CCDC160

Summary

CCDC160 (coiled-coil domain containing 160, HGNC:37286) is a protein-coding gene on chromosome Xq26.2, encoding Coiled-coil domain-containing protein 160 (A6NGH7).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 48 total — 4 pathogenic
• MANE Select transcript: NM_001353453

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37286
Approved symbol	CCDC160
Name	coiled-coil domain containing 160
Location	Xq26.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000203952
Ensembl biotype	protein_coding
Entrez	347475

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000370809, ENST00000517294, ENST00000695460, ENST00000695461, ENST00000918519

RefSeq mRNA: 3 — MANE Select: NM_001353453 NM_001101357, NM_001353453, NM_001393996

CCDS: CCDS48171

Canonical transcript exons

ENST00000695460 — 3 exons

Exon	Start	End
ENSE00001453673	134244777	134246842
ENSE00003963878	134238750	134238840
ENSE00003963880	134237182	134237343

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 84.56.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5883 / max 113.8635, expressed in 347 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197594	1.0266	329
197596	0.3849	158
197595	0.1768	107

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	84.56	gold quality
buccal mucosa cell	CL:0002336	79.88	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	79.35	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.63	gold quality
bronchial epithelial cell	CL:0002328	76.19	gold quality
bronchus	UBERON:0002185	74.59	gold quality
metanephros cortex	UBERON:0010533	71.52	gold quality
right uterine tube	UBERON:0001302	70.11	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	69.49	gold quality
ventricular zone	UBERON:0003053	69.25	gold quality
minor salivary gland	UBERON:0001830	68.63	gold quality
saliva-secreting gland	UBERON:0001044	68.57	gold quality
spinal cord	UBERON:0002240	67.18	gold quality
hypothalamus	UBERON:0001898	67.12	gold quality
fallopian tube	UBERON:0003889	67.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	66.38	gold quality
mucosa of paranasal sinus	UBERON:0005030	65.90	silver quality
substantia nigra	UBERON:0002038	65.49	gold quality
adult mammalian kidney	UBERON:0000082	65.13	gold quality
mouth mucosa	UBERON:0003729	64.98	gold quality
metanephros	UBERON:0000081	63.74	gold quality
nasal cavity mucosa	UBERON:0001826	63.48	gold quality
hindlimb stylopod muscle	UBERON:0004252	63.24	gold quality
amygdala	UBERON:0001876	62.81	gold quality
midbrain	UBERON:0001891	62.55	gold quality
nasal cavity epithelium	UBERON:0005384	62.21	gold quality
Brodmann (1909) area 9	UBERON:0013540	62.13	gold quality
prefrontal cortex	UBERON:0000451	61.69	gold quality
gall bladder	UBERON:0002110	61.67	gold quality
pigmented layer of retina	UBERON:0001782	61.66	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-9388	yes	10.98
E-ANND-3	yes	5.77

Regulation

Is transcription factor: no

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc160	ENSMUSG00000073207
rattus_norvegicus	Ccdc160	ENSRNOG00000046484
drosophila_melanogaster	acj6	FBGN0000028
drosophila_melanogaster	vvl	FBGN0086680
caenorhabditis_elegans		WBGENE00000441
caenorhabditis_elegans		WBGENE00006818

Paralogs (17): POU2F2 (ENSG00000028277), POU1F1 (ENSG00000064835), POU4F3 (ENSG00000091010), POU6F2 (ENSG00000106536), POU2F3 (ENSG00000137709), POU2F1 (ENSG00000143190), POU4F2 (ENSG00000151615), POU4F1 (ENSG00000152192), HDX (ENSG00000165259), POU6F1 (ENSG00000184271), POU3F2 (ENSG00000184486), POU3F1 (ENSG00000185668), POU3F4 (ENSG00000196767), POU3F3 (ENSG00000198914), POU5F1 (ENSG00000204531), POU5F1B (ENSG00000212993), POU5F2 (ENSG00000248483)

Protein

Protein identifiers

Coiled-coil domain-containing protein 160 — A6NGH7 (reviewed: A6NGH7)

All UniProt accessions (1): A6NGH7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CCDC160 family.

RefSeq proteins (3): NP_001094827, NP_001340382, NP_001380925 (=MANE)

Domains & families (InterPro)

UniProt features (6 total): region of interest 2, compositionally biased region 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NGH7-F1	72.79	0.42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MEISSNER_ES_ICP_WITH_H3K4ME3, MEISSNER_BRAIN_ICP_WITH_H3K4ME3, MIKKELSEN_ES_ICP_WITH_H3K4ME3, chrXq26, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_DN, ZFP91_TARGET_GENES, GSE11924_TFH_VS_TH1_CD4_TCELL_DN, GAO_SMALL_INTESTINE_24W_C6_GOBLET_CELLS, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_ADRENAL_SCHWANN_CELLS, DESCARTES_FETAL_LUNG_CILIATED_EPITHELIAL_CELLS, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

986 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC160	CFAP210	Q0VFZ6	557
CCDC160	EFHC2	Q5JST6	533
CCDC160	C1orf105	O95561	510
CCDC160	CCDC190	Q86UF4	497
CCDC160	FAM174C	Q9BVV8	495
CCDC160	USP46	P62068	483
CCDC160	CCDC60	Q8IWA6	477
CCDC160	SLC25A53	Q5H9E4	467
CCDC160	CCDC13	Q8IYE1	463
CCDC160	DEFB123	Q8N688	449
CCDC160	USP26	Q9BXU7	434
CCDC160	SLC22A31	A6NKX4	432
CCDC160	SPMIP6	Q8NCR6	430
CCDC160	MAP6D1	Q9H9H5	430
CCDC160	TEKT2	Q9UIF3	412
CCDC160	TMEM129	A0AVI4	412

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CCDC160	TSC1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (1): CCDC160 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTZ2, A3RM20, A4UHQ4, A6H7E2, A6NGH7, A9JSR5, B0BK70, O55527, O74982, P04861, P04862, P06747, P0C137, P0C139, P0C142, P14253, P14254, P33493, P35940, P40167, P69479, P69480, P69738, Q0GBX8, Q13352, Q14BK3, Q2T9U9, Q2YDE5, Q32L17, Q3UYG1, Q4KLZ4, Q4VKV6, Q5I0J4, Q5RE16, Q66HB6, Q6AXY9, Q810N5, Q8IR45, Q8IYM0, Q8NCU1

Diamond homologs: A6NGH7, Q2T9U9, Q3UYG1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	0
Uncertain significance	32
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
3245602	NC_000023.10:g.(?132670152)(133634107_?)del	Pathogenic
4279193	GRCh37/hg19 Xq26.2(chrX:133376542-133524283)x1	Pathogenic
443632	GRCh37/hg19 Xq26.2-26.3(chrX:133081342-135086194)x0	Pathogenic
57217	GRCh38/hg38 Xq26.2-26.3(chrX:133909683-135211108)x1	Pathogenic

SpliceAI

478 predictions. Top by Δscore:

Variant	Effect	Δscore
X:134237343:GGT:G	donor_loss	1.0000
X:134237344:G:C	donor_loss	1.0000
X:134238017:G:GT	donor_gain	1.0000
X:134243891:G:GT	donor_gain	1.0000
X:134243895:T:TA	donor_gain	1.0000
X:134243896:A:AA	donor_gain	1.0000
X:134237344:G:GG	donor_gain	0.9900
X:134237345:T:A	donor_loss	0.9900
X:134238007:C:T	donor_gain	0.9900
X:134243161:C:T	donor_gain	0.9900
X:134243943:G:GT	donor_gain	0.9900
X:134244771:TTTCA:T	acceptor_loss	0.9900
X:134244772:TTCA:T	acceptor_loss	0.9900
X:134244775:A:AG	acceptor_gain	0.9900
X:134244775:A:T	acceptor_loss	0.9900
X:134244776:G:GA	acceptor_loss	0.9900
X:134244776:G:GG	acceptor_gain	0.9900
X:134244776:GAT:G	acceptor_gain	0.9900
X:134244776:GATA:G	acceptor_gain	0.9900
X:134243177:A:G	donor_gain	0.9800
X:134244776:GA:G	acceptor_gain	0.9800
X:134243164:A:G	donor_gain	0.9700
X:134244767:T:TA	acceptor_gain	0.9700
X:134244776:GATAT:G	acceptor_gain	0.9700
X:134244763:ATTTT:A	acceptor_gain	0.9500
X:134238841:G:GG	donor_gain	0.9200
X:134243160:GCAAA:G	donor_gain	0.9200
X:134243184:GTC:G	donor_gain	0.9200
X:134243185:TCT:T	donor_gain	0.9200
X:134243891:GAA:G	donor_gain	0.9200

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000040709 (X:134239483 G>A), RS1000639973 (X:134237073 G>A), RS1000644689 (X:134244166 G>A), RS1001015074 (X:134243830 T>C,G), RS1001344595 (X:134238257 C>T), RS1001349022 (X:134245112 T>C), RS1002243431 (X:134235326 A>G), RS1002286925 (X:134246140 G>A), RS1002345141 (X:134235842 C>T), RS1002376558 (X:134236067 G>A), RS1002648395 (X:134243059 C>G), RS1002724617 (X:134246587 T>C,G), RS1003019751 (X:134240634 G>C), RS1003050881 (X:134240969 G>T), RS1004089597 (X:134242516 C>G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:194070

GenCC curated gene-disease

Mondo (1): Wilms tumor 1 (MONDO:0008679)

Orphanet (1): Nephroblastoma (Orphanet:654)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002358_9	Pit-and-Fissure caries	2.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases methylation	2
propionaldehyde	increases expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
Sunitinib	decreases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Nickel	decreases expression	1
Dihydrotestosterone	increases expression	1
Tretinoin	decreases expression	1
Triclosan	decreases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00038207	PHASE2	COMPLETED	Liposomal Vincristine for Pediatric and Adolescent Patients With Relapsed Malignancies
NCT00335556	PHASE2	COMPLETED	Combination Chemotherapy, Radiation Therapy, and/or Surgery in Treating Patients With High-Risk Kidney Tumors
NCT00011414	PHASE1	COMPLETED	Phase I Trial of Tariquidar (XR9576) in Combination With Doxorubicin, Vinorelbine, or Docetaxel in Pediatric Patients With Solid Tumors
NCT02164097	PHASE1	TERMINATED	ODSH + ICE Chemotherapy in Pediatric Solid Tumors
NCT00503893	Not specified	UNKNOWN	Genetics of Wilms’ Tumor and/or the Associated Conditions of Aniridia, Hemihypertrophy, and Genitourinary Anomalies
NCT05179850	Not specified	UNKNOWN	Computer Aided Diagnostic Tool on Computed Tomography Images for Diagnosis of Retroperitoneal Tumor in Children