CCDC180

Summary

CCDC180 (coiled-coil domain containing 180, HGNC:29303) is a protein-coding gene on chromosome 9q22.33, encoding Coiled-coil domain-containing protein 180 (Q9P1Z9).

The protein encoded by this gene contains a coiled-coil domain. Alternative splicing results in multiple transcript variants encoding different isoforms. A single nucleotide polymorphism (SNP) in this gene has been associated with increased susceptibility to Behcet’s Disease (PMID: 19442274).

Source: NCBI Gene 100499483 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 274 total
• MANE Select transcript: NM_020893

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29303
Approved symbol	CCDC180
Name	coiled-coil domain containing 180
Location	9q22.33
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434I2420, BDAG1, FAP76, CFAP76
Ensembl gene	ENSG00000197816
Ensembl biotype	protein_coding
OMIM	621141
Entrez	100499483

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 6 protein_coding_CDS_not_defined, 6 retained_intron, 3 protein_coding

ENST00000460482, ENST00000471314, ENST00000472746, ENST00000483504, ENST00000487976, ENST00000494917, ENST00000526038, ENST00000527182, ENST00000528678, ENST00000529487, ENST00000530011, ENST00000530551, ENST00000534189, ENST00000867263, ENST00000960338

RefSeq mRNA: 2 — MANE Select: NM_020893 NM_001348010, NM_020893

CCDS: CCDS35077

Canonical transcript exons

ENST00000529487 — 37 exons

Exon	Start	End
ENSE00001903814	97307659	97307806
ENSE00003464124	97376763	97378751
ENSE00003465367	97325019	97325192
ENSE00003466530	97317065	97317228
ENSE00003469658	97371595	97371706
ENSE00003493137	97362196	97362441
ENSE00003506624	97361726	97361898
ENSE00003514467	97354569	97354713
ENSE00003532477	97314393	97314521
ENSE00003532693	97322833	97322921
ENSE00003552252	97359982	97360101
ENSE00003565102	97326554	97326669
ENSE00003565391	97318463	97318582
ENSE00003565556	97323781	97323903
ENSE00003569386	97343340	97343563
ENSE00003572382	97309414	97309604
ENSE00003589607	97354892	97355008
ENSE00003593133	97328020	97328146
ENSE00003600927	97364051	97364128
ENSE00003616867	97369922	97370082
ENSE00003619782	97370641	97370778
ENSE00003622838	97347314	97347489
ENSE00003625214	97366559	97366700
ENSE00003632427	97320126	97320205
ENSE00003632557	97314618	97314728
ENSE00003639033	97375454	97375589
ENSE00003641120	97330154	97330193
ENSE00003642689	97314851	97314946
ENSE00003645573	97349111	97349291
ENSE00003650084	97330322	97330767
ENSE00003651535	97357627	97357725
ENSE00003658667	97350409	97350555
ENSE00003672901	97365673	97365739
ENSE00003676351	97313236	97313345
ENSE00003686731	97312113	97312201
ENSE00003693726	97374543	97374648
ENSE00003898006	97307983	97308132

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 96.94.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2626 / max 100.5920, expressed in 76 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
97545	0.1237	49
97546	0.0671	33
97547	0.0505	3
97549	0.0123	5
97548	0.0090	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	96.94	gold quality
sural nerve	UBERON:0015488	94.11	gold quality
left testis	UBERON:0004533	91.35	gold quality
right testis	UBERON:0004534	90.88	gold quality
testis	UBERON:0000473	90.34	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.65	gold quality
cerebellar cortex	UBERON:0002129	86.97	gold quality
cerebellar hemisphere	UBERON:0002245	86.97	gold quality
cerebellum	UBERON:0002037	86.89	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.94	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.35	gold quality
primary visual cortex	UBERON:0002436	82.32	gold quality
fallopian tube	UBERON:0003889	82.22	gold quality
superior frontal gyrus	UBERON:0002661	82.14	gold quality
corpus callosum	UBERON:0002336	81.05	gold quality
right frontal lobe	UBERON:0002810	80.79	gold quality
right lobe of thyroid gland	UBERON:0001119	80.68	gold quality
hypothalamus	UBERON:0001898	80.61	gold quality
endometrium	UBERON:0001295	80.53	gold quality
Ammon’s horn	UBERON:0001954	80.10	gold quality
caudate nucleus	UBERON:0001873	80.07	gold quality
left ovary	UBERON:0002119	79.99	gold quality
cortex of kidney	UBERON:0001225	79.98	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	79.89	gold quality
thyroid gland	UBERON:0002046	79.74	gold quality
ovary	UBERON:0000992	79.58	gold quality
left lobe of thyroid gland	UBERON:0001120	79.41	gold quality
brain	UBERON:0000955	79.36	gold quality
right ovary	UBERON:0002118	79.29	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting CCDC180, 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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-548Q	98.71	65.35	563
HSA-MIR-6757-5P	98.08	65.50	724
HSA-MIR-4778-5P	97.96	68.06	1634
HSA-MIR-4736	97.96	65.89	1287
HSA-MIR-219B-5P	97.91	65.80	531
HSA-MIR-5581-5P	97.91	66.50	965
HSA-MIR-4294	97.86	65.72	1110

Literature-anchored findings (GeneRIF, showing 1)

• High CCDC180 expression is associated with Liposarcoma . (PMID:30790560)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc180	ENSMUSG00000035539
rattus_norvegicus	Ccdc180	ENSRNOG00000010412

Paralogs (1): STRA6 (ENSG00000137868)

Protein

Protein identifiers

Coiled-coil domain-containing protein 180 — Q9P1Z9 (reviewed: Q9P1Z9)

All UniProt accessions (1): A0A6E1Y6F7

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q9P1Z9-2	2	yes
Q9P1Z9-3	3

RefSeq proteins (1): NP_065944* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027914	DUF4456	Domain
IPR028089	DUF4455	Domain

Pfam: PF14643, PF14644

UniProt features (27 total): sequence variant 8, compositionally biased region 6, sequence conflict 5, region of interest 4, coiled-coil region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P1Z9-F1	69.84	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (showing top): chr9q22, DOUGLAS_BMI1_TARGETS_UP, WHITFIELD_CELL_CYCLE_G1_S, TOP2B_TARGET_GENES, ZFP82_TARGET_GENES, ZNF8_TARGET_GENES, MIR153_5P, MIR4728_5P, MIR6785_5P, MIR149_3P, MIR6883_5P, MIR4652_3P, MIR4778_5P, MIR6759_3P, GSE13306_TREG_VS_TCONV_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
extracellular vesicle	1

Protein interactions and networks

STRING

631 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC180	TDRD7	Q8NHU6	916
CCDC180	CDK17	Q00537	829
CCDC180	CFAP92	Q9ULG3	667
CCDC180	SPATA17	Q96L03	632
CCDC180	CPVL	Q9H3G5	604
CCDC180	CABLES1	Q8TDN4	589
CCDC180	UBAC2	Q8NBM4	584
CCDC180	CDK18	Q07002	549
CCDC180	UBASH3B	Q8TF42	542
CCDC180	BLOC1S5	Q8TDH9	453
CCDC180	DLEC1	Q9Y238	447
CCDC180	SPAG17	Q6Q759	447
CCDC180	SPAG6	O75602	447
CCDC180	CFAP99	D6REC4	447
CCDC180	A0A087WYV9	A0A087WYV9	447

IntAct

23 interactions, top by confidence:

A	B	Type	Score
YBX1	HNRNPR	psi-mi:“MI:0915”(physical association)	0.770
CCDC180	MYH9	psi-mi:“MI:0915”(physical association)	0.400
BCL10	CCDC180	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	BUB1	psi-mi:“MI:0915”(physical association)	0.370
CDKN2A	CCDC180	psi-mi:“MI:0915”(physical association)	0.370
CTNNA1	CCDC180	psi-mi:“MI:0915”(physical association)	0.370
DLC1	CCDC180	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	ERBB2	psi-mi:“MI:0915”(physical association)	0.370
FLCN	CCDC180	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	MCC	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	MLH1	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	MLH3	psi-mi:“MI:0915”(physical association)	0.370
MSH2	CCDC180	psi-mi:“MI:0915”(physical association)	0.370
NRAS	CCDC180	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	PDGFRL	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	PMS2	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	PTEN	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	PTPN12	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	RB1	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	SMAD4	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	SRC	psi-mi:“MI:0915”(physical association)	0.370
CCDC180	STK11	psi-mi:“MI:0915”(physical association)	0.370

ESM2 similar proteins: A2AJB1, A5D8V7, A6QQM8, A7MBH5, A7S8T5, A8E4X8, B0BMJ2, B1H228, D3Z5T1, D6REC4, O60826, P86182, Q1RMI8, Q2M329, Q32KY1, Q32LK9, Q3UX62, Q494V2, Q4R8V8, Q4V8F7, Q4V909, Q571B6, Q5JU67, Q5SPX1, Q5SV66, Q5T5N4, Q5T5S1, Q5XI03, Q5XI65, Q62036, Q6NTM6, Q6NVC9, Q7T0Y4, Q80VN0, Q8BSN3, Q8BVV7, Q8CDV6, Q8N9B5, Q8NA47, Q8TF30

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 23 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.

GO biological processes:

GO term	Partners	Fold	FDR
in utero embryonic development	5	16.4×	7e-04
negative regulation of cell population proliferation	5	9.6×	5e-03
intracellular signal transduction	5	8.7×	6e-03
spermatogenesis	5	8.0×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	236
Likely benign	32
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

6047 predictions. Top by Δscore:

Variant	Effect	Δscore
9:97309395:T:A	acceptor_gain	1.0000
9:97309405:T:TA	acceptor_gain	1.0000
9:97309406:G:A	acceptor_gain	1.0000
9:97309601:ACAG:A	donor_gain	1.0000
9:97309602:CAG:C	donor_gain	1.0000
9:97309603:AG:A	donor_gain	1.0000
9:97309603:AGG:A	donor_loss	1.0000
9:97309604:GG:G	donor_gain	1.0000
9:97309605:G:GG	donor_gain	1.0000
9:97313231:CGCA:C	acceptor_loss	1.0000
9:97313233:CA:C	acceptor_loss	1.0000
9:97313234:A:AG	acceptor_gain	1.0000
9:97313235:G:GT	acceptor_gain	1.0000
9:97313235:GTTC:G	acceptor_gain	1.0000
9:97313235:GTTCC:G	acceptor_gain	1.0000
9:97313322:G:GT	donor_gain	1.0000
9:97313347:T:A	donor_loss	1.0000
9:97314522:G:GG	donor_gain	1.0000
9:97314612:GCGTA:G	acceptor_loss	1.0000
9:97314613:C:CA	acceptor_gain	1.0000
9:97314613:CGTA:C	acceptor_loss	1.0000
9:97314614:GTA:G	acceptor_loss	1.0000
9:97314616:A:AG	acceptor_gain	1.0000
9:97314616:A:AT	acceptor_loss	1.0000
9:97314617:G:GG	acceptor_gain	1.0000
9:97314724:ATAAA:A	donor_gain	1.0000
9:97314725:TAAA:T	donor_gain	1.0000
9:97314726:AAA:A	donor_gain	1.0000
9:97314727:AA:A	donor_gain	1.0000
9:97314729:G:GG	donor_gain	1.0000

AlphaMissense

11331 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:97375458:T:A	W1615R	0.997
9:97375458:T:C	W1615R	0.997
9:97375573:G:C	R1653P	0.995
9:97375460:G:C	W1615C	0.993
9:97375460:G:T	W1615C	0.993
9:97375569:G:C	A1652P	0.990
9:97328099:A:C	S625R	0.986
9:97328101:C:A	S625R	0.986
9:97328101:C:G	S625R	0.986
9:97320169:T:A	W419R	0.983
9:97320169:T:C	W419R	0.983
9:97354947:T:C	L1112P	0.983
9:97366562:T:C	F1395L	0.983
9:97366564:C:A	F1395L	0.983
9:97366564:C:G	F1395L	0.983
9:97360021:T:A	W1179R	0.981
9:97360021:T:C	W1179R	0.981
9:97360055:T:C	L1190P	0.981
9:97371659:T:C	L1562P	0.981
9:97318558:G:C	R396P	0.979
9:97375459:G:C	W1615S	0.979
9:97354986:T:C	L1125P	0.978
9:97357679:T:C	L1150P	0.975
9:97347340:T:C	L886P	0.973
9:97354952:T:C	F1114L	0.972
9:97354954:C:A	F1114L	0.972
9:97354954:C:G	F1114L	0.972
9:97357636:T:C	S1136P	0.972
9:97360034:T:C	L1183P	0.972
9:97360044:G:C	R1186S	0.971

dbSNP variants (sampled 300 via entrez): RS1000007344 (9:97363337 A>T), RS1000015137 (9:97342860 C>G,T), RS1000037827 (9:97319929 C>A,T), RS1000117965 (9:97325484 A>G), RS1000125566 (9:97329311 G>C), RS1000145321 (9:97321844 G>A), RS1000219203 (9:97377992 G>A,T), RS1000268315 (9:97331169 A>G), RS1000274140 (9:97371615 C>T), RS1000341000 (9:97331465 A>C), RS1000364838 (9:97376014 A>G), RS1000433798 (9:97365340 G>GC), RS1000478713 (9:97324995 C>G), RS1000527760 (9:97324364 G>A), RS1000645933 (9:97370321 C>T)

Disease associations

OMIM: gene MIM:621141 | 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

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases mutagenesis	3
Smoke	decreases expression, increases abundance, increases expression	2
Valproic Acid	decreases expression	2
beauvericin	affects cotreatment, decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	increases expression	1
butyraldehyde	decreases expression	1
cyanoginosin LR	decreases expression	1
enniatins	affects cotreatment, decreases expression	1
bisphenol S	increases expression	1
Fulvestrant	increases methylation	1
Leflunomide	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	decreases expression	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