CCDC190

Summary

CCDC190 (coiled-coil domain containing 190, HGNC:28736) is a protein-coding gene on chromosome 1q23.3, encoding Coiled-coil domain-containing protein 190 (Q86UF4).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_001394065

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28736
Approved symbol	CCDC190
Name	coiled-coil domain containing 190
Location	1q23.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC48998
Ensembl gene	ENSG00000185860
Ensembl biotype	protein_coding
Entrez	339512

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000367910, ENST00000367911, ENST00000367912, ENST00000524691, ENST00000524710, ENST00000876170

RefSeq mRNA: 2 — MANE Select: NM_001394065 NM_001394065, NM_178550

CCDS: CCDS44269, CCDS91094

Canonical transcript exons

ENST00000367912 — 4 exons

Exon	Start	End
ENSE00001445908	162851020	162855359
ENSE00001445910	162855632	162855755
ENSE00001445911	162859460	162859658
ENSE00003937405	162861008	162861175

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 93.78.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2209 / max 45.4964, expressed in 105 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15679	0.1926	93
15682	0.0283	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	93.78	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.02	gold quality
bronchus	UBERON:0002185	92.87	gold quality
lower esophagus mucosa	UBERON:0035834	89.64	gold quality
epithelium of nasopharynx	UBERON:0001951	86.98	gold quality
mucosa of paranasal sinus	UBERON:0005030	86.94	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.05	gold quality
right coronary artery	UBERON:0001625	77.14	gold quality
nasal cavity epithelium	UBERON:0005384	75.47	gold quality
nasal cavity mucosa	UBERON:0001826	73.57	gold quality
trachea	UBERON:0003126	72.37	gold quality
left coronary artery	UBERON:0001626	71.38	gold quality
coronary artery	UBERON:0001621	70.15	gold quality
thoracic aorta	UBERON:0001515	70.11	gold quality
descending thoracic aorta	UBERON:0002345	69.93	gold quality
ascending aorta	UBERON:0001496	69.89	gold quality
aorta	UBERON:0000947	68.39	gold quality
popliteal artery	UBERON:0002250	67.38	gold quality
tibial artery	UBERON:0007610	67.33	gold quality
esophagus mucosa	UBERON:0002469	63.84	gold quality
right lung	UBERON:0002167	61.08	gold quality
gall bladder	UBERON:0002110	55.13	gold quality
corpus callosum	UBERON:0002336	54.23	gold quality
pharyngeal mucosa	UBERON:0000355	53.82	gold quality
caudate nucleus	UBERON:0001873	53.60	gold quality
mucosa of stomach	UBERON:0001199	52.60	gold quality
esophagus	UBERON:0001043	50.40	gold quality
putamen	UBERON:0001874	50.29	gold quality
smooth muscle tissue	UBERON:0001135	49.88	gold quality
lung	UBERON:0002048	49.67	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting CCDC190, 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-656-3P	100.00	72.15	2788
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-3913-3P	99.74	66.53	938
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4696	99.48	67.48	1040
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-6853-3P	99.36	70.79	1558
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-3916	98.99	68.04	2155
HSA-MIR-6859-5P	98.99	68.07	2049
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-4742-3P	98.73	69.82	1803
HSA-MIR-4703-5P	98.53	70.13	1645
HSA-MIR-3942-5P	98.52	69.51	1517
HSA-MIR-4766-3P	98.48	67.94	1347
HSA-MIR-891A-3P	98.05	67.99	970
HSA-MIR-6502-3P	97.86	65.43	569
HSA-MIR-7111-3P	97.80	66.75	1467
HSA-MIR-3928-3P	97.61	66.53	1096

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc190	ENSMUSG00000070532
rattus_norvegicus	Ccdc190	ENSRNOG00000025005

Protein

Protein identifiers

Coiled-coil domain-containing protein 190 — Q86UF4 (reviewed: Q86UF4)

All UniProt accessions (2): A0A8J8YXK0, Q86UF4

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q86UF4-1	1	yes
Q86UF4-2	2

RefSeq proteins (2): NP_001380994, NP_848645 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031525	CC190	Family

Pfam: PF15768

UniProt features (11 total): compositionally biased region 3, splice variant 3, region of interest 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-Q86UF4-F1	65.14	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, RICKMAN_HEAD_AND_NECK_CANCER_E, UBN1_TARGET_GENES, ZNF274_TARGET_GENES, MIR335_3P, MIR8068, MIR3125, MIR4703_5P, MIR3942_5P, MIR1276, MIR5197_5P, MIR4766_3P, MIR9851_3P, MIR593_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

246 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC190	KLHDC9	Q8NEP7	675
CCDC190	ASB17	Q8WXJ9	597
CCDC190	TAS2R1	Q9NYW7	554
CCDC190	CFAP210	Q0VFZ6	542
CCDC190	C2orf66	Q6UXQ4	515
CCDC190	CCDC160	A6NGH7	497
CCDC190	CCDC169	A6NNP5	479
CCDC190	NPY2R	P49146	463
CCDC190	CCDC60	Q8IWA6	458
CCDC190	NPAS4	Q8IUM7	456
CCDC190	CCDC74B	Q96LY2	447
CCDC190	ALOXE3	Q9BYJ1	446
CCDC190	CCDC13	Q8IYE1	433
CCDC190	AGTR2	P50052	432
CCDC190	CENATAC	Q86UT8	431

IntAct

4 interactions, top by confidence:

A	B	Type	Score
CCDC190	PPIB	psi-mi:“MI:0915”(physical association)	0.400
CCDC190	NPM1	psi-mi:“MI:0915”(physical association)	0.400
PPP1R14C	CCDC190	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (5): C1orf110 (Reconstituted Complex), C1orf110 (Proximity Label-MS), PPP1R14C (Proximity Label-MS), C1orf110 (Proximity Label-MS), APP (Reconstituted Complex)

ESM2 similar proteins: A0A1B0GUA9, A0JNH1, A1L170, A2TJV2, A6H7B4, A6NFA0, A6NGY1, A6X8Z5, A7YY35, B2RQL2, D3Z1D3, M0RD54, P43359, Q05860, Q0VF49, Q1RMX6, Q1RN00, Q2M1Z3, Q32LI3, Q3URK1, Q5EBJ4, Q5M831, Q5RJL0, Q62100, Q640N3, Q64256, Q642A3, Q66H53, Q66LM6, Q68D20, Q68DA7, Q68US1, Q6AXN6, Q6AYA8, Q6IR42, Q711Q0, Q80VY2, Q86UF4, Q8IY42, Q8TDR4

Diamond homologs: Q1RMX6, Q3URK1, Q86UF4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

265 predictions. Top by Δscore:

Variant	Effect	Δscore
1:162859456:TTAC:T	donor_loss	0.9900
1:162859458:ACC:A	donor_loss	0.9900
1:162859459:C:CG	donor_loss	0.9900
1:162859459:CCTTG:C	donor_gain	0.9900
1:162855759:C:CC	acceptor_gain	0.9800
1:162855753:TTT:T	acceptor_gain	0.9700
1:162855754:TT:T	acceptor_gain	0.9700
1:162855756:C:CC	acceptor_gain	0.9700
1:162855760:T:C	acceptor_gain	0.9600
1:162859458:A:AC	donor_gain	0.9600
1:162859459:C:CC	donor_gain	0.9600
1:162855358:CT:C	acceptor_gain	0.9400
1:162855360:C:CC	acceptor_gain	0.9400
1:162855360:C:G	acceptor_gain	0.9400
1:162855359:TCTGA:T	acceptor_gain	0.9300
1:162855751:GGTTT:G	acceptor_gain	0.9300
1:162855752:GTTT:G	acceptor_gain	0.9300
1:162855752:GTTTC:G	acceptor_loss	0.9300
1:162855755:TC:T	acceptor_loss	0.9300
1:162855757:T:A	acceptor_loss	0.9300
1:162855356:TGCT:T	acceptor_gain	0.9200
1:162855769:A:C	acceptor_loss	0.8900
1:162855643:AG:A	donor_gain	0.8800
1:162855761:T:TC	acceptor_gain	0.8800
1:162855627:CTTA:C	donor_loss	0.8700
1:162855630:ACC:A	donor_loss	0.8700
1:162855755:TCTG:T	acceptor_loss	0.8700
1:162855756:CTGC:C	acceptor_loss	0.8700
1:162855758:GCTT:G	acceptor_loss	0.8700
1:162855760:T:G	acceptor_loss	0.8700

AlphaMissense

2076 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:162854843:A:C	F277L	0.952
1:162854843:A:T	F277L	0.952
1:162854845:A:G	F277L	0.952
1:162859577:C:G	A24P	0.922
1:162854847:A:T	I276K	0.902
1:162859489:A:G	L53P	0.900
1:162854858:G:C	S272R	0.889
1:162854858:G:T	S272R	0.889
1:162854860:T:G	S272R	0.889
1:162859543:A:G	L35P	0.889
1:162859571:C:G	A26P	0.889
1:162859498:T:G	Q50P	0.888
1:162859586:C:G	A21P	0.881
1:162859477:A:G	L57P	0.879
1:162854891:G:C	H261Q	0.875
1:162854891:G:T	H261Q	0.875
1:162859501:T:A	E49V	0.866
1:162854847:A:C	I276R	0.858
1:162859510:A:G	L46P	0.858
1:162854895:C:G	R260P	0.856
1:162859552:A:G	L32P	0.853
1:162854936:G:C	F246L	0.843
1:162854936:G:T	F246L	0.843
1:162854938:A:G	F246L	0.843
1:162859500:C:A	E49D	0.840
1:162859500:C:G	E49D	0.840
1:162854893:G:C	H261D	0.837
1:162859564:A:G	L28P	0.836
1:162859581:C:A	K22N	0.830
1:162859581:C:G	K22N	0.830

dbSNP variants (sampled 300 via entrez): RS1000203446 (1:162859683 T>C), RS1000412395 (1:162865484 G>A), RS1000575137 (1:162861646 T>A,G), RS1000893657 (1:162870497 A>C), RS1001198558 (1:162851928 G>A), RS1001463845 (1:162858196 C>A,T), RS1001617805 (1:162852162 G>T), RS1001628323 (1:162851597 C>T), RS1001805038 (1:162864578 C>G,T), RS1001871237 (1:162862694 T>A), RS1001890726 (1:162869271 A>G), RS1001923306 (1:162869037 G>A), RS1002182497 (1:162869251 C>T), RS1002215804 (1:162852174 A>G), RS1002310002 (1:162856669 G>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

4 associations (top):

Study	Trait	p-value
GCST001787_11	Colorectal cancer	9.000000e-06
GCST003488_4	Response to fenofibrate (triglyceride levels)	2.000000e-06
GCST011494_87	Daytime nap	3.000000e-07
GCST012282_2	BMI x environmental factors (excluding physical activity) interaction	5.000000e-07

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0007681	triglyceride change measurement
EFO:0007828	daytime rest measurement
EFO:0004340	body mass index
EFO:0006527	smoking status measurement
EFO:0009374	energy intake measurement
EFO:0009695	household income
EFO:0010810	protein intake measurement
EFO:0010811	carbohydrate intake measurement
EFO:0011015	educational attainment

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
Tobacco Smoke Pollution	affects expression, decreases expression	2
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
3,4,5,4’-tetramethoxystilbene	affects expression	1
(+)-JQ1 compound	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Folic Acid	affects cotreatment, decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Methotrexate	decreases expression, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Asbestos, Crocidolite	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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