CCDC112

Summary

CCDC112 (coiled-coil domain containing 112, HGNC:28599) is a protein-coding gene on chromosome 5q22.3, encoding Coiled-coil domain-containing protein 112 (Q8NEF3).

Located in centriolar satellite.

Source: NCBI Gene 153733 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_001040440

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28599
Approved symbol	CCDC112
Name	coiled-coil domain containing 112
Location	5q22.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC39633
Ensembl gene	ENSG00000164221
Ensembl biotype	protein_coding
Entrez	153733

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000379611, ENST00000395557, ENST00000502975, ENST00000503027, ENST00000506442, ENST00000512261, ENST00000513730, ENST00000881296, ENST00000881297, ENST00000881298, ENST00000918123, ENST00000944213

RefSeq mRNA: 6 — MANE Select: NM_001040440 NM_001040440, NM_001375896, NM_001375897, NM_001375898, NM_001375899, NM_152549

CCDS: CCDS34213, CCDS4117, CCDS93761

Canonical transcript exons

ENST00000379611 — 10 exons

Exon	Start	End
ENSE00001082580	115268882	115269000
ENSE00001082586	115269703	115269798
ENSE00001082602	115271213	115271626
ENSE00001082604	115275216	115275606
ENSE00001522103	115267190	115267918
ENSE00002026823	115296427	115296654
ENSE00003477105	115279647	115279768
ENSE00003517999	115276965	115277054
ENSE00003566027	115275994	115276069
ENSE00003694314	115284787	115284908

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 96.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.8323 / max 147.4148, expressed in 1628 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63004	7.5755	1624
63003	0.1461	37
63002	0.0380	3
62998	0.0231	4
62999	0.0203	5
63000	0.0160	6
63001	0.0132	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	96.98	gold quality
ganglionic eminence	UBERON:0004023	95.32	gold quality
ventricular zone	UBERON:0003053	91.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.54	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.70	gold quality
monocyte	CL:0000576	88.01	gold quality
calcaneal tendon	UBERON:0003701	87.46	gold quality
leukocyte	CL:0000738	87.40	gold quality
body of pancreas	UBERON:0001150	86.99	gold quality
right testis	UBERON:0004534	85.55	gold quality
left testis	UBERON:0004533	85.52	gold quality
testis	UBERON:0000473	84.99	gold quality
sperm	CL:0000019	84.51	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	83.51	gold quality
pancreas	UBERON:0001264	83.08	gold quality
mucosa of transverse colon	UBERON:0004991	82.90	gold quality
sural nerve	UBERON:0015488	82.88	gold quality
rectum	UBERON:0001052	82.58	gold quality
epithelial cell of pancreas	CL:0000083	82.04	silver quality
spinal cord	UBERON:0002240	81.84	gold quality
transverse colon	UBERON:0001157	80.61	gold quality
corpus callosum	UBERON:0002336	80.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	79.64	gold quality
popliteal artery	UBERON:0002250	79.59	gold quality
tibial artery	UBERON:0007610	79.57	gold quality
cerebellar cortex	UBERON:0002129	79.28	gold quality
cerebellar hemisphere	UBERON:0002245	79.21	gold quality
right coronary artery	UBERON:0001625	79.05	gold quality
descending thoracic aorta	UBERON:0002345	78.97	gold quality
smooth muscle tissue	UBERON:0001135	78.80	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.70
E-CURD-114	yes	6.97
E-MTAB-6379	no	251.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

42 targeting CCDC112, 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-1252-5P	100.00	69.80	2774
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-2053	99.57	69.15	1635
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-7849-3P	99.47	68.17	1224
HSA-MIR-6165	99.44	67.12	1389
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-513B-3P	98.76	68.12	1577
HSA-MIR-16-1-3P	98.70	69.23	1538
HSA-MIR-4731-3P	98.56	68.60	1860
HSA-MIR-4712-3P	98.52	65.39	822

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc112	ENSMUSG00000071855
rattus_norvegicus	Ccdc112	ENSRNOG00000003559

Paralogs (1): CCDC148 (ENSG00000153237)

Protein

Protein identifiers

Coiled-coil domain-containing protein 112 — Q8NEF3 (reviewed: Q8NEF3)

Alternative names: Mutated in bladder cancer protein 1

All UniProt accessions (2): D6RF76, Q8NEF3

UniProt curated annotations — full annotation on UniProt →

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NEF3-1	1	yes
Q8NEF3-2	2

RefSeq proteins (6): NP_001035530, NP_001362825, NP_001362826, NP_001362827, NP_001362828, NP_689762 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039902	CCDC148/CCDC112	Family

UniProt features (11 total): sequence variant 4, region of interest 2, coiled-coil region 2, chain 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NEF3-F1	82.18	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

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

GO Cellular Component (3): centriolar satellite (GO:0034451), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
centrosome	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

540 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC112	ESYT1	Q9BSJ8	765
CCDC112	TEX29	Q8N6K0	669
CCDC112	TEX9	Q8N6V9	584
CCDC112	MCOLN3	Q8TDD5	505
CCDC112	CCDC14	Q49A88	446
CCDC112	NEXMIF	Q5QGS0	438
CCDC112	KIAA0753	Q2KHM9	430
CCDC112	CCDC13	Q8IYE1	393
CCDC112	ODF2L	Q9ULJ1	389
CCDC112	GRIK4	Q16099	375
CCDC112	CEP131	Q9UPN4	371
CCDC112	IQCF3	P0C7M6	370
CCDC112	C3orf62	Q6ZUJ4	369
CCDC112	CCDC183	Q5T5S1	349
CCDC112	ST8SIA4	Q92187	345

IntAct

33 interactions, top by confidence:

A	B	Type	Score
TEX9	CCDC112	psi-mi:“MI:0915”(physical association)	0.630
CCDC112	TEX9	psi-mi:“MI:0915”(physical association)	0.630
FSD2	CCDC112	psi-mi:“MI:0915”(physical association)	0.560
CCDC112	TNIP1	psi-mi:“MI:0915”(physical association)	0.560
CCDC112	KRT31	psi-mi:“MI:0915”(physical association)	0.560
KRT40	CCDC112	psi-mi:“MI:0915”(physical association)	0.560
CCDC112	FSD2	psi-mi:“MI:0915”(physical association)	0.560
TNIP1	CCDC112	psi-mi:“MI:0915”(physical association)	0.560
KRT31	CCDC112	psi-mi:“MI:0915”(physical association)	0.560
CCDC112	LURAP1	psi-mi:“MI:0915”(physical association)	0.550
TRIM44	ODAD3	psi-mi:“MI:0914”(association)	0.530
LTBR	ZNF724	psi-mi:“MI:0914”(association)	0.530
TNFRSF8	DAPK3	psi-mi:“MI:0914”(association)	0.530
TEX9	NOL4	psi-mi:“MI:0914”(association)	0.530
CCDC112	TPM1	psi-mi:“MI:0915”(physical association)	0.400
CCDC112	HSP90B1	psi-mi:“MI:0915”(physical association)	0.400
CCDC112	SPTAN1	psi-mi:“MI:0915”(physical association)	0.400
CCDC85B	CCDC112	psi-mi:“MI:0915”(physical association)	0.370
TANK	CNOT1	psi-mi:“MI:0914”(association)	0.350
LURAP1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
ING5	CCDC85C	psi-mi:“MI:0914”(association)	0.350
KCNA4	POLRMT	psi-mi:“MI:0914”(association)	0.350
TNFRSF1B	MAP3K7	psi-mi:“MI:0914”(association)	0.350
CEP128	CCDC66	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (43): CCDC112 (Two-hybrid), CCDC112 (Two-hybrid), CCDC112 (Two-hybrid), CCDC112 (Two-hybrid), CCDC112 (Affinity Capture-MS), CCDC112 (Affinity Capture-MS), CCDC112 (Two-hybrid), TEX9 (Two-hybrid), LURAP1 (Two-hybrid), CCDC112 (Synthetic Lethality), CCDC112 (Proximity Label-MS), CCDC112 (Proximity Label-MS), CCDC112 (Proximity Label-MS), CCDC112 (Affinity Capture-MS), CCDC112 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IFG5, A0A480NP79, A0A974E306, A0AUP1, A0AUT1, A0JLY1, A4IJ21, A7S8T5, A8I9E8, D6REC4, E1BJL9, F1N7G5, O88346, P02641, Q0VC09, Q0VFZ6, Q1RM03, Q2KIQ2, Q2TA16, Q32KY1, Q32LJ7, Q32LN4, Q3TVW5, Q3USS3, Q4R698, Q4R7T8, Q4R8R3, Q5RE49, Q61884, Q6AXN9, Q6AXQ8, Q6AYL4, Q6PBA8, Q7T0Y4, Q7TNB2, Q7Z4T9, Q8BRC6, Q8N443, Q8NEF3, Q8NEH6

Diamond homologs: A0AUP1, Q4R8R3, Q8NEF3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	4
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

1374 predictions. Top by Δscore:

Variant	Effect	Δscore
5:115268876:TCTTA:T	donor_loss	1.0000
5:115268877:CTTA:C	donor_loss	1.0000
5:115268878:TTACC:T	donor_loss	1.0000
5:115268879:TA:T	donor_loss	1.0000
5:115268880:A:AC	donor_gain	1.0000
5:115268880:A:AT	donor_loss	1.0000
5:115268881:C:CC	donor_gain	1.0000
5:115268996:TCAAC:T	acceptor_gain	1.0000
5:115268997:CAAC:C	acceptor_gain	1.0000
5:115268997:CAACC:C	acceptor_gain	1.0000
5:115268998:AAC:A	acceptor_gain	1.0000
5:115268998:AACC:A	acceptor_loss	1.0000
5:115268999:ACC:A	acceptor_loss	1.0000
5:115269000:CCTG:C	acceptor_loss	1.0000
5:115269001:C:CC	acceptor_gain	1.0000
5:115269002:T:A	acceptor_loss	1.0000
5:115269008:C:CT	acceptor_gain	1.0000
5:115269009:A:T	acceptor_gain	1.0000
5:115275992:A:AC	donor_gain	1.0000
5:115275993:C:CC	donor_gain	1.0000
5:115276065:AACAA:A	acceptor_gain	1.0000
5:115276066:ACAA:A	acceptor_gain	1.0000
5:115276067:CAA:C	acceptor_gain	1.0000
5:115276067:CAAC:C	acceptor_gain	1.0000
5:115276068:AA:A	acceptor_gain	1.0000
5:115276070:C:CC	acceptor_gain	1.0000
5:115276070:CT:C	acceptor_loss	1.0000
5:115276071:T:A	acceptor_loss	1.0000
5:115276959:A:AC	donor_gain	1.0000
5:115276959:ACTT:A	donor_loss	1.0000

AlphaMissense

3547 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:115267905:A:G	W438R	0.994
5:115267905:A:T	W438R	0.994
5:115276057:A:G	L72P	0.986
5:115267903:C:A	W438C	0.985
5:115267903:C:G	W438C	0.985
5:115276011:T:A	K87N	0.985
5:115276011:T:G	K87N	0.985
5:115277003:A:G	L55P	0.985
5:115276028:C:G	A82P	0.981
5:115275595:A:G	L97P	0.979
5:115267918:C:A	R433S	0.971
5:115267918:C:G	R433S	0.971
5:115275360:A:C	F175L	0.970
5:115275360:A:T	F175L	0.970
5:115275362:A:G	F175L	0.970
5:115275257:A:G	W210R	0.969
5:115275257:A:T	W210R	0.969
5:115268936:C:G	R415P	0.968
5:115268968:C:A	R404S	0.965
5:115268968:C:G	R404S	0.965
5:115271222:A:C	F358L	0.965
5:115271222:A:T	F358L	0.965
5:115271224:A:G	F358L	0.965
5:115267900:T:A	R439S	0.961
5:115267900:T:G	R439S	0.961
5:115269785:A:G	L366P	0.960
5:115276066:A:T	V69D	0.960
5:115268946:A:G	W412R	0.959
5:115268946:A:T	W412R	0.959
5:115275386:A:G	W167R	0.958

dbSNP variants (sampled 300 via entrez): RS1000096384 (5:115293146 G>A), RS1000297120 (5:115282767 T>C), RS1000351090 (5:115294287 T>C), RS1000376464 (5:115294456 A>T), RS1000528379 (5:115277711 A>T), RS1000596809 (5:115288737 C>A), RS1000619775 (5:115278325 A>G), RS1000712016 (5:115286033 T>C,G), RS1000763453 (5:115285681 T>A,C), RS1001154831 (5:115272560 G>A), RS1001212301 (5:115277464 A>G), RS1001252074 (5:115295288 T>G), RS1001708059 (5:115289722 T>C), RS1001750079 (5:115295665 A>G), RS1001785016 (5:115282678 TG>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

1 associations (top):

Study	Trait	p-value
GCST012099_4	Hypertrophic cardiomyopathy (sarcomere negative)	2.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, decreases expression, decreases methylation	2
aristolochic acid I	decreases expression	1
deoxynivalenol	increases expression	1
terbufos	decreases methylation	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	increases expression	1
potassium chromate(VI)	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Cisplatin	decreases expression, affects cotreatment	1
Clorgyline	increases expression	1
Cytarabine	increases expression	1
Fonofos	decreases methylation	1
Lipopolysaccharides	increases expression, decreases expression, affects response to substance	1
Naled	affects expression	1
Parathion	decreases methylation	1
Phthalic Acids	increases methylation	1
Plant Oils	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Vanadates	decreases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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