CCDC178

Summary

CCDC178 (coiled-coil domain containing 178, HGNC:29588) is a protein-coding gene on chromosome 18q12.1, encoding Coiled-coil domain-containing protein 178 (Q5BJE1). May play a crucial role in head shaping and sperm flagellum formation.

Located in ciliary basal body.

Source: NCBI Gene 374864 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 141 total
• MANE Select transcript: NM_001105528

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29588
Approved symbol	CCDC178
Name	coiled-coil domain containing 178
Location	18q12.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ44050
Ensembl gene	ENSG00000166960
Ensembl biotype	protein_coding
OMIM	621139
Entrez	374864

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000300227, ENST00000383096, ENST00000399177, ENST00000403303, ENST00000406524, ENST00000577268, ENST00000577766, ENST00000579916, ENST00000579947, ENST00000581524, ENST00000581852, ENST00000583550, ENST00000583930

RefSeq mRNA: 5 — MANE Select: NM_001105528 NM_001105528, NM_001308126, NM_001371120, NM_001371121, NM_198995

CCDS: CCDS11906, CCDS42424, CCDS77174

Canonical transcript exons

ENST00000383096 — 23 exons

Exon	Start	End
ENSE00001108200	33215550	33215695
ENSE00001108209	33211896	33212055
ENSE00001141952	33226793	33226855
ENSE00001141975	33267202	33267297
ENSE00001141987	33323491	33323633
ENSE00001198459	33224775	33224936
ENSE00001198470	33266916	33267052
ENSE00001366990	33245245	33245428
ENSE00001368226	33092761	33092910
ENSE00001368996	33370050	33370189
ENSE00001371533	33346211	33346411
ENSE00001373942	33348890	33348975
ENSE00001375105	33389540	33389629
ENSE00001378954	33293159	33293312
ENSE00001382109	33356324	33356346
ENSE00001382818	33397149	33397208
ENSE00001386372	33412031	33412110
ENSE00001389125	32974547	32974681
ENSE00001404301	33439962	33440081
ENSE00001494848	33223106	33223219
ENSE00001494884	33440653	33440721
ENSE00002720405	32937406	32938091
ENSE00003654283	33333174	33333394

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 92.54.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1311 / max 14.5812, expressed in 52 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
171609	0.0856	38
171610	0.0454	19

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	92.54	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.90	gold quality
left testis	UBERON:0004533	82.67	gold quality
right testis	UBERON:0004534	82.51	gold quality
testis	UBERON:0000473	81.62	gold quality
omental fat pad	UBERON:0010414	81.36	gold quality
peritoneum	UBERON:0002358	81.25	gold quality
adipose tissue of abdominal region	UBERON:0007808	81.07	gold quality
adipose tissue	UBERON:0001013	78.38	gold quality
subcutaneous adipose tissue	UBERON:0002190	77.90	gold quality
spleen	UBERON:0002106	76.05	gold quality
left ovary	UBERON:0002119	74.13	gold quality
right ovary	UBERON:0002118	73.59	gold quality
adrenal tissue	UBERON:0018303	70.85	gold quality
parietal pleura	UBERON:0002400	70.42	gold quality
endocervix	UBERON:0000458	70.06	gold quality
ovary	UBERON:0000992	69.66	gold quality
visceral pleura	UBERON:0002401	69.29	gold quality
gall bladder	UBERON:0002110	69.15	gold quality
ectocervix	UBERON:0012249	69.01	gold quality
prostate gland	UBERON:0002367	68.97	gold quality
tibial nerve	UBERON:0001323	68.35	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.10	gold quality
smooth muscle tissue	UBERON:0001135	66.96	gold quality
buccal mucosa cell	CL:0002336	66.88	silver quality
adult mammalian kidney	UBERON:0000082	66.64	gold quality
thoracic mammary gland	UBERON:0005200	66.45	gold quality
metanephros cortex	UBERON:0010533	66.35	gold quality
mammary gland	UBERON:0001911	66.07	gold quality
vagina	UBERON:0000996	64.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-119	yes	31.77
E-ANND-3	yes	4.89
E-MTAB-6678	no	2.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting CCDC178, 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-6873-3P	100.00	71.42	2626
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-582-5P	99.47	70.79	2635
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-12113	99.32	67.54	1072
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-4717-3P	99.06	66.34	1072
HSA-MIR-3164	99.02	68.39	1071

Literature-anchored findings (GeneRIF, showing 2)

