CCDC42

Summary

CCDC42 (coiled-coil domain containing 42, HGNC:26528) is a protein-coding gene on chromosome 17p13.1, encoding Coiled-coil domain-containing protein 42 (Q96M95). Essential for male fertility.

Predicted to be involved in spermatid development. Predicted to act upstream of or within acrosome assembly; centrosome cycle; and cilium assembly. Predicted to be located in several cellular components, including microtubule cytoskeleton; sperm head-tail coupling apparatus; and sperm principal piece.

Source: NCBI Gene 146849 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 51 total
• MANE Select transcript: NM_144681

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26528
Approved symbol	CCDC42
Name	coiled-coil domain containing 42
Location	17p13.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32734, CCDC42A
Ensembl gene	ENSG00000161973
Ensembl biotype	protein_coding
Entrez	146849

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000293845, ENST00000539522, ENST00000581598, ENST00000857512, ENST00000857513

RefSeq mRNA: 2 — MANE Select: NM_144681 NM_001158261, NM_144681

CCDS: CCDS11145, CCDS54088

Canonical transcript exons

ENST00000293845 — 7 exons

Exon	Start	End
ENSE00001061740	8743626	8743730
ENSE00001061741	8741474	8741671
ENSE00001061742	8744079	8744184
ENSE00001061744	8735390	8735611
ENSE00001061745	8735096	8735254
ENSE00001104353	8729935	8730207
ENSE00001231184	8744527	8744836

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 95.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4873 / max 586.8616, expressed in 5 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164449	0.4683	5
208058	0.0190	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	95.98	gold quality
right testis	UBERON:0004534	95.55	gold quality
testis	UBERON:0000473	93.06	gold quality
adult organism	UBERON:0007023	90.49	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.38	gold quality
sperm	CL:0000019	86.64	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	67.34	gold quality
ascending aorta	UBERON:0001496	64.33	gold quality
thoracic aorta	UBERON:0001515	64.04	gold quality
tibialis anterior	UBERON:0001385	62.91	silver quality
right coronary artery	UBERON:0001625	61.91	gold quality
granulocyte	CL:0000094	61.54	gold quality
descending thoracic aorta	UBERON:0002345	60.70	gold quality
ileal mucosa	UBERON:0000331	58.26	silver quality
pancreatic ductal cell	CL:0002079	57.01	silver quality
aorta	UBERON:0000947	56.43	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
epithelial cell of pancreas	CL:0000083	54.29	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
coronary artery	UBERON:0001621	54.01	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
left coronary artery	UBERON:0001626	53.87	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
jejunal mucosa	UBERON:0000399	53.06	gold quality
deltoid	UBERON:0001476	51.99	gold quality
popliteal artery	UBERON:0002250	50.87	gold quality
tibial artery	UBERON:0007610	50.84	gold quality
myocardium	UBERON:0002349	50.25	gold quality
skin of hip	UBERON:0001554	49.60	silver quality
biceps brachii	UBERON:0001507	48.11	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting CCDC42, 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-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-625-5P	99.02	68.64	2031
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-5000-3P	98.79	65.63	1251
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-4436A	98.05	64.83	1140
HSA-MIR-12128	96.67	66.98	1471

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc42	ENSMUSG00000045915
rattