CCDC170

Summary

CCDC170 (coiled-coil domain containing 170, HGNC:21177) is a protein-coding gene on chromosome 6q25.1, encoding Coiled-coil domain-containing protein 170 (Q8IYT3). Plays a role in Golgi-associated microtubules organization and stabilization.

The function of this gene and its encoded protein is not known. Several genome-wide association studies have implicated the region around this gene to be involved in breast cancer and bone mineral density, but no link to this specific gene has been found.

Source: NCBI Gene 80129 — RefSeq curated summary.

At a glance

• GWAS associations: 67
• Clinical variants (ClinVar): 122 total — 1 likely-pathogenic
• MANE Select transcript: NM_025059

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21177
Approved symbol	CCDC170
Name	coiled-coil domain containing 170
Location	6q25.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23305, bA282P11.1
Ensembl gene	ENSG00000120262
Ensembl biotype	protein_coding
Entrez	80129

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000239374, ENST00000537358, ENST00000544131, ENST00000867015, ENST00000867016, ENST00000867017, ENST00000971556, ENST00000971557

RefSeq mRNA: 1 — MANE Select: NM_025059 NM_025059

CCDS: CCDS43515

Canonical transcript exons

ENST00000239374 — 11 exons

Exon	Start	End
ENSE00000813741	151544572	151544716
ENSE00000813743	151573174	151573491
ENSE00000813744	151585889	151586089
ENSE00000813745	151593107	151593280
ENSE00000813747	151615443	151615679
ENSE00000896373	151548304	151548489
ENSE00001128561	151536318	151536446
ENSE00001323120	151617947	151621193
ENSE00001952106	151494017	151494185
ENSE00003476893	151538045	151538301
ENSE00003675199	151596335	151596577

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 96.58.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4174 / max 57.6523, expressed in 576 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
70608	0.8478	416
70610	0.4433	235
70609	0.1119	50
70611	0.0143	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	96.58	gold quality
epithelium of bronchus	UBERON:0002031	95.91	gold quality
bronchus	UBERON:0002185	94.57	gold quality
right uterine tube	UBERON:0001302	92.43	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.41	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.40	gold quality
calcaneal tendon	UBERON:0003701	85.00	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.51	gold quality
monocyte	CL:0000576	76.26	gold quality
nasal cavity epithelium	UBERON:0005384	76.23	gold quality
sperm	CL:0000019	76.20	gold quality
mononuclear cell	CL:0000842	76.12	gold quality
leukocyte	CL:0000738	75.65	gold quality
adrenal tissue	UBERON:0018303	75.44	gold quality
male germ cell	CL:0000015	74.76	silver quality
right adrenal gland cortex	UBERON:0035827	74.36	gold quality
sural nerve	UBERON:0015488	74.19	gold quality
left ovary	UBERON:0002119	73.74	gold quality
right adrenal gland	UBERON:0001233	73.72	gold quality
endometrium	UBERON:0001295	73.37	gold quality
adrenal gland	UBERON:0002369	73.09	gold quality
left adrenal gland cortex	UBERON:0035825	73.08	gold quality
left adrenal gland	UBERON:0001234	73.00	gold quality
epithelium of nasopharynx	UBERON:0001951	73.00	gold quality
nasopharynx	UBERON:0001728	72.99	gold quality
adrenal cortex	UBERON:0001235	71.68	gold quality
nasal cavity mucosa	UBERON:0001826	71.51	gold quality
stromal cell of endometrium	CL:0002255	71.36	gold quality
right ovary	UBERON:0002118	71.34	gold quality
decidua	UBERON:0002450	70.73	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	64.31
E-MTAB-10287	yes	27.24
E-HCAD-1	yes	27.08
E-GEOD-130148	yes	13.31
E-ANND-3	yes	10.41
E-CURD-11	no	41.66
E-MTAB-7249	no	17.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

110 targeting CCDC170, 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-3646	100.00	73.56	5283
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-3912-5P	99.95	66.11	925
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3140-3P	99.88	68.47	2069

Literature-anchored findings (GeneRIF, showing 14)

• SNPs associated with breast cancer differ for Asian, European, and African ancestry groups (PMID:20661439)
• Our findings suggest that ESR1 and C6orf97 gene polymorphism is associated with fracture and vertebral fracture risk in Chinese postmenopausal women. (PMID:24481879)
• ESR1-CCDC170 rearrangements are found in an aggressive subset of estrogen receptor-positive breast cancers (PMID:25099679)
• Variation in rs3757318 of C6orf97 is associated with breast cancer risk. (PMID:25338983)
• Data suggest that rs2046210 SNPs located in the region of C6ORF97 (CCDC170)-estrogen receptor alpha (ESR1) might have substantial roles not only in carcinogenesis but also in progression toward a more aggressive phenotype in breast cancer patients. (PMID:25370037)
• Genetic variation at the WLS and CCDC170/ESR1 loci were found to be significantly associated with bone mineral density (PMID:26911590)
• Expression of ESR1, RMND1 and CCDC170 associated with variants in separate enhancer elements predisposing breast cancer. [meta-analysis] (PMID:26928228)
• Findings demonstrate that CCDC170 plays an essential role in Golgi-associated microtubules organization and stabilization, and implicate a mechanism for how perturbations in the CCDC170 gene may contribute to the hallmark changes in cell polarity and motility seen in breast cancer. (PMID:28687497)
• The study shows that an association of theRMND1/CCDC170-ESR1 single nucleotide polymorphisms can exist with osteopenia, osteoporosis, or fragility fracture. (PMID:30601066)
• COL1A1, CCDC170, and ESR1 single nucleotide polymorphisms associated with distal radius fracture in postmenopausal Mexican women. (PMID:31246104)
• Therapeutic role of recurrent ESR1-CCDC170 gene fusions in breast cancer endocrine resistance. (PMID:32771039)
• CCDC170 affects breast cancer apoptosis through IRE1 pathway. (PMID:33291081)
• Three functional polymorphisms in CCDC170 were associated with osteoporosis phenotype. (PMID:33785515)
• Relationship between rs7586085, GALNT3 and CCDC170 gene polymorphisms and the risk of osteoporosis among the Chinese Han population. (PMID:35414641)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc170	ENSDARG00000016161
mus_musculus	Ccdc170	ENSMUSG00000019767
rattus_norvegicus	Ccdc170	ENSRNOG00000024280
drosophila_melanogaster	CG43338	FBGN0263079
caenorhabditis_elegans		WBGENE00016160

Protein

Protein identifiers

Coiled-coil domain-containing protein 170 — Q8IYT3 (reviewed: Q8IYT3)

All UniProt accessions (1): Q8IYT3

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in Golgi-associated microtubules organization and stabilization.

Subunit / interactions. Binds Golgi-associated microtubules.

Subcellular location. Golgi apparatus.

RefSeq proteins (1): NP_079335* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039139	CCDC170-like	Family

UniProt features (14 total): sequence variant 8, coiled-coil region 3, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IYT3-F1	82.06	0.40

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 72 (showing top): GOZGIT_ESR1_TARGETS_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, chr6q25, CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY, GOMF_CYTOSKELETAL_PROTEIN_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, DOANE_BREAST_CANCER_ESR1_UP, GOBP_MICROTUBULE_CYTOSKELETON_ORGANIZATION, LTE2_UP.V1_UP, RAF_UP.V1_DN, MIR153_5P, MIR3662

GO Biological Process (1): microtubule cytoskeleton organization (GO:0000226)

GO Molecular Function (2): microtubule binding (GO:0008017), protein binding (GO:0005515)

GO Cellular Component (3): Golgi apparatus (GO:0005794), cell junction (GO:0030054), ciliary basal body (GO:0036064)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoskeleton organization	1
microtubule-based process	1
tubulin binding	1
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
microtubule organizing center	1
cilium	1

Protein interactions and networks

STRING

2025 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC170	DCPH1	Q9H993	788
CCDC170	ESR1	P03372	757
CCDC170	RMND1	Q9NWS8	754
CCDC170	ZBTB2	Q8N680	584
CCDC170	ZBTB40	Q9NUA8	571
CCDC170	GPATCH1	Q9BRR8	568
CCDC170	CFAP90	A4QMS7	488
CCDC170	ESR2	Q92731	473
CCDC170	TOX3	O15405	460
CCDC170	TMEM135	Q86UB9	458
CCDC170	SYNE1	Q8NF91	452
CCDC170	PLEKHG1	Q9ULL1	447
CCDC170	MTRF1L	Q9UGC7	446
CCDC170	SGSM3	Q96HU1	445
CCDC170	TEPSIN	Q96N21	445

IntAct

13 interactions, top by confidence:

A	B	Type	Score
MIS18A	DCTN6	psi-mi:“MI:0914”(association)	0.640
CCDC170	CCNH	psi-mi:“MI:0915”(physical association)	0.560
CCNH	CCDC170	psi-mi:“MI:0915”(physical association)	0.560
CCDC170	RBM17	psi-mi:“MI:0915”(physical association)	0.560
RDH11	CCDC170	psi-mi:“MI:0915”(physical association)	0.400
M		psi-mi:“MI:0914”(association)	0.350
EXOC1	CCDC170	psi-mi:“MI:0915”(physical association)	0.000
RBM17	CCDC170	psi-mi:“MI:0915”(physical association)	0.000
thrS	CCDC170	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): CCDC170 (Two-hybrid), CCDC170 (Affinity Capture-MS), CCDC170 (Affinity Capture-MS), CCDC170 (Affinity Capture-MS), RBM17 (Two-hybrid), RDH11 (Proximity Label-MS), CCDC170 (Affinity Capture-MS), CCDC170 (Affinity Capture-MS), CCDC170 (Affinity Capture-MS), S100A5 (Cross-Linking-MS (XL-MS)), CCDC170 (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8QCI3, A3KGV1, B6MFW3, F6ZDS4, G5E861, O15078, O94986, P61584, P70336, P85001, P85120, Q15276, Q3V6T2, Q498G2, Q4R703, Q5BJF6, Q5EE04, Q5NVN6, Q5R5R4, Q5SNZ0, Q5TZ80, Q5VU43, Q5ZJ27, Q5ZKK5, Q66GS9, Q66KE8, Q6A078, Q6AYX5, Q6GQ73, Q6NRB0, Q6NRC9, Q6NY15, Q6P5D4, Q6VGS5, Q80UF4, Q86SQ7, Q86VS8, Q8BIL5, Q8BUK6, Q8CJ99

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	100
Likely benign	2
Benign	5

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
810049	GRCh37/hg19 6q25.1(chr6:151742378-151869624)x1	Likely pathogenic

SpliceAI

2193 predictions. Top by Δscore:

Variant	Effect	Δscore
6:151494182:CGAGG:C	donor_loss	1.0000
6:151494184:AGGTA:A	donor_loss	1.0000
6:151494185:GGTA:G	donor_loss	1.0000
6:151494186:GT:G	donor_loss	1.0000
6:151536294:T:TA	acceptor_gain	1.0000
6:151536297:A:AG	acceptor_gain	1.0000
6:151536297:ATTTT:A	acceptor_gain	1.0000
6:151536298:T:G	acceptor_gain	1.0000
6:151536301:T:TA	acceptor_gain	1.0000
6:151536302:G:A	acceptor_gain	1.0000
6:151536442:CTGAG:C	donor_loss	1.0000
6:151536443:TGAG:T	donor_loss	1.0000
6:151536445:AGGTA:A	donor_loss	1.0000
6:151536447:G:GA	donor_loss	1.0000
6:151536447:G:GG	donor_gain	1.0000
6:151536448:T:A	donor_loss	1.0000
6:151538039:T:G	acceptor_gain	1.0000
6:151538043:A:AG	acceptor_gain	1.0000
6:151538044:G:GA	acceptor_gain	1.0000
6:151538261:GAAT:G	donor_gain	1.0000
6:151538273:A:T	donor_gain	1.0000
6:151538285:T:G	donor_gain	1.0000
6:151538302:G:GG	donor_gain	1.0000
6:151544697:A:G	donor_gain	1.0000
6:151544699:G:GT	donor_gain	1.0000
6:151586090:G:GG	donor_gain	1.0000
6:151586119:G:GT	donor_gain	1.0000
6:151593098:T:TA	acceptor_gain	1.0000
6:151593099:G:A	acceptor_gain	1.0000
6:151593105:A:AG	acceptor_gain	1.0000

AlphaMissense

4741 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:151593204:G:C	R464P	0.947
6:151548388:G:C	A225P	0.942
6:151548419:T:C	L235P	0.940
6:151618035:T:C	L679P	0.937
6:151593129:T:C	L439P	0.927
6:151617957:T:C	F653S	0.921
6:151617969:T:A	V657E	0.921
6:151538132:G:C	A92P	0.916
6:151548394:G:C	A227P	0.916
6:151596573:T:C	L569P	0.913
6:151548397:A:C	S228R	0.911
6:151548399:C:A	S228R	0.911
6:151548399:C:G	S228R	0.911
6:151615480:T:C	L583P	0.906
6:151593116:T:C	F435L	0.899
6:151593118:T:A	F435L	0.899
6:151593118:T:G	F435L	0.899
6:151596336:T:C	L490P	0.899
6:151617948:T:C	L650P	0.897
6:151548406:A:C	T231P	0.896
6:151593216:T:C	L468P	0.896
6:151573241:T:C	L281P	0.895
6:151544652:T:C	L175P	0.894
6:151618035:T:A	L679H	0.888
6:151596543:T:C	L559P	0.873
6:151617956:T:C	F653L	0.873
6:151617958:C:A	F653L	0.873
6:151617958:C:G	F653L	0.873
6:151596548:G:C	A561P	0.866
6:151615459:A:C	Q576P	0.865

dbSNP variants (sampled 300 via entrez): RS1000043357 (6:151579327 G>T), RS1000090263 (6:151578459 A>C), RS1000115317 (6:151504731 G>C), RS1000119207 (6:151558122 C>A,T), RS1000129524 (6:151555816 A>T), RS1000156934 (6:151617765 A>G), RS1000197120 (6:151526596 A>G), RS1000215452 (6:151516131 G>A), RS1000219105 (6:151602187 T>C), RS1000240843 (6:151599381 G>A), RS1000254896 (6:151526329 C>T), RS1000307778 (6:151521573 A>C), RS1000315200 (6:151561368 C>G), RS1000371750 (6:151532090 G>C), RS1000391951 (6:151606523 T>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:615363

GenCC curated gene-disease

Mondo (1): estrogen resistance syndrome (MONDO:0014148)

Orphanet (1): Estrogen resistance syndrome (Orphanet:785)

HPO phenotypes

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

GWAS associations

67 associations (top):

Study	Trait	p-value
GCST000180_7	Bone mineral density (spine)	4.000000e-11
GCST000180_8	Bone mineral density (spine)	2.000000e-08
GCST000181_5	Bone mineral density (hip)	2.000000e-07
GCST000295_1	Bone mineral density (spine)	2.000000e-10
GCST000343_1	Breast cancer	2.000000e-15
GCST000678_11	Breast cancer	3.000000e-06
GCST001063_1	Chronic myeloid leukemia	2.000000e-06
GCST001482_9	Lumbar spine bone mineral density	4.000000e-35
GCST001585_22	Breast size	6.000000e-11
GCST001870_5	Bone mineral density	1.000000e-09
GCST002276_3	Bone mineral density	9.000000e-13
GCST002333_3	Bone properties (heel)	3.000000e-18
GCST002335_7	Bone properties (heel)	2.000000e-10
GCST003380_3	Bone mineral density (spine)	2.000000e-07
GCST003985_4	Breast size	1.000000e-11
GCST004350_15	Bone ultrasound measurement (velocity of sound)	3.000000e-09
GCST004350_2	Bone ultrasound measurement (velocity of sound)	1.000000e-11
GCST004351_15	Bone ultrasound measurement (broadband ultrasound attenuation)	2.000000e-10
GCST004351_21	Bone ultrasound measurement (broadband ultrasound attenuation)	3.000000e-07
GCST004351_6	Bone ultrasound measurement (broadband ultrasound attenuation)	3.000000e-08
GCST004549_20	Endometriosis	4.000000e-08
GCST004549_35	Endometriosis	1.000000e-07
GCST005795_23	Femoral neck bone mineral density	2.000000e-13
GCST005796_9	Lumbar spine bone mineral density	4.000000e-14
GCST006288_137	Heel bone mineral density	1.000000e-70
GCST006288_138	Heel bone mineral density	1.000000e-34
GCST006288_468	Heel bone mineral density	9.000000e-80
GCST006288_469	Heel bone mineral density	3.000000e-24
GCST006288_562	Heel bone mineral density	4.000000e-150
GCST006288_563	Heel bone mineral density	4.000000e-54

EFO canonical traits (14, from GWAS)

EFO ID	Trait name
EFO:0005654	velocity of sound measurement
EFO:0004514	bone quantitative ultrasound measurement
EFO:0007701	spine bone mineral density
EFO:0007785	femoral neck bone mineral density
EFO:0009270	heel bone mineral density
EFO:0009443	BRCAX breast cancer
EFO:0007620	volumetric bone mineral density
EFO:0004574	total cholesterol measurement
EFO:0004309	platelet count
EFO:0004327	electrocardiography
EFO:0007702	hip bone mineral density
EFO:0004842	eosinophil count
EFO:0004587	lymphocyte count
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	3
sodium arsenite	decreases expression, increases expression	2
Aflatoxin B1	affects expression, decreases expression	2
methyleugenol	decreases expression	1
triphenyl phosphate	affects expression	1
butyraldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
pentabromodiphenyl ether	increases expression	1
bromovanin	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arbutin	decreases expression	1
Cadmium	decreases expression	1
Estradiol	decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
N-Nitrosopyrrolidine	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
8-Bromo Cyclic Adenosine Monophosphate	decreases expression	1
Cyclosporine	decreases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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