• CCDC178 as a novel candidate oncogene involved in anoikis resistance and hepatocellular carcinoma (HCC) metastasis, and raise the possibility that CCDC178 may be a new therapeutic target for HCC. (PMID:28319061)
• Homeobox Protein BarH-like 1 Promotes Gastric Cancer Progression by Activating Coiled-Coil Domain-Containing Protein 178. (PMID:38358459)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc178	ENSMUSG00000024306
rattus_norvegicus	Ccdc178	ENSRNOG00000022156

Protein

Protein identifiers

Coiled-coil domain-containing protein 178 — Q5BJE1 (reviewed: Q5BJE1)

All UniProt accessions (7): Q5BJE1, A0A0A0MS97, F8W7A7, J3KRT5, J3KSU3, J3QKU2, J3QRM8

UniProt curated annotations — full annotation on UniProt →

Function. May play a crucial role in head shaping and sperm flagellum formation.

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

Isoforms (4)

UniProt ID	Names	Canonical?
Q5BJE1-1	1	yes
Q5BJE1-2	2
Q5BJE1-3	3
Q5BJE1-4	4

RefSeq proteins (5): NP_001098998, NP_001295055, NP_001358049, NP_001358050, NP_945346 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038826	CCDC178	Family

UniProt features (16 total): sequence variant 5, coiled-coil region 4, sequence conflict 3, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5BJE1-F1	76.69	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): GOBP_MALE_GAMETE_GENERATION, GOCC_MICROTUBULE_ORGANIZING_CENTER, CATTTCA_MIR203, chr18q12, GTGTTGA_MIR505, GOCC_CENTROSOME, AAAGACA_MIR511, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, ATGTCAC_MIR489, GTCAGGA_MIR378, GTGACTT_MIR224, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, TGGAAA_NFAT_Q4_01, GOCC_CILIUM

GO Biological Process (2): spermatid development (GO:0007286), manchette assembly (GO:1905198)

GO Molecular Function (0):

GO Cellular Component (2): centrosome (GO:0005813), ciliary basal body (GO:0036064)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule organizing center	2
germ cell development	1
spermatid differentiation	1
spermatid development	1
cellular component assembly	1
centriole	1
cilium	1

Protein interactions and networks

STRING

364 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC178	RMP24	Q32NC0	507
CCDC178	CCDC167	Q9P0B6	465
CCDC178	CCDC34	Q96HJ3	453
CCDC178	GAREM1	Q9H706	447
CCDC178	CCDC8	Q9H0W5	447
CCDC178	OR5H1	A6NKK0	447
CCDC178	CCDC106	Q9BWC9	422
CCDC178	OR7E24	Q6IFN5	397
CCDC178	RPRD1A	Q96P16	394
CCDC178	CCDC121	Q6ZUS5	394
CCDC178	RTTN	Q86VV8	390
CCDC178	PHGR1	C9JFL3	374
CCDC178	CCDC69	A6NI79	369
CCDC178	SPDYC	Q5MJ68	366
CCDC178	CCDC88A	Q3V6T2	357

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CCDC178	HNRNPU	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (6): CCDC178 (Proximity Label-MS), CCDC178 (Positive Genetic), HNRNPA2B1 (Cross-Linking-MS (XL-MS)), EEA1 (Cross-Linking-MS (XL-MS)), CHTOP (Cross-Linking-MS (XL-MS)), IGF2BP1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2A2Z9, A6NC57, A8MYB1, A9JSR5, A9ZSY0, D3ZNV2, E9PVB3, O94252, P0A1K3, P0A1K4, P0C221, P0C7W6, Q01649, Q08B20, Q0VBY1, Q10006, Q10221, Q1MTQ0, Q2T9Z6, Q2TA00, Q2YDH9, Q3KPU6, Q5AI71, Q5BJE1, Q5I0J4, Q5PQJ9, Q5T0U0, Q5VUR7, Q66HB6, Q6AXT4, Q6AY08, Q6GM07, Q80X59, Q810N9, Q8BVM7, Q8BVN0, Q8CDV0, Q8IVF6, Q8IWF9, Q8N6Q1

Diamond homologs: Q5BJE1, Q8CDV0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	113
Likely benign	18
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4596 predictions. Top by Δscore:

Variant	Effect	Δscore
18:32974542:CCTA:C	donor_loss	1.0000
18:32974543:CTA:C	donor_loss	1.0000
18:32974544:TACCT:T	donor_loss	1.0000
18:32974545:A:T	donor_loss	1.0000
18:32974546:CC:C	donor_loss	1.0000
18:32974575:T:A	donor_gain	1.0000
18:32974677:CAGAG:C	acceptor_gain	1.0000
18:32974682:C:CC	acceptor_gain	1.0000
18:33215544:ACTT:A	donor_loss	1.0000
18:33215545:CTT:C	donor_loss	1.0000
18:33215545:CTTA:C	donor_gain	1.0000
18:33215546:TTAC:T	donor_loss	1.0000
18:33215547:TACT:T	donor_loss	1.0000
18:33215548:A:AC	donor_gain	1.0000
18:33215549:C:CT	donor_gain	1.0000
18:33215549:CT:C	donor_gain	1.0000
18:33215549:CTT:C	donor_gain	1.0000
18:33215549:CTTT:C	donor_gain	1.0000
18:33215549:CTTTA:C	donor_gain	1.0000
18:33215691:TTACT:T	acceptor_gain	1.0000
18:33215692:TACT:T	acceptor_gain	1.0000
18:33215696:C:CC	acceptor_gain	1.0000
18:33224773:A:AC	donor_gain	1.0000
18:33224774:C:CC	donor_gain	1.0000
18:33224774:CA:C	donor_gain	1.0000
18:33224774:CAA:C	donor_gain	1.0000
18:33224942:A:T	acceptor_gain	1.0000
18:33226855:CCTA:C	acceptor_gain	1.0000
18:33245262:CTT:C	donor_gain	1.0000
18:33245427:TG:T	acceptor_gain	1.0000

AlphaMissense

5826 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:33346327:C:G	R181P	0.978
18:33346319:C:G	A184P	0.977
18:32974671:A:G	L800P	0.969
18:33346339:A:G	L177P	0.955
18:33346351:A:G	L173P	0.951
18:33346240:A:G	L210P	0.948
18:33212018:C:G	A706P	0.943
18:33346215:C:A	Q218H	0.935
18:33346215:C:G	Q218H	0.935
18:33346219:A:T	V217E	0.935
18:33346325:C:G	A182P	0.930
18:33346216:T:G	Q218P	0.928
18:33346310:C:G	A187P	0.928
18:33211920:T:A	R738S	0.925
18:33211920:T:G	R738S	0.925
18:33370143:G:C	S85R	0.925
18:33370143:G:T	S85R	0.925
18:33370145:T:G	S85R	0.925
18:33346361:C:G	A170P	0.924
18:33245354:A:G	L495P	0.922
18:33092871:C:G	A760P	0.921
18:32974680:A:G	L797P	0.919
18:33267030:A:G	L432P	0.919
18:33293169:A:G	L389P	0.918
18:33346223:C:G	A216P	0.918
18:33346256:A:G	W205R	0.915
18:33346256:A:T	W205R	0.915
18:33212004:A:C	F710L	0.912
18:33212004:A:T	F710L	0.912
18:33212006:A:G	F710L	0.912

dbSNP variants (sampled 300 via entrez): RS1000001512 (18:33132567 A>C), RS1000011197 (18:32994974 T>C), RS1000021691 (18:33286817 T>C), RS1000028427 (18:33011716 G>A), RS1000028476 (18:33382290 C>T), RS1000038821 (18:33224743 C>T), RS1000040892 (18:33098591 T>C), RS1000045099 (18:33049014 A>G), RS1000048813 (18:33014262 G>A), RS1000061650 (18:33272655 T>C), RS1000062175 (18:33230981 G>A), RS1000069655 (18:33373705 C>T), RS1000072214 (18:33329886 T>A), RS1000078648 (18:33233859 C>T), RS1000079127 (18:33195941 T>C)

Disease associations

OMIM: gene MIM:621139 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002119_3	Metabolite levels (X-11787)	9.000000e-06
GCST002875_51	Diisocyanate-induced asthma	5.000000e-06
GCST003264_499	Post bronchodilator FEV1/FVC ratio	3.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005276	hydroxy-leucine measurement
EFO:0006995	response to diisocyanate
EFO:0004713	FEV/FVC ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	4
Aflatoxin B1	decreases methylation, increases methylation	2
bisphenol A	affects methylation	1
sodium arsenite	increases expression	1
tobacco tar	decreases reaction, increases expression	1
benzo(e)pyrene	decreases methylation	1
diallyl disulfide	decreases reaction, increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
MT19c compound	decreases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Arsenic	affects methylation	1
Cisplatin	increases expression	1
Copper	decreases expression, affects cotreatment	1
Methapyrilene	decreases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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