CCDC116

Summary

CCDC116 (coiled-coil domain containing 116, HGNC:26688) is a protein-coding gene on chromosome 22q11.21, encoding Coiled-coil domain-containing protein 116 (Q8IYX3).

Located in centrosome. Implicated in lung cancer.

Source: NCBI Gene 164592 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 165 total — 23 pathogenic, 2 likely-pathogenic
• MANE Select transcript: NM_152612

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26688
Approved symbol	CCDC116
Name	coiled-coil domain containing 116
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Aliases	FLJ36046
Ensembl gene	ENSG00000161180
Ensembl biotype	protein_coding
Entrez	164592

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000292779, ENST00000425975, ENST00000607942

RefSeq mRNA: 2 — MANE Select: NM_152612 NM_001331066, NM_152612

CCDS: CCDS13791, CCDS87008

Canonical transcript exons

ENST00000292779 — 5 exons

Exon	Start	End
ENSE00001056711	21634022	21634570
ENSE00001136182	21634685	21635266
ENSE00001136193	21633120	21633253
ENSE00001261060	21636432	21637329
ENSE00001309084	21632760	21632827

Expression profiles

Bgee: expression breadth ubiquitous, 146 present calls, max score 86.81.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3658 / max 65.4073, expressed in 67 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
191191	0.3559	66
191190	0.0100	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	86.81	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.05	gold quality
right testis	UBERON:0004534	85.85	gold quality
testis	UBERON:0000473	83.03	gold quality
sperm	CL:0000019	75.66	silver quality
buccal mucosa cell	CL:0002336	65.94	gold quality
popliteal artery	UBERON:0002250	64.80	gold quality
tibial artery	UBERON:0007610	64.78	gold quality
aorta	UBERON:0000947	64.21	gold quality
left coronary artery	UBERON:0001626	63.96	gold quality
stromal cell of endometrium	CL:0002255	63.76	gold quality
ascending aorta	UBERON:0001496	63.75	gold quality
thoracic aorta	UBERON:0001515	63.75	gold quality
body of uterus	UBERON:0009853	63.17	gold quality
descending thoracic aorta	UBERON:0002345	62.92	gold quality
coronary artery	UBERON:0001621	62.51	gold quality
endocervix	UBERON:0000458	61.93	gold quality
right coronary artery	UBERON:0001625	61.91	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	61.30	gold quality
muscle layer of sigmoid colon	UBERON:0035805	61.12	gold quality
lower esophagus muscularis layer	UBERON:0035833	60.80	gold quality
lower esophagus	UBERON:0013473	60.74	gold quality
left ovary	UBERON:0002119	60.36	gold quality
tibial nerve	UBERON:0001323	60.01	gold quality
mucosa of stomach	UBERON:0001199	59.87	gold quality
ectocervix	UBERON:0012249	59.73	gold quality
right ovary	UBERON:0002118	59.70	gold quality
left uterine tube	UBERON:0001303	59.48	gold quality
omental fat pad	UBERON:0010414	59.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	59.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting CCDC116, 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-4482-3P	99.98	72.50	3147
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-1296-3P	99.72	64.04	636
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-138-2-3P	98.91	68.33	1643
HSA-MIR-3944-5P	98.50	67.55	997
HSA-MIR-653-3P	98.31	67.71	1542
HSA-MIR-10398-5P	97.12	64.94	1051
HSA-MIR-301A-5P	96.88	68.07	931
HSA-MIR-301B-5P	96.88	67.75	946
HSA-MIR-4652-5P	96.46	64.22	553

Literature-anchored findings (GeneRIF, showing 2)

• The CCDC116 protein is expressed in all islet cell types except the glucagon and ghrelin cells. (PMID:23072936)
• Our results suggest that a slight change in CCDC116 expression in normal tissues can confer risk to corresponding cancers. (PMID:28653172)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc116	ENSMUSG00000022768
rattus_norvegicus	Ccdc116	ENSRNOG00000001860

Protein

Protein identifiers

Coiled-coil domain-containing protein 116 — Q8IYX3 (reviewed: Q8IYX3)

All UniProt accessions (2): C9JW89, Q8IYX3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8IYX3-2	2	yes
Q8IYX3-1	1
Q8IYX3-3	3

RefSeq proteins (2): NP_001317995, NP_689825* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031532	DUF4702	Family

Pfam: PF15774

UniProt features (19 total): sequence variant 6, region of interest 4, compositionally biased region 4, splice variant 2, chain 1, modified residue 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IYX3-F1	50.59	0.02

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): 386

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, GOCC_MICROTUBULE_ORGANIZING_CENTER, FREAC3_01, GOCC_CENTROSOME, OCT1_06, YATGNWAAT_OCT_C, MEISSNER_NPC_HCP_WITH_H3K4ME2, OCT_Q6, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_DN, MIR10398_5P, GSE13485_DAY1_VS_DAY7_YF17D_VACCINE_PBMC_UP, GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_DN, GSE14308_TH1_VS_TH17_UP, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_UP

GO Biological Process (0):

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

GO Cellular Component (3): centrosome (GO:0005813), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
centriole	1
microtubule organizing center	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

482 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC116	CFAP184	Q2M329	585
CCDC116	SPMIP4	Q8N865	583
CCDC116	CFAP96	A7E2U8	580
CCDC116	CCDC38	Q502W7	541
CCDC116	EFCAB5	A4FU69	507
CCDC116	C5orf52	A6NGY3	506
CCDC116	SPMIP9	Q96LM6	497
CCDC116	CFAP263	Q9H0I3	487
CCDC116	CCDC146	Q8IYE0	484
CCDC116	PRRG3	Q9BZD7	469
CCDC116	YDJC	A8MPS7	464
CCDC116	OR5K2	Q8NHB8	460
CCDC116	LRRC72	A6NJI9	452
CCDC116	LRRC52	Q8N7C0	450
CCDC116	CFAP97D1	B2RV13	447

IntAct

105 interactions, top by confidence:

A	B	Type	Score
CCDC116	MDFI	psi-mi:“MI:0915”(physical association)	0.780
MDFI	CCDC116	psi-mi:“MI:0915”(physical association)	0.780
CCDC116	TRAF1	psi-mi:“MI:0915”(physical association)	0.720
CCDC116	USHBP1	psi-mi:“MI:0915”(physical association)	0.720
TRAF1	CCDC116	psi-mi:“MI:0915”(physical association)	0.720
USHBP1	CCDC116	psi-mi:“MI:0915”(physical association)	0.720
CCDC116	BEX3	psi-mi:“MI:0915”(physical association)	0.670
MTUS2	CCDC116	psi-mi:“MI:0915”(physical association)	0.670
BEX3	CCDC116	psi-mi:“MI:0915”(physical association)	0.670
CCDC116	MTUS2	psi-mi:“MI:0915”(physical association)	0.670
CCDC116	FAM9B	psi-mi:“MI:0915”(physical association)	0.560
TFIP11	CCDC116	psi-mi:“MI:0915”(physical association)	0.560
FAM9B	CCDC116	psi-mi:“MI:0915”(physical association)	0.560
CCDC116	CARD10	psi-mi:“MI:0915”(physical association)	0.560
CCDC116	COG6	psi-mi:“MI:0915”(physical association)	0.560
CCDC116	HSF2BP	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (46): CCDC116 (Two-hybrid), CCDC116 (Two-hybrid), CCDC116 (Two-hybrid), CCDC116 (Two-hybrid), CCDC116 (Two-hybrid), CCDC116 (Two-hybrid), FAM9B (Two-hybrid), CCDC116 (Two-hybrid), CCDC116 (Two-hybrid), CCDC116 (Two-hybrid), MTUS2 (Two-hybrid), NGFRAP1 (Two-hybrid), TRAF1 (Two-hybrid), CEP44 (Two-hybrid), PAPSS1 (Affinity Capture-MS)

ESM2 similar proteins: A0A096LP49, A0A8V8TNH8, A0A8V8TPE2, A2VE02, A5D7I0, A6NDY2, A6NGG8, A6NIJ5, A6NNJ1, A8MXJ8, A8MYA2, B1ASB6, B2RW88, D6RGX4, O60269, P0C7V4, P0C7W8, P0C7W9, P0C7X0, P0DV75, P0DV76, Q2KIS6, Q2NL68, Q3SY00, Q4R736, Q4V8B5, Q5RCQ2, Q5SZB4, Q5VZ46, Q5XIK6, Q658T7, Q66JV7, Q6NS69, Q6PAC4, Q6ZMY3, Q76N32, Q7TSA6, Q7Z591, Q80VW7, Q80X53

Diamond homologs: Q4V8B5, Q80X53, Q8IYX3, Q95LR6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	23
Likely pathogenic	2
Uncertain significance	110
Likely benign	18
Benign	8

Top pathogenic / likely-pathogenic (25)

Variant ID	HGVS	Classification
146776	GRCh38/hg38 22q11.21-11.22(chr22:21454649-22562620)x3	Pathogenic
146777	GRCh38/hg38 22q11.21-11.22(chr22:21454649-22562620)x1	Pathogenic
147610	GRCh38/hg38 22q11.21-11.22(chr22:21444416-22574173)x1	Pathogenic
148420	GRCh38/hg38 22q11.21-11.22(chr22:21151069-22617194)x1	Pathogenic
150486	GRCh38/hg38 22q11.21-11.22(chr22:21151097-22562620)x1	Pathogenic
151375	GRCh38/hg38 22q11.21-11.22(chr22:21583391-22647760)x3	Pathogenic
153062	GRCh38/hg38 22q11.21-11.22(chr22:21447344-22655838)x1	Pathogenic
155200	GRCh38/hg38 22q11.21-11.22(chr22:21454661-22617194)x1	Pathogenic
1706504	GRCh37/hg19 22q11.21-11.22(chr22:21462566-22962196)x1	Pathogenic
1807776	GRCh37/hg19 22q11.21-11.22(chr22:21465662-22962962)x1	Pathogenic
1808649	GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x3	Pathogenic
253531	GRCh37/hg19 22q11.21-11.22(chr22:21923858-23025727)x3	Pathogenic
2685673	GRCh37/hg19 22q11.21-11.22(chr22:21465662-22997928)x1	Pathogenic
441808	GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962196)x1	Pathogenic
442574	GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x1	Pathogenic
565017	GRCh37/hg19 22q11.21-11.22(chr22:21800470-22962196)x1	Pathogenic
565024	GRCh37/hg19 22q11.21-11.22(chr22:21465661-22962196)x1	Pathogenic
57332	GRCh38/hg38 22q11.21-11.22(chr22:21151069-22562663)x1	Pathogenic
57444	GRCh38/hg38 22q11.21-11.22(chr22:21603122-22562663)x1	Pathogenic
59282	GRCh38/hg38 22q11.21-11.22(chr22:21623411-22617259)x1	Pathogenic
59328	GRCh38/hg38 22q11.21-11.22(chr22:21623411-22651271)x3	Pathogenic
599193	NC_000022.10:g.21808950_22963000del1154051	Pathogenic
830215	NC_000022.10:g.(21822774_21914652)_(22922798_23025613)del	Pathogenic
253360	GRCh37/hg19 22q11.21-11.22(chr22:21923858-22963000)x1	Likely pathogenic
625623	GRCh37/hg19 22q11.21-11.22(chr22:21800032-23237674)	Likely pathogenic

SpliceAI

621 predictions. Top by Δscore:

Variant	Effect	Δscore
22:21634565:G:T	donor_gain	1.0000
22:21634568:GGG:G	donor_gain	1.0000
22:21634569:GGG:G	donor_gain	1.0000
22:21636418:C:CA	acceptor_gain	1.0000
22:21636419:G:A	acceptor_gain	1.0000
22:21636422:T:A	acceptor_gain	1.0000
22:21636427:T:G	acceptor_gain	1.0000
22:21636430:AG:A	acceptor_loss	1.0000
22:21636431:GA:G	acceptor_gain	1.0000
22:21636431:GAGC:G	acceptor_gain	1.0000
22:21636431:GAGCC:G	acceptor_gain	1.0000
22:21632825:CTGG:C	donor_loss	0.9900
22:21632826:TGG:T	donor_loss	0.9900
22:21632827:GGT:G	donor_loss	0.9900
22:21632828:G:C	donor_loss	0.9900
22:21632829:TGAG:T	donor_loss	0.9900
22:21632830:G:GT	donor_loss	0.9900
22:21633118:A:AG	acceptor_gain	0.9900
22:21633119:G:GG	acceptor_gain	0.9900
22:21634565:G:GT	donor_gain	0.9900
22:21636426:A:AG	acceptor_gain	0.9900
22:21636427:T:TA	acceptor_gain	0.9900
22:21636427:TGCAG:T	acceptor_gain	0.9900
22:21636429:CAG:C	acceptor_gain	0.9900
22:21636430:A:AG	acceptor_gain	0.9900
22:21636430:AGA:A	acceptor_gain	0.9900
22:21636431:G:GT	acceptor_gain	0.9900
22:21636431:GAG:G	acceptor_gain	0.9900
22:21632828:G:GG	donor_gain	0.9800
22:21633115:C:G	acceptor_gain	0.9800

AlphaMissense

4013 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:21636598:T:C	L457P	0.974
22:21636652:T:C	L475P	0.974
22:21636585:T:C	F453L	0.971
22:21636587:C:A	F453L	0.971
22:21636587:C:G	F453L	0.971
22:21634175:T:C	F76L	0.965
22:21634177:C:A	F76L	0.965
22:21634177:C:G	F76L	0.965
22:21634226:G:C	A93P	0.963
22:21636589:A:T	E454V	0.960
22:21635021:G:C	A320P	0.959
22:21635069:T:C	F336L	0.957
22:21635071:C:A	F336L	0.957
22:21635071:C:G	F336L	0.957
22:21636578:G:C	K450N	0.957
22:21636578:G:T	K450N	0.957
22:21636590:A:C	E454D	0.957
22:21636590:A:T	E454D	0.957
22:21636643:T:C	L472P	0.955
22:21634157:T:C	F70L	0.954
22:21634159:T:A	F70L	0.954
22:21634159:T:G	F70L	0.954
22:21635013:T:A	V317D	0.952
22:21635001:T:C	L313P	0.951
22:21636643:T:A	L472H	0.950
22:21636624:T:C	F466L	0.945
22:21636626:C:A	F466L	0.945
22:21636626:C:G	F466L	0.945
22:21636668:G:C	K480N	0.945
22:21636668:G:T	K480N	0.945

dbSNP variants (sampled 300 via entrez): RS1000521787 (22:21637225 C>A,T), RS1000611225 (22:21631204 G>A), RS1000993326 (22:21632244 C>T), RS1001329710 (22:21630945 G>A,T), RS1002034996 (22:21637200 C>A), RS1002101081 (22:21635978 G>A,C), RS1002285661 (22:21632329 G>A,C), RS1002482034 (22:21633153 G>A), RS1002532974 (22:21637566 CAGG>C), RS1003128268 (22:21634001 G>A,C), RS1003815855 (22:21633624 C>T), RS1004640317 (22:21635893 C>A,T), RS1004949475 (22:21635678 G>A,C), RS1005697000 (22:21634019 C>G), RS1006107649 (22:21632903 C>G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:611867

GenCC curated gene-disease

Mondo (1): chromosome 22q11.2 deletion syndrome, distal (MONDO:0012740)

Orphanet (1): Distal 22q11.2 microdeletion syndrome (Orphanet:261330)

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001725_108	Inflammatory bowel disease	1.000000e-16
GCST004131_48	Inflammatory bowel disease	4.000000e-15
GCST004132_118	Crohn’s disease	1.000000e-15
GCST004133_48	Ulcerative colitis	9.000000e-06
GCST007827_18	Alzheimer’s disease or HDL levels (pleiotropy)	4.000000e-12
GCST90002407_192	White blood cell count	2.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C567511	Chromosome 22q11.2 Deletion Syndrome, Distal (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation, increases expression	2
sodium arsenite	decreases expression	1
15-acetyldeoxynivalenol	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Phenobarbital	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Thiram	increases expression	1
Valproic Acid	increases methylation	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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