CCDC60

Summary

CCDC60 (coiled-coil domain containing 60, HGNC:28610) is a protein-coding gene on chromosome 12q24.23, encoding Coiled-coil domain-containing protein 60 (Q8IWA6).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 120 total — 1 likely-pathogenic
• MANE Select transcript: NM_178499

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28610
Approved symbol	CCDC60
Name	coiled-coil domain containing 60
Location	12q24.23
Locus type	gene with protein product
Status	Approved
Aliases	MGC39827
Ensembl gene	ENSG00000183273
Ensembl biotype	protein_coding
Entrez	160777

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000327554, ENST00000535685, ENST00000536742, ENST00000539847, ENST00000546345, ENST00000886826, ENST00000886827

RefSeq mRNA: 1 — MANE Select: NM_178499 NM_178499

CCDS: CCDS9190

Canonical transcript exons

ENST00000327554 — 14 exons

Exon	Start	End
ENSE00001293751	119488759	119488866
ENSE00001302072	119516623	119516707
ENSE00001304398	119522939	119523001
ENSE00001306511	119528615	119528746
ENSE00001316899	119500078	119500168
ENSE00001320528	119520121	119520192
ENSE00001324050	119540614	119541040
ENSE00001328635	119523693	119523818
ENSE00001330437	119505069	119505303
ENSE00001330853	119530874	119531063
ENSE00003530164	119479094	119479201
ENSE00003610618	119471994	119472164
ENSE00003625798	119428683	119428762
ENSE00003847826	119334729	119335266

Expression profiles

Bgee: expression breadth ubiquitous, 150 present calls, max score 90.85.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.5802 / max 52.3259, expressed in 169 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128296	0.4085	148
128295	0.0939	35
128294	0.0304	13
128297	0.0260	13
206925	0.0214	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	90.85	gold quality
right uterine tube	UBERON:0001302	90.74	gold quality
bronchus	UBERON:0002185	89.47	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.20	gold quality
epithelium of nasopharynx	UBERON:0001951	87.49	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.76	gold quality
mucosa of paranasal sinus	UBERON:0005030	81.64	gold quality
left testis	UBERON:0004533	80.11	gold quality
right testis	UBERON:0004534	79.61	gold quality
testis	UBERON:0000473	78.35	gold quality
pigmented layer of retina	UBERON:0001782	76.50	gold quality
nasal cavity mucosa	UBERON:0001826	75.41	gold quality
sperm	CL:0000019	74.69	silver quality
rectum	UBERON:0001052	72.44	gold quality
fallopian tube	UBERON:0003889	70.32	gold quality
oviduct epithelium	UBERON:0004804	68.29	gold quality
myocardium	UBERON:0002349	67.90	gold quality
prostate gland	UBERON:0002367	67.38	gold quality
urinary bladder	UBERON:0001255	67.36	gold quality
secondary oocyte	CL:0000655	66.07	gold quality
vagina	UBERON:0000996	65.98	gold quality
endocervix	UBERON:0000458	64.58	gold quality
seminal vesicle	UBERON:0000998	64.28	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	62.73	gold quality
esophagus mucosa	UBERON:0002469	62.70	gold quality
ectocervix	UBERON:0012249	62.40	gold quality
uterine cervix	UBERON:0000002	62.25	gold quality
tonsil	UBERON:0002372	62.07	gold quality
adult organism	UBERON:0007023	62.07	gold quality
vastus lateralis	UBERON:0001379	61.66	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting CCDC60, 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-3925-3P	100.00	69.95	1237
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-548AI	99.69	69.24	1494
HSA-MIR-548BA	99.69	69.14	1514
HSA-MIR-570-5P	99.69	69.24	1494
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-873-5P	98.84	66.90	1348
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-4463	98.56	66.05	1071
HSA-MIR-4691-5P	98.41	66.77	1343
HSA-MIR-6792-3P	98.41	66.86	1359
HSA-MIR-4712-5P	97.24	67.79	775
HSA-MIR-770-5P	97.24	68.10	758
HSA-MIR-6734-5P	95.70	65.56	950

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc60	ENSMUSG00000043913
rattus_norvegicus	Ccdc60	ENSRNOG00000032684

Protein

Protein identifiers

Coiled-coil domain-containing protein 60 — Q8IWA6 (reviewed: Q8IWA6)

All UniProt accessions (3): Q8IWA6, F5H2N8, F5H5H4

RefSeq proteins (1): NP_848594* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031526	DUF4698	Family

Pfam: PF15769

UniProt features (11 total): region of interest 3, sequence variant 3, compositionally biased region 2, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IWA6-F1	67.25	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): EFC_Q6, TATA_C, RFX1_01, chr12q24, DODD_NASOPHARYNGEAL_CARCINOMA_DN, STAT6_01, RAO_BOUND_BY_SALL4_ISOFORM_B, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, CDP_02, GATA1_05, MIR1276, MIR3925_3P, MIR873_5P, MIR770_5P, MIR4712_5P

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

462 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC60	TEX9	Q8N6V9	543
CCDC60	CFAP210	Q0VFZ6	532
CCDC60	FAM178B	Q8IXR5	518
CCDC60	UBXN11	Q5T124	507
CCDC60	EPS8L2	Q9H6S3	487
CCDC60	CCDC160	A6NGH7	477
CCDC60	GLOD4	Q9HC38	476
CCDC60	SYTL1	Q8IYJ3	473
CCDC60	FRMD8	Q9BZ67	470
CCDC60	CCDC190	Q86UF4	458
CCDC60	LCA5L	O95447	457
CCDC60	CATSPERB	Q9H7T0	441
CCDC60	RABL2A	Q9UBK7	434
CCDC60	PKN3	Q6P5Z2	419
CCDC60	HSF2	Q03933	416

IntAct

8 interactions, top by confidence:

A	B	Type	Score
MTUS2	CCDC60	psi-mi:“MI:0915”(physical association)	0.670
CCDC60	MTUS2	psi-mi:“MI:0915”(physical association)	0.670
CCDC60	DCP1B	psi-mi:“MI:0914”(association)	0.530
CCDC60	ZNF593	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350

BioGRID (18): CCDC60 (Two-hybrid), CCDC60 (Reconstituted Complex), CCDC60 (Affinity Capture-MS), FAM204A (Affinity Capture-MS), FAM32A (Affinity Capture-MS), UPF3B (Affinity Capture-MS), ZNF593 (Affinity Capture-MS), DCP1B (Affinity Capture-MS), RBM42 (Affinity Capture-MS), CCDC60 (Biochemical Activity), CCDC60 (Affinity Capture-MS), FAM32A (Affinity Capture-MS), DCP1B (Affinity Capture-MS), FAM204A (Affinity Capture-MS), UGGT2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GVB3, A0A1B0GVH6, A2RRY8, A4IGV6, A6NHR8, B3DHS1, E1B9I5, O74317, O95561, P03319, P03320, P0C9Z5, P0C9Z6, P10260, P36353, P40744, P40745, Q06616, Q09280, Q09424, Q2KIL1, Q2KIR0, Q32KT7, Q32LB6, Q3T028, Q3TTI8, Q496A3, Q5NC83, Q5SQS8, Q5XIU7, Q68FQ8, Q6DFB0, Q6ZNM6, Q6ZV65, Q811V6, Q8IWA6, Q8N9R6, Q8R0E5, Q8TAL5, Q8WTQ4

Diamond homologs: Q3ZAV0, Q8C4J0, Q8IWA6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	105
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3063271	GRCh37/hg19 12q24.21-24.23(chr12:116718608-120115397)x1	Likely pathogenic

SpliceAI

2834 predictions. Top by Δscore:

Variant	Effect	Δscore
12:119335264:CAGG:C	donor_loss	1.0000
12:119335267:GTAA:G	donor_loss	1.0000
12:119428759:GCCG:G	donor_gain	1.0000
12:119428762:GGTG:G	donor_loss	1.0000
12:119428763:G:T	donor_loss	1.0000
12:119428764:T:A	donor_loss	1.0000
12:119428765:GAGT:G	donor_loss	1.0000
12:119471985:T:G	acceptor_gain	1.0000
12:119479200:GT:G	donor_gain	1.0000
12:119479202:G:GG	donor_gain	1.0000
12:119488867:G:GG	donor_gain	1.0000
12:119505064:TTTA:T	acceptor_loss	1.0000
12:119505066:TAG:T	acceptor_loss	1.0000
12:119505067:A:AG	acceptor_gain	1.0000
12:119505067:A:AT	acceptor_loss	1.0000
12:119505068:G:GA	acceptor_gain	1.0000
12:119505302:GA:G	donor_gain	1.0000
12:119505304:G:GG	donor_gain	1.0000
12:119523819:G:GG	donor_gain	1.0000
12:119530863:T:TA	acceptor_gain	1.0000
12:119530864:G:A	acceptor_gain	1.0000
12:119530871:AAGGT:A	acceptor_loss	1.0000
12:119530872:AGGT:A	acceptor_loss	1.0000
12:119530873:G:GT	acceptor_loss	1.0000
12:119531059:TTGAG:T	donor_loss	1.0000
12:119531060:TGAGG:T	donor_loss	1.0000
12:119531061:GAGG:G	donor_loss	1.0000
12:119531063:GGTAA:G	donor_loss	1.0000
12:119531064:G:C	donor_loss	1.0000
12:119335263:GCAG:G	donor_gain	0.9900

AlphaMissense

3673 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:119488793:T:A	W162R	0.996
12:119488793:T:C	W162R	0.996
12:119528745:T:A	W454R	0.996
12:119528745:T:C	W454R	0.996
12:119488805:G:C	A166P	0.995
12:119531025:T:A	W505R	0.995
12:119531025:T:C	W505R	0.995
12:119530948:T:C	L479P	0.994
12:119488779:T:C	L157P	0.993
12:119488788:T:C	L160P	0.993
12:119540621:G:C	R520P	0.993
12:119488781:T:C	C158R	0.992
12:119488797:T:C	L163P	0.992
12:119540662:T:A	W534R	0.992
12:119540662:T:C	W534R	0.992
12:119488783:T:G	C158W	0.991
12:119488856:T:A	W183R	0.991
12:119488856:T:C	W183R	0.991
12:119500142:T:A	W208R	0.991
12:119500142:T:C	W208R	0.991
12:119523778:G:C	A397P	0.991
12:119530885:T:C	L458P	0.991
12:119488800:T:C	L164P	0.990
12:119531056:C:A	A515D	0.990
12:119531027:G:C	W505C	0.989
12:119531027:G:T	W505C	0.989
12:119530897:T:C	L462P	0.988
12:119540666:T:C	L535P	0.988
12:119488809:T:C	L167P	0.987
12:119530874:G:C	W454C	0.987

dbSNP variants (sampled 300 via entrez): RS1000005053 (12:119393763 G>A), RS1000013209 (12:119541448 A>G), RS1000018659 (12:119400709 C>T), RS1000033404 (12:119348602 T>C), RS1000045336 (12:119425909 A>G), RS1000045504 (12:119507274 C>T), RS1000048627 (12:119470701 C>A,T), RS1000073450 (12:119520956 G>A), RS1000082184 (12:119346724 G>A,T), RS1000086607 (12:119420001 C>T), RS1000099155 (12:119442450 T>C), RS1000100058 (12:119435096 T>C), RS1000127430 (12:119413037 C>T), RS1000134783 (12:119436923 T>G), RS1000140819 (12:119386870 T>C)

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

5 associations (top):

Study	Trait	p-value
GCST000096_9	Aging traits	6.000000e-07
GCST000163_1	Schizophrenia	1.000000e-06
GCST003073_15	Cerebral amyloid deposition (PET imaging)	9.000000e-07
GCST003073_6	Cerebral amyloid deposition (PET imaging)	8.000000e-07
GCST008876_28	Non-lobar intracerebral hemorrhage (MTAG)	4.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004328	exercise test
EFO:0007707	cerebral amyloid deposition measurement
EFO:0010178	non-lobar intracerebral hemorrhage

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
bisphenol A	affects cotreatment, increases methylation	1
sodium arsenite	increases expression	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	affects cotreatment, increases expression	1
abrine	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	affects methylation	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Dactinomycin	affects cotreatment, increases expression	1
Doxorubicin	affects expression	1
Tobacco Smoke Pollution	decreases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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