenohypophysis	UBERON:0002196	88.97	gold quality
telencephalon	UBERON:0001893	88.83	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	88.69	gold quality
forebrain	UBERON:0001890	88.46	gold quality
brain	UBERON:0000955	88.04	gold quality
central nervous system	UBERON:0001017	88.00	gold quality
pituitary gland	UBERON:0000007	87.92	gold quality
cerebral cortex	UBERON:0000956	87.89	gold quality
Ammon’s horn	UBERON:0001954	87.41	gold quality
left adrenal gland cortex	UBERON:0035825	87.09	gold quality
right adrenal gland cortex	UBERON:0035827	87.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting CCDC106, 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-4775	99.98	75.00	6394
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-4427	99.34	70.33	1854
HSA-MIR-665	97.60	65.64	1781
HSA-MIR-1538	85.86	60.08	75
HSA-MIR-4745-3P	83.50	60.58	126
HSA-MIR-3186-3P	82.87	62.46	32

Literature-anchored findings (GeneRIF, showing 6)

• CCDC106 promotes the degradation of p53 protein and inhibits its transactivity. (PMID:20159018)
• Our studies revealed that CCDC106 is associated with non-small cell lung cancer progression and unfavorable prognosis. CCDC106 enhanced Cyclin A2 and Cyclin B1 expression and promoted A549 and H1299 cell proliferation, which depended on AKT signaling. These results suggest that CCDC106 may be a novel target for lung cancer treatment. (PMID:28460455)
• Study revealed a CK2/CCDC106/p53 signaling axis in the progression of breast and cervical cancers. (PMID:30885251)
• HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer. (PMID:33023834)
• CCDC106 promotes the proliferation and invasion of ovarian cancer cells by suppressing p21 transcription through a p53-independent pathway. (PMID:35484984)
• HPV-CCDC106 integration promotes cervical cancer progression by facilitating the high expression of CCDC106 after HPV E6 splicing. (PMID:35854676)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc106a	ENSDARG00000004211
danio_rerio	ccdc106b	ENSDARG00000058578
mus_musculus	Ccdc106	ENSMUSG00000035228

Protein

Protein identifiers

Coiled-coil domain-containing protein 106 — Q9BWC9 (reviewed: Q9BWC9)

All UniProt accessions (5): Q9BWC9, K7EMI9, K7EMP7, K7ER22, K7ES29

UniProt curated annotations — full annotation on UniProt →

Function. Promotes the degradation of p53/TP53 protein and inhibits its transactivity.

Subunit / interactions. Interacts with p53/TP53.

Subcellular location. Nucleus.

RefSeq proteins (6): NP_001357396, NP_001357397, NP_001357398, NP_001357399, NP_001357400, NP_037433 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031591	CCDC106	Family

Pfam: PF15794

UniProt features (8 total): compositionally biased region 3, chain 1, region of interest 1, coiled-coil region 1, short sequence motif 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BWC9-F1	73.31	0.40

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 (1): 130

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): GCACCTT_MIR18A_MIR18B, RNGTGGGC_UNKNOWN, TGCGCANK_UNKNOWN, TGACCTY_ERR1_Q2, SMID_BREAST_CANCER_LUMINAL_B_UP, MODULE_99, ZIC1_01, CTCAAGA_MIR526B, YGCGYRCGC_UNKNOWN, AGGTGCA_MIR500, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, CGCTGCT_MIR503, BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING, BRCA1_DN.V1_DN, SREBP_Q3

GO Biological Process (0):

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

GO Cellular Component (3): nucleoplasm (GO:0005654), cytosol (GO:0005829), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
nuclear lumen	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

458 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC106	CCDC154	A6NI56	605
CCDC106	CCDC34	Q96HJ3	604
CCDC106	RSPRY1	Q96DX4	595
CCDC106	NUDT13	Q86X67	540
CCDC106	ZC3H15	Q8WU90	539
CCDC106	AKAP13	Q12802	536
CCDC106	SNX15	Q9NRS6	535
CCDC106	NMT2	O60551	516
CCDC106	FIZ1	Q96SL8	513
CCDC106	MRPS34	P82930	507
CCDC106	RCBTB1	Q8NDN9	507
CCDC106	CCDC192	P0DO97	507
CCDC106	TP53	P04637	506
CCDC106	TMEM63C	Q9P1W3	495
CCDC106	RNF150	Q9ULK6	483

IntAct

107 interactions, top by confidence:

A	B	Type	Score
CCDC106	ATF4	psi-mi:“MI:0915”(physical association)	0.870
ATF4	CCDC106	psi-mi:“MI:0915”(physical association)	0.870
FAM9B	CCDC106	psi-mi:“MI:0915”(physical association)	0.780
CCDC106	FAM9B	psi-mi:“MI:0915”(physical association)	0.780
TP53	CCDC106	psi-mi:“MI:0403”(colocalization)	0.610
CCDC106	TP53	psi-mi:“MI:0915”(physical association)	0.610
PSH1	CCDC106	psi-mi:“MI:0915”(physical association)	0.560
CCDC106	PSH1	psi-mi:“MI:0915”(physical association)	0.560
EIF1AD	CCDC106	psi-mi:“MI:0915”(physical association)	0.560
MAGEA11	CCDC106	psi-mi:“MI:0915”(physical association)	0.560
SDCBP	CCDC106	psi-mi:“MI:0915”(physical association)	0.560
NKAPD1	CCDC106	psi-mi:“MI:0915”(physical association)	0.560
KBTBD7	CCDC106	psi-mi:“MI:0915”(physical association)	0.560
NAA10	CCDC106	psi-mi:“MI:0915”(physical association)	0.560
MAGOHB	CCDC106	psi-mi:“MI:0915”(physical association)	0.560
NUTF2	CCDC106	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (78): CCDC106 (Two-hybrid), FAM9B (Two-hybrid), CCDC106 (Affinity Capture-MS), TERF2IP (Affinity Capture-MS), NEFM (Affinity Capture-MS), TERF2 (Affinity Capture-MS), CAMK1 (Affinity Capture-MS), CCDC106 (Affinity Capture-Western), TERF2 (Affinity Capture-MS), TERF2IP (Affinity Capture-MS), CAMK1 (Affinity Capture-MS), CCDC106 (Affinity Capture-MS), NEFM (Affinity Capture-MS), CCDC106 (Two-hybrid), CSNK2B (Affinity Capture-Western)

ESM2 similar proteins: A0JP43, A1YEW9, A2D4U8, A2D5N1, A2D671, A2T6K9, A8T6P4, B8AE37, F6QRE9, G3V9A7, O60238, P48785, P79149, Q0IIJ3, Q0P6D6, Q15170, Q15361, Q15390, Q2KIJ9, Q3T013, Q3ULM0, Q3ZBJ9, Q4V7L5, Q5H9J7, Q5NVG8, Q5PPP3, Q5PR69, Q5RFN3, Q5W0A0, Q66HD8, Q67XL4, Q6K678, Q86X53, Q8BP27, Q8BPM6, Q8C627, Q8N4S0, Q8R5H6, Q91W45, Q921P9

Diamond homologs: Q1LZ89, Q3ULM0, Q9BWC9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 61 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
Response of EIF2AK4 (GCN2) to amino acid deficiency	5	16.3×	3e-03
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	5	14.3×	3e-03
Regulation of expression of SLITs and ROBOs	5	10.2×	9e-03
Major pathway of rRNA processing in the nucleolus and cytosol	5	9.1×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	41
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
145961	GRCh38/hg38 19q13.42-13.43(chr19:55550939-57031576)x1	Likely pathogenic

SpliceAI

1872 predictions. Top by Δscore:

Variant	Effect	Δscore
19:55649078:G:GG	donor_gain	1.0000
19:55649083:GAAGC:G	donor_gain	1.0000
19:55649087:C:G	donor_gain	1.0000
19:55649203:A:AG	acceptor_gain	1.0000
19:55649204:G:GT	acceptor_gain	1.0000
19:55649204:GT:G	acceptor_gain	1.0000
19:55649306:GAGG:G	donor_gain	1.0000
19:55649308:GG:G	donor_gain	1.0000
19:55649308:GGGTG:G	donor_loss	1.0000
19:55649309:GG:G	donor_gain	1.0000
19:55649310:G:C	donor_loss	1.0000
19:55649310:G:GG	donor_gain	1.0000
19:55649311:T:A	donor_loss	1.0000
19:55649397:T:A	acceptor_gain	1.0000
19:55649399:T:TA	acceptor_gain	1.0000
19:55649406:A:AG	acceptor_gain	1.0000
19:55649407:G:GC	acceptor_gain	1.0000
19:55649407:GA:G	acceptor_gain	1.0000
19:55649407:GAGC:G	acceptor_gain	1.0000
19:55649407:GAGCC:G	acceptor_gain	1.0000
19:55649521:G:GT	donor_gain	1.0000
19:55649584:GGTG:G	donor_loss	1.0000
19:55649586:T:A	donor_loss	1.0000
19:55651442:G:T	donor_gain	1.0000
19:55651491:GCGAG:G	donor_gain	1.0000
19:55651494:AGG:A	donor_loss	1.0000
19:55651495:GGTG:G	donor_loss	1.0000
19:55651497:T:G	donor_loss	1.0000
19:55652414:C:CA	acceptor_gain	1.0000
19:55652421:A:AG	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000012144 (19:55653544 A>G,T), RS1000130663 (19:55652137 TGTCGGGGG>T), RS1001037145 (19:55652939 G>A,C), RS1001076803 (19:55645534 G>A), RS1001193099 (19:55651861 A>G), RS1001434632 (19:55647129 T>C,G), RS1001767385 (19:55649732 C>G,T), RS1001869315 (19:55653276 G>A), RS1002350503 (19:55646537 A>G), RS1002423863 (19:55653364 G>A,C,T), RS1002800272 (19:55648318 C>A,T), RS1002809659 (19:55645948 C>T), RS1002842079 (19:55645674 C>T), RS1002903888 (19:55652901 C>G,T), RS1002964688 (19:55652363 T>C)

Disease associations

OMIM: gene MIM:613478 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
bisphenol A	decreases methylation	1
mancozeb	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
abrine	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	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Urethane	decreases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases expression, increases abundance	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	PHASE1/PHASE2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	PHASE1/PHASE2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	EARLY_PHASE1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	EARLY_PHASE1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974	Not specified	ACTIVE_NOT_RECRUITING	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery