CCDC117

Summary

CCDC117 (coiled-coil domain containing 117, HGNC:26599) is a protein-coding gene on chromosome 22q12.1, encoding Coiled-coil domain-containing protein 117 (Q8IWD4). Facilitates DNA repair, cell cycle progression, and cell proliferation through its interaction with CIAO2B.

Involved in positive regulation of DNA repair and positive regulation of cell population proliferation. Located in mitotic spindle.

Source: NCBI Gene 150275 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 77 total — 1 pathogenic
• MANE Select transcript: NM_173510

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26599
Approved symbol	CCDC117
Name	coiled-coil domain containing 117
Location	22q12.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ33814
Ensembl gene	ENSG00000159873
Ensembl biotype	protein_coding
Entrez	150275

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 nonsense_mediated_decay

ENST00000249064, ENST00000421503, ENST00000432510, ENST00000444523, ENST00000448492, ENST00000453543, ENST00000936867, ENST00000936868

RefSeq mRNA: 4 — MANE Select: NM_173510 NM_001284263, NM_001284264, NM_001284265, NM_173510

CCDS: CCDS13846, CCDS63435, CCDS63436

Canonical transcript exons

ENST00000249064 — 5 exons

Exon	Start	End
ENSE00001947975	28786089	28789295
ENSE00003476010	28780948	28781172
ENSE00003657143	28773725	28773778
ENSE00003659098	28783508	28783645
ENSE00003850931	28772695	28773034

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 96.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.5455 / max 698.1642, expressed in 1811 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
191571	23.0483	1811
191572	0.2543	26
191573	0.2429	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	96.91	gold quality
secondary oocyte	CL:0000655	96.66	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	95.63	gold quality
ileal mucosa	UBERON:0000331	94.36	gold quality
oviduct epithelium	UBERON:0004804	94.07	gold quality
oocyte	CL:0000023	93.69	gold quality
tibialis anterior	UBERON:0001385	92.18	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.15	gold quality
colonic epithelium	UBERON:0000397	92.06	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	91.80	gold quality
cartilage tissue	UBERON:0002418	91.78	gold quality
endometrium	UBERON:0001295	89.39	gold quality
adrenal tissue	UBERON:0018303	89.20	gold quality
bone marrow cell	CL:0002092	89.04	gold quality
testis	UBERON:0000473	88.69	gold quality
deltoid	UBERON:0001476	88.66	gold quality
right testis	UBERON:0004534	88.07	gold quality
tonsil	UBERON:0002372	87.25	gold quality
placenta	UBERON:0001987	87.16	gold quality
bone marrow	UBERON:0002371	87.12	gold quality
left testis	UBERON:0004533	87.11	gold quality
liver	UBERON:0002107	86.90	gold quality
upper arm skin	UBERON:0004263	86.72	gold quality
lower lobe of lung	UBERON:0008949	86.51	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.50	gold quality
right lobe of liver	UBERON:0001114	86.48	gold quality
mucosa of sigmoid colon	UBERON:0004993	86.09	gold quality
lymph node	UBERON:0000029	86.07	gold quality
tendon of biceps brachii	UBERON:0008188	86.05	gold quality
cortical plate	UBERON:0005343	85.80	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

169 targeting CCDC117, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc117	ENSDARG00000091872
mus_musculus	Ccdc117	ENSMUSG00000020482
rattus_norvegicus	Ccdc117	ENSRNOG00000010706

Protein

Protein identifiers

Coiled-coil domain-containing protein 117 — Q8IWD4 (reviewed: Q8IWD4)

All UniProt accessions (4): Q8IWD4, B0QYH1, B0QYH3, F8WBN8

UniProt curated annotations — full annotation on UniProt →

Function. Facilitates DNA repair, cell cycle progression, and cell proliferation through its interaction with CIAO2B.

Subunit / interactions. Interacts with CIAO2B; the interaction is direct. Interacts with MMS19; the interaction is indirect.

Subcellular location. Cytoplasm. Cytoskeleton. Spindle. Nucleus.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8IWD4-1	1	yes
Q8IWD4-2	2
Q8IWD4-3	3
Q8IWD4-4	4

RefSeq proteins (4): NP_001271192, NP_001271193, NP_001271194, NP_775781* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031630	CCDC117	Family

Pfam: PF15810

UniProt features (15 total): splice variant 3, compositionally biased region 3, region of interest 2, sequence variant 2, modified residue 2, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IWD4-F1	60.99	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): 48, 53

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 164 (showing top): GGGACCA_MIR133A_MIR133B, TGGTGCT_MIR29A_MIR29B_MIR29C, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_REGULATION_OF_DNA_REPAIR, FOXD3_01, PATIL_LIVER_CANCER, CCTGTGA_MIR513, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_DNA_DAMAGE_RESPONSE, GOBP_POSITIVE_REGULATION_OF_DNA_REPAIR, HFH1_01, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_STRESS, TAATGTG_MIR323

GO Biological Process (2): positive regulation of cell population proliferation (GO:0008284), positive regulation of DNA repair (GO:0045739)

