CCDC142

Summary

CCDC142 (coiled-coil domain containing 142, HGNC:25889) is a protein-coding gene on chromosome 2p13.1, encoding Coiled-coil domain-containing protein 142 (Q17RM4).

At a glance

• Clinical variants (ClinVar): 124 total
• MANE Select transcript: NM_001365575

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25889
Approved symbol	CCDC142
Name	coiled-coil domain containing 142
Location	2p13.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14397
Ensembl gene	ENSG00000135637
Ensembl biotype	protein_coding
Entrez	84865

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 10 protein_coding, 4 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000290418, ENST00000393965, ENST00000454193, ENST00000471713, ENST00000472962, ENST00000473278, ENST00000474681, ENST00000486335, ENST00000497232, ENST00000715459, ENST00000904896, ENST00000904897, ENST00000904898, ENST00000904899, ENST00000904900, ENST00000969127, ENST00000969128

RefSeq mRNA: 2 — MANE Select: NM_001365575 NM_001365575, NM_032779

CCDS: CCDS1945, CCDS92784

Canonical transcript exons

ENST00000393965 — 9 exons

Exon	Start	End
ENSE00001199322	74474916	74475115
ENSE00001316287	74475612	74475726
ENSE00001326102	74472832	74474802
ENSE00001327085	74481817	74482998
ENSE00003493809	74480956	74481086
ENSE00003522329	74475225	74475402
ENSE00003523597	74481223	74481372
ENSE00003560921	74481452	74481538
ENSE00003633716	74480769	74480882

Expression profiles

Bgee: expression breadth ubiquitous, 202 present calls, max score 86.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.2872 / max 34.2600, expressed in 1567 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29217	3.2278	1364
29216	0.9229	613
29215	0.1365	43

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	86.59	gold quality
granulocyte	CL:0000094	83.67	gold quality
right lobe of liver	UBERON:0001114	81.61	gold quality
mucosa of transverse colon	UBERON:0004991	80.64	gold quality
ventricular zone	UBERON:0003053	79.94	gold quality
bone marrow cell	CL:0002092	79.67	gold quality
monocyte	CL:0000576	79.01	gold quality
leukocyte	CL:0000738	79.01	gold quality
cortical plate	UBERON:0005343	78.89	gold quality
cerebellar hemisphere	UBERON:0002245	78.71	gold quality
cerebellar cortex	UBERON:0002129	78.68	gold quality
right adrenal gland	UBERON:0001233	78.61	gold quality
colonic epithelium	UBERON:0000397	78.46	gold quality
apex of heart	UBERON:0002098	78.45	gold quality
right adrenal gland cortex	UBERON:0035827	78.43	gold quality
small intestine Peyer’s patch	UBERON:0003454	78.37	gold quality
stromal cell of endometrium	CL:0002255	78.36	gold quality
ganglionic eminence	UBERON:0004023	78.30	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.28	gold quality
sural nerve	UBERON:0015488	78.09	gold quality
cerebellum	UBERON:0002037	77.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.92	gold quality
transverse colon	UBERON:0001157	77.91	gold quality
small intestine	UBERON:0002108	77.79	gold quality
right ovary	UBERON:0002118	77.60	gold quality
left adrenal gland cortex	UBERON:0035825	77.51	gold quality
right lobe of thyroid gland	UBERON:0001119	77.50	gold quality
left adrenal gland	UBERON:0001234	77.43	gold quality
metanephros cortex	UBERON:0010533	77.32	gold quality
spleen	UBERON:0002106	76.86	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	15.84
E-HCAD-6	no	325.71
E-ANND-3	no	2.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting CCDC142, 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-6876-5P	100.00	67.68	2126
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-4320	99.75	65.80	793
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-1287-3P	99.63	66.93	492
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-6506-5P	99.04	65.66	1386
HSA-MIR-4699-5P	98.99	67.50	1210
HSA-MIR-3149	98.77	67.13	1639
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-619-5P	98.57	64.97	1988

Literature-anchored findings (GeneRIF, showing 1)

• A fragment of the CCDC142-TTC31 intergenic region was cloned;this fragment functions as bidirectional promoter. (PMID:21790010)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc142	ENSDARG00000101377
mus_musculus	Ccdc142	ENSMUSG00000107499
rattus_norvegicus	Ccdc142	ENSRNOG00000058785
drosophila_melanogaster	CG13842	FBGN0039009

Protein

Protein identifiers

Coiled-coil domain-containing protein 142 — Q17RM4 (reviewed: Q17RM4)

All UniProt accessions (2): Q17RM4, H7C450

Isoforms (3)

UniProt ID	Names	Canonical?
Q17RM4-1	1	yes
Q17RM4-2	2
Q17RM4-3	3

RefSeq proteins (2): NP_001352504, NP_116168 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026700	CCDC142	Family
IPR055350	CCDC142_C	Domain
IPR056901	CC142_N	Domain

Pfam: PF14923, PF25081

UniProt features (8 total): region of interest 2, splice variant 2, chain 1, coiled-coil region 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q17RM4-F1	70.05	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): chr2p13, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, ARNT2_TARGET_GENES, CIITA_TARGET_GENES, DIDO1_TARGET_GENES, HOXB4_TARGET_GENES, LHX9_TARGET_GENES, ZNF407_TARGET_GENES, MIR1290, MIR7151_3P, MIR6778_3P, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_DN, MIR504_3P, MIR6856_3P, MIR1281

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

476 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC142	TTC31	Q49AM3	670
CCDC142	C2orf81	A6NN90	592
CCDC142	WDR54	Q9H977	555
CCDC142	DQX1	Q8TE96	500
CCDC142	MRPL53	Q96EL3	475
CCDC142	CCDC192	P0DO97	474
CCDC142	INO80B	Q9C086	465
CCDC142	M1AP	Q8TC57	460
CCDC142	LBX2	Q6XYB7	436
CCDC142	GOLGA8H	P0CJ92	415
CCDC142	POLE4	Q9NR33	413
CCDC142	GOLGA8R	I6L899	400
CCDC142	C16orf78	Q8WTQ4	399
CCDC142	SEMA4F	O95754	381
CCDC142	CLDN18	P56856	348
CCDC142	BRICD5	Q6PL45	348

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CCDC142	HSPA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): CCDC142 (Affinity Capture-RNA), CCDC142 (Affinity Capture-RNA), HSPA8 (Affinity Capture-MS), HSPA1B (Affinity Capture-MS), HSPA1L (Affinity Capture-MS), OMA1 (Affinity Capture-MS), PPP2CA (Affinity Capture-MS), MUL1 (Affinity Capture-MS), CCDC142 (Proximity Label-MS), CCDC142 (Affinity Capture-RNA), CCDC142 (Affinity Capture-MS), CCDC142 (Affinity Capture-RNA)

ESM2 similar proteins: A2A3L6, A5PJC7, A6NCS6, A6NGR9, A8VU90, D2I4M3, E1BDF2, P03972, P27106, P49000, P79295, Q14296, Q17RC7, Q17RM4, Q3MIN7, Q3T0Y9, Q3UK37, Q3UR50, Q3UR97, Q3UV16, Q400G9, Q53GL7, Q58EX7, Q642B3, Q6NUI2, Q6PJG6, Q6ZUA9, Q6ZW31, Q810I0, Q86SX3, Q86XR2, Q8BH06, Q8BP97, Q8CAI1, Q8K4C2, Q8N398, Q8NAC3, Q8NAG6, Q8TE82, Q969T3

Diamond homologs: Q17RM4, Q8CAI1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	111
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1985 predictions. Top by Δscore:

Variant	Effect	Δscore
2:74472330:C:A	donor_gain	1.0000
2:74472333:T:TA	donor_gain	1.0000
2:74472369:T:TA	donor_gain	1.0000
2:74472369:TCC:T	donor_gain	1.0000
2:74472370:C:A	donor_gain	1.0000
2:74472402:T:TA	donor_gain	1.0000
2:74474914:A:AC	donor_gain	1.0000
2:74474915:C:CC	donor_gain	1.0000
2:74474915:CAG:C	donor_gain	1.0000
2:74474931:T:TA	donor_gain	1.0000
2:74474942:TGAG:T	donor_gain	1.0000
2:74475114:GG:G	acceptor_gain	1.0000
2:74475116:C:CC	acceptor_gain	1.0000
2:74475568:ACCC:A	donor_gain	1.0000
2:74475569:CCCC:C	donor_gain	1.0000
2:74475571:C:CA	donor_gain	1.0000
2:74480764:CTCA:C	donor_loss	1.0000
2:74480766:CA:C	donor_loss	1.0000
2:74480768:CCTGG:C	donor_loss	1.0000
2:74480883:C:CC	acceptor_gain	1.0000
2:74480963:T:TA	donor_gain	1.0000
2:74481219:TCAC:T	donor_loss	1.0000
2:74481222:C:CT	donor_loss	1.0000
2:74483320:A:AG	acceptor_gain	1.0000
2:74483321:G:GG	acceptor_gain	1.0000
2:74472342:TCTCC:T	donor_gain	0.9900
2:74472344:TC:T	donor_gain	0.9900
2:74472345:C:CT	donor_gain	0.9900
2:74472557:T:TA	donor_gain	0.9900
2:74472558:C:A	donor_gain	0.9900

AlphaMissense

4737 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:74475227:G:C	F598L	0.995
2:74475227:G:T	F598L	0.995
2:74475229:A:G	F598L	0.995
2:74475228:A:G	F598S	0.994
2:74475262:A:G	W587R	0.991
2:74475262:A:T	W587R	0.991
2:74475087:C:G	D609H	0.986
2:74475662:A:G	F523S	0.985
2:74475095:A:G	L606P	0.982
2:74475631:C:A	W533C	0.982
2:74475631:C:G	W533C	0.982
2:74475086:T:G	D609A	0.981
2:74474626:A:G	W725R	0.978
2:74474626:A:T	W725R	0.978
2:74475086:T:A	D609V	0.977
2:74475379:A:G	Y548H	0.976
2:74475228:A:C	F598C	0.975
2:74475633:A:G	W533R	0.975
2:74475633:A:T	W533R	0.975
2:74474624:C:A	W725C	0.974
2:74474624:C:G	W725C	0.974
2:74475086:T:C	D609G	0.974
2:74475085:G:C	D609E	0.972
2:74475085:G:T	D609E	0.972
2:74475095:A:T	L606H	0.971
2:74475378:T:C	Y548C	0.969
2:74474612:C:A	R729S	0.964
2:74474612:C:G	R729S	0.964
2:74475375:G:T	A549D	0.964
2:74474613:C:A	R729M	0.962

dbSNP variants (sampled 300 via entrez): RS1000023195 (2:74479770 T>A,G), RS1000312320 (2:74480118 G>A), RS1000398231 (2:74477480 A>G), RS1000687841 (2:74479254 C>A,T), RS1000739746 (2:74478880 G>A), RS1000866090 (2:74474445 G>A,C), RS1000870266 (2:74472763 C>G), RS1001365143 (2:74481282 G>A), RS1001761969 (2:74478382 G>A,C), RS1001869294 (2:74476152 T>C), RS1002032833 (2:74472963 C>G,T), RS1002085195 (2:74472777 G>A,C), RS1002335268 (2:74482980 T>C), RS1002757495 (2:74477961 G>A), RS1002936676 (2:74484341 G>A,T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	2
Cyclosporine	decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Leflunomide	decreases expression	1
Cannabidiol	decreases expression	1
Catechin	affects cotreatment, decreases expression	1
Diazinon	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1
Sodium Selenite	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1
Particulate Matter	increases methylation	1

Clinical trials (associated diseases)

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