CCDC152

Summary

CCDC152 (coiled-coil domain containing 152, HGNC:34438) is a protein-coding gene on chromosome 5p12, encoding Coiled-coil domain-containing protein 152 (Q4G0S7).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 64 total — 3 pathogenic
• MANE Select transcript: NM_001134848

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34438
Approved symbol	CCDC152
Name	coiled-coil domain containing 152
Location	5p12
Locus type	gene with protein product
Status	Approved
Aliases	LOC100129792
Ensembl gene	ENSG00000198865
Ensembl biotype	protein_coding
OMIM	621274
Entrez	100129792

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 9 protein_coding

ENST00000361970, ENST00000388827, ENST00000881080, ENST00000881081, ENST00000927600, ENST00000927601, ENST00000927602, ENST00000927603, ENST00000927604

RefSeq mRNA: 1 — MANE Select: NM_001134848 NM_001134848

CCDS: CCDS47203

Canonical transcript exons

ENST00000361970 — 9 exons

Exon	Start	End
ENSE00001435187	42799659	42802439
ENSE00001489256	42799375	42799458
ENSE00001489257	42796829	42796956
ENSE00001489259	42783474	42783576
ENSE00001489260	42779458	42779522
ENSE00001489262	42769597	42769665
ENSE00001489265	42762443	42762548
ENSE00001489268	42759120	42759208
ENSE00001489269	42756818	42756885

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 99.77.

FANTOM5 (CAGE): breadth broad, TPM avg 2.3680 / max 325.6449, expressed in 624 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
56284	2.3680	624

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	99.77	gold quality
renal medulla	UBERON:0000362	99.15	gold quality
cardia of stomach	UBERON:0001162	99.14	gold quality
pylorus	UBERON:0001166	99.05	gold quality
buccal mucosa cell	CL:0002336	98.99	gold quality
nipple	UBERON:0002030	98.90	gold quality
ventral tegmental area	UBERON:0002691	98.84	gold quality
medulla oblongata	UBERON:0001896	98.78	gold quality
trigeminal ganglion	UBERON:0001675	98.75	gold quality
inferior vagus X ganglion	UBERON:0005363	98.72	gold quality
trachea	UBERON:0003126	98.71	gold quality
superior vestibular nucleus	UBERON:0007227	98.70	gold quality
superior surface of tongue	UBERON:0007371	98.70	gold quality
endothelial cell	CL:0000115	98.68	gold quality
subthalamic nucleus	UBERON:0001906	98.67	gold quality
dorsal plus ventral thalamus	UBERON:0001897	98.64	gold quality
lateral globus pallidus	UBERON:0002476	98.56	gold quality
dorsal root ganglion	UBERON:0000044	98.48	gold quality
pericardium	UBERON:0002407	98.39	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.38	gold quality
lateral nuclear group of thalamus	UBERON:0002736	98.31	gold quality
substantia nigra pars compacta	UBERON:0001965	98.27	gold quality
mucosa of paranasal sinus	UBERON:0005030	98.12	gold quality
superficial temporal artery	UBERON:0001614	98.10	gold quality
saphenous vein	UBERON:0007318	97.92	gold quality
upper leg skin	UBERON:0004262	97.90	gold quality
pharyngeal mucosa	UBERON:0000355	97.87	gold quality
urethra	UBERON:0000057	97.74	gold quality
vena cava	UBERON:0004087	97.48	gold quality
upper arm skin	UBERON:0004263	97.48	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-9543	yes	5223.04
E-ANND-3	yes	7.31
E-CURD-112	no	3.56

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting CCDC152, 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-4282	99.99	75.36	6408
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349

Literature-anchored findings (GeneRIF, showing 1)

• Identification of a novel endogenous long non-coding RNA that inhibits selenoprotein P translation. (PMID:34142161)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc152	ENSMUSG00000091119
rattus_norvegicus	Ccdc152	ENSRNOG00000039473

Protein

Protein identifiers

Coiled-coil domain-containing protein 152 — Q4G0S7 (reviewed: Q4G0S7)

All UniProt accessions (1): Q4G0S7

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Detected in stomach.

Isoforms (2)

UniProt ID	Names	Canonical?
Q4G0S7-1	1	yes
Q4G0S7-2	2

RefSeq proteins (1): NP_001128320* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038827	CCDC152	Family

UniProt features (6 total): sequence conflict 2, chain 1, coiled-coil region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q4G0S7-F1	87.17	0.71

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, LIU_COMMON_CANCER_GENES, LEE_DIFFERENTIATING_T_LYMPHOCYTE, CHAMP1_TARGET_GENES, IGLV5_37_TARGET_GENES, KAECH_NAIVE_VS_DAY15_EFF_CD8_TCELL_UP, MIR4422, MIR548AZ_5P, MIR548T_5P, MIR448, MIR511_5P, MIR8084, MIR4742_5P, MIR451B, MIR4318

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

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC152	SELENOP	P49908	476
CCDC152	NT5DC1	Q5TFE4	472
CCDC152	WDR70	Q9NW82	461
CCDC152	ZBTB35	P52739	456
CCDC152	FANCD2OS	Q96PS1	443
CCDC152	NIM1K	Q8IY84	429
CCDC152	EVA1C	P58658	412
CCDC152	DPY19L1	Q2PZI1	397
CCDC152	SELENOS	Q9BQE4	388
CCDC152	SNX22	Q96L94	365
CCDC152	FAM8A1	Q9UBU6	364
CCDC152	SECISBP2	Q96T21	360
CCDC152	CACNG5	Q9UF02	346
CCDC152	NRAP	Q86VF7	325
CCDC152	C16orf54	Q6UWD8	324

IntAct

13 interactions, top by confidence:

A	B	Type	Score
CCDC152	TXLNB	psi-mi:“MI:0915”(physical association)	0.560
CCDC152	NTAQ1	psi-mi:“MI:0915”(physical association)	0.560
CDC37	CCDC152	psi-mi:“MI:0915”(physical association)	0.560
FARS2	CCDC152	psi-mi:“MI:0915”(physical association)	0.560
TXLNB	CCDC152	psi-mi:“MI:0915”(physical association)	0.000
NTAQ1	CCDC152	psi-mi:“MI:0915”(physical association)	0.000
CDC37	CCDC152	psi-mi:“MI:0915”(physical association)	0.000
FARS2	CCDC152	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): CCDC152 (Two-hybrid), CCDC152 (Two-hybrid), CCDC152 (Two-hybrid), CCDC152 (Two-hybrid), CCDC152 (Affinity Capture-MS)

ESM2 similar proteins: A2AUM9, A6PWD2, A7MD70, B1AJZ9, E9Q1U1, O35550, O35551, O75330, O94986, P0CB05, P97779, Q00547, Q03410, Q05D60, Q08DR9, Q13439, Q15276, Q15431, Q3KR99, Q3UPP8, Q498G2, Q4G0S7, Q4R703, Q4R7H3, Q4V7C8, Q53EZ4, Q5U3Z6, Q60563, Q61595, Q62209, Q6NRC9, Q6NRW2, Q6P3P1, Q6TFL3, Q70FJ1, Q80UF4, Q86SQ7, Q8BT07, Q8BVC4, Q8CDI7

Diamond homologs: Q32LM7, Q4G0S7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	52
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
144612	GRCh38/hg38 5p13.1-12(chr5:41901984-42896060)x1	Pathogenic
1710914	GRCh37/hg19 5p13.1-12(chr5:41879852-42906725)x1	Pathogenic
1710915	GRCh37/hg19 5p13.1-12(chr5:41879852-42913979)x1	Pathogenic

SpliceAI

1575 predictions. Top by Δscore:

Variant	Effect	Δscore
5:42759114:TTTCA:T	acceptor_loss	1.0000
5:42759115:TTCAG:T	acceptor_loss	1.0000
5:42759116:TCAGG:T	acceptor_loss	1.0000
5:42759117:CAGGC:C	acceptor_loss	1.0000
5:42759118:A:AG	acceptor_gain	1.0000
5:42759118:A:AT	acceptor_loss	1.0000
5:42759119:G:GA	acceptor_gain	1.0000
5:42759119:G:T	acceptor_loss	1.0000
5:42759119:GGC:G	acceptor_gain	1.0000
5:42759208:GGTA:G	donor_loss	1.0000
5:42759209:G:C	donor_loss	1.0000
5:42759210:T:G	donor_loss	1.0000
5:42762438:TACA:T	acceptor_loss	1.0000
5:42762439:ACAG:A	acceptor_loss	1.0000
5:42762440:CAGA:C	acceptor_loss	1.0000
5:42762441:A:AC	acceptor_loss	1.0000
5:42762441:A:AG	acceptor_gain	1.0000
5:42762442:G:GA	acceptor_gain	1.0000
5:42762442:GA:G	acceptor_gain	1.0000
5:42762442:GAA:G	acceptor_gain	1.0000
5:42762442:GAAA:G	acceptor_gain	1.0000
5:42770869:T:TG	donor_gain	1.0000
5:42796818:A:AG	acceptor_gain	1.0000
5:42796819:T:G	acceptor_gain	1.0000
5:42796827:A:AG	acceptor_gain	1.0000
5:42796827:AGTT:A	acceptor_gain	1.0000
5:42796828:G:GA	acceptor_gain	1.0000
5:42796828:GT:G	acceptor_gain	1.0000
5:42796828:GTT:G	acceptor_gain	1.0000
5:42796828:GTTG:G	acceptor_gain	1.0000

AlphaMissense

1720 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:42769630:T:C	L76P	0.966
5:42796946:T:C	L183P	0.956
5:42796904:T:C	L169P	0.955
5:42799705:T:C	L230P	0.949
5:42759180:T:C	L20P	0.946
5:42799663:T:C	L216P	0.944
5:42779473:T:C	L93P	0.942
5:42799661:A:C	K215N	0.931
5:42799661:A:T	K215N	0.931
5:42759191:T:C	F24L	0.913
5:42759193:C:A	F24L	0.913
5:42759193:C:G	F24L	0.913
5:42769609:T:C	L69P	0.894
5:42799450:T:G	Y212D	0.891
5:42799684:A:T	K223I	0.890
5:42799708:G:C	R231P	0.889
5:42799659:A:G	K215E	0.883
5:42783499:T:C	L118P	0.879
5:42799381:G:C	A189P	0.873
5:42799455:A:C	R213S	0.873
5:42799455:A:T	R213S	0.873
5:42796952:T:C	L185P	0.863
5:42799660:A:C	K215T	0.855
5:42799388:T:C	L191P	0.851
5:42799776:T:C	F254L	0.843
5:42799778:T:A	F254L	0.843
5:42799778:T:G	F254L	0.843
5:42799660:A:T	K215I	0.839
5:42762477:T:C	L41P	0.835
5:42799375:T:C	F187L	0.831

dbSNP variants (sampled 300 via entrez): RS1000043725 (5:42780216 C>T), RS1000082216 (5:42790035 A>G), RS1000135604 (5:42767698 C>A,T), RS1000148916 (5:42776392 A>G), RS1000276238 (5:42796119 A>T), RS1000287059 (5:42795936 T>C), RS1000359077 (5:42770366 G>A), RS1000374417 (5:42783134 T>C,G), RS1000443062 (5:42782880 T>C), RS1000650294 (5:42800588 A>T), RS1000717844 (5:42771456 A>C), RS1000822274 (5:42778052 C>T), RS1000879843 (5:42794432 A>T), RS1000927187 (5:42760964 T>C), RS1000979861 (5:42785098 T>A,C)

Disease associations

OMIM: gene MIM:621274 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008839_144	Height	2.000000e-24

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
Air Pollutants	affects expression, increases abundance, decreases expression	2
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
lasiocarpine	increases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
incobotulinumtoxinA	affects expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Formaldehyde	increases expression	1
Methotrexate	increases expression	1
Naphthoquinones	increases expression	1
Ozone	affects expression, increases abundance	1
Phenylmercuric Acetate	affects cotreatment, decreases expression	1
Smoke	decreases expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	increases expression	1
Valproic Acid	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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