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

GO Cellular Component (5): nucleus (GO:0005634), mitotic spindle (GO:0072686), cytoplasm (GO:0005737), spindle (GO:0005819), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	2
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
DNA repair	1
regulation of DNA repair	1
positive regulation of response to stimulus	1
positive regulation of DNA metabolic process	1
binding	1
intracellular membrane-bounded organelle	1
spindle	1
intracellular anatomical structure	1
cellular anatomical structure	1
microtubule cytoskeleton	1

Protein interactions and networks

STRING

456 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC117	VEPH1	Q14D04	607
CCDC117	MEGF11	A6BM72	596
CCDC117	MSANTD4	Q8NCY6	533
CCDC117	PTAFR	P25105	493
CCDC117	TCEANC2	Q96MN5	450
CCDC117	SLC16A4	O15374	449
CCDC117	CNTNAP5	Q8WYK1	440
CCDC117	MOSPD1	Q9UJG1	438
CCDC117	RBIS	Q8N0T1	436
CCDC117	AP4E1	Q9UPM8	429
CCDC117	EBPL	Q9BY08	414
CCDC117	GGPS1	O95749	410
CCDC117	ARID4B	Q4LE39	406
CCDC117	CHEK2	O96017	404
CCDC117	NCAPH	Q15003	391

IntAct

28 interactions, top by confidence:

A	B	Type	Score
HSP90AB1	HSP90AA1	psi-mi:“MI:0914”(association)	0.840
STIP1	CCDC117	psi-mi:“MI:0914”(association)	0.770
CCDC117	STIP1	psi-mi:“MI:0915”(physical association)	0.770
CCDC117	HSP90AA1	psi-mi:“MI:0914”(association)	0.740
CCDC117	HSP90AA1	psi-mi:“MI:0915”(physical association)	0.740
HSP90AA1	CHUK	psi-mi:“MI:0914”(association)	0.670
HSP90AA1	USP19	psi-mi:“MI:0914”(association)	0.530
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
RAB6B	SBF1	psi-mi:“MI:0914”(association)	0.530
HSPA2	DNAJC13	psi-mi:“MI:0914”(association)	0.530
HSP90AB1	CCDC117	psi-mi:“MI:0915”(physical association)	0.400
CCDC117		psi-mi:“MI:0915”(physical association)	0.400
	CCDC117	psi-mi:“MI:0915”(physical association)	0.400
HSP90AA1	URI1	psi-mi:“MI:0914”(association)	0.350
HSP90AA1	ST13	psi-mi:“MI:0914”(association)	0.350
SLC35B2	HSPA8	psi-mi:“MI:0914”(association)	0.350
STIP1	HSPA8	psi-mi:“MI:0914”(association)	0.350
hspa1a_hspa1b_human-1	SHTN1	psi-mi:“MI:0914”(association)	0.350
BAG1	PSMD11	psi-mi:“MI:0914”(association)	0.350
CCDC117	USP19	psi-mi:“MI:0914”(association)	0.350
CCDC117	OBSL1	psi-mi:“MI:0914”(association)	0.350
HSP90AB1	MGST3	psi-mi:“MI:0914”(association)	0.350
HSP90AB1	EL52	psi-mi:“MI:0914”(association)	0.350
STIP1	EL52	psi-mi:“MI:0914”(association)	0.350

BioGRID (60): HSPA8 (Affinity Capture-MS), HSPA1L (Affinity Capture-MS), STIP1 (Affinity Capture-MS), HSP90AB1 (Affinity Capture-MS), HSP90AA4P (Affinity Capture-MS), HSPA4 (Affinity Capture-MS), OBSL1 (Affinity Capture-MS), STIP1 (Affinity Capture-MS), HSP90AA4P (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), HSPBP1 (Affinity Capture-MS), CCDC117 (Affinity Capture-MS), BAG1 (Affinity Capture-MS), HSP90AA1 (Affinity Capture-MS), CCDC117 (Proximity Label-MS)

ESM2 similar proteins: A0PJS5, A3KNX5, A8K830, F8VPY8, O54968, P01102, P01105, P12979, P15173, P28322, P41161, P41164, P43268, P49812, P50549, P53450, Q14140, Q16633, Q29RM2, Q2KIC2, Q2KJA4, Q4G112, Q56TN0, Q56TT7, Q5M7N6, Q5M9G5, Q5R815, Q5ZKN5, Q60795, Q64693, Q66IT9, Q6NYT3, Q6PB51, Q6PBC9, Q7YR76, Q7YS81, Q80V38, Q80VF6, Q8BGR5, Q8BXQ8

Diamond homologs: Q5M9G5, Q6PB51, Q8IWD4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 22 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
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand	5	50.9×	7e-06
Regulation of HSF1-mediated heat shock response	5	36.6×	1e-05

GO biological processes:

GO term	Partners	Fold	FDR
protein folding	6	31.0×	5e-06
protein stabilization	6	20.1×	3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	57
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
979602	GRCh37/hg19 22q12.1-12.2(chr22:28291202-30450920)x1	Pathogenic

SpliceAI

780 predictions. Top by Δscore:

Variant	Effect	Δscore
22:28773724:GT:G	acceptor_gain	1.0000
22:28773771:GATGA:G	donor_gain	1.0000
22:28773774:GATGA:G	donor_gain	1.0000
22:28773775:A:G	donor_gain	1.0000
22:28773775:ATGA:A	donor_gain	1.0000
22:28773776:TGA:T	donor_gain	1.0000
22:28773777:GA:G	donor_gain	1.0000
22:28773777:GAG:G	donor_gain	1.0000
22:28773778:AGT:A	donor_loss	1.0000
22:28773779:G:GG	donor_gain	1.0000
22:28773779:GT:G	donor_loss	1.0000
22:28773780:TAA:T	donor_loss	1.0000
22:28780946:A:AG	acceptor_gain	1.0000
22:28780947:G:GA	acceptor_gain	1.0000
22:28780947:GT:G	acceptor_gain	1.0000
22:28780947:GTT:G	acceptor_gain	1.0000
22:28781149:G:GT	donor_gain	1.0000
22:28781172:GGTAA:G	donor_loss	1.0000
22:28781173:G:GA	donor_loss	1.0000
22:28781174:T:G	donor_loss	1.0000
22:28783491:T:A	acceptor_gain	1.0000
22:28783497:A:AG	acceptor_gain	1.0000
22:28783497:AATT:A	acceptor_gain	1.0000
22:28783506:A:AG	acceptor_gain	1.0000
22:28783506:AG:A	acceptor_gain	1.0000
22:28783507:G:GG	acceptor_gain	1.0000
22:28783507:GG:G	acceptor_gain	1.0000
22:28783507:GGATA:G	acceptor_gain	1.0000
22:28783646:G:GG	donor_gain	1.0000
22:28773016:G:GT	donor_gain	0.9900

AlphaMissense

1844 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:28786109:T:C	L208P	0.999
22:28786117:T:A	W211R	0.999
22:28786117:T:C	W211R	0.999
22:28786119:G:C	W211C	0.999
22:28786119:G:T	W211C	0.999
22:28781154:T:C	L149P	0.997
22:28786109:T:A	L208H	0.997
22:28786112:T:A	V209D	0.997
22:28783567:T:C	L175P	0.996
22:28786118:G:C	W211S	0.996
22:28781163:T:G	I152S	0.995
22:28783510:T:C	I156T	0.995
22:28783567:T:A	L175H	0.995
22:28783641:T:C	S200P	0.995
22:28786115:T:C	L210P	0.994
22:28781154:T:A	L149H	0.992
22:28783510:T:A	I156K	0.992
22:28783570:T:A	V176D	0.992
22:28783597:T:C	L185S	0.992
22:28786109:T:G	L208R	0.992
22:28786104:G:A	M206I	0.991
22:28786104:G:C	M206I	0.991
22:28786104:G:T	M206I	0.991
22:28783567:T:G	L175R	0.990
22:28783573:T:C	L177P	0.990
22:28783576:C:T	S178F	0.990
22:28786115:T:A	L210H	0.989
22:28786117:T:G	W211G	0.989
22:28781163:T:A	I152N	0.988
22:28786107:G:C	E207D	0.988

dbSNP variants (sampled 300 via entrez): RS1000013517 (22:28772123 C>T), RS1000081161 (22:28776796 C>A), RS1000105391 (22:28773398 A>C,G,T), RS1000132976 (22:28773606 C>A,T), RS1000145420 (22:28777654 C>G), RS1000335118 (22:28778457 A>G), RS1000643713 (22:28785937 AAAAAG>A), RS1000702101 (22:28789441 A>G), RS1000729853 (22:28789708 A>G), RS1000779695 (22:28785659 A>G), RS1001192892 (22:28783272 C>G,T), RS1001422757 (22:28781736 C>T), RS1001624132 (22:28770841 C>A,T), RS1001628406 (22:28781252 A>G), RS1002053872 (22:28770974 G>A,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

4 associations (top):

Study	Trait	p-value
GCST002553_2	Pancreatic cancer	1.000000e-08
GCST002568_9	Esophageal squamous cell carcinoma	4.000000e-07
GCST003985_20	Breast size	7.000000e-07
GCST010083_280	Hemoglobin levels	3.000000e-19

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004509	hemoglobin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, decreases methylation	2
Tobacco Smoke Pollution	increases expression	2
Cadmium Chloride	decreases expression, increases expression, increases methylation	2
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
arsenite	affects binding, decreases reaction	1
butyraldehyde	decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
jinfukang	decreases 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
Resveratrol	affects cotreatment, increases expression	1
Caffeine	affects phosphorylation	1
Cisplatin	increases expression	1
Coumestrol	affects cotreatment, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ethyl Methanesulfonate	increases expression	1
Gallic Acid	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Smoke	decreases expression	1
Testosterone	decreases expression	1
Dronabinol	increases expression	1
Valproic Acid	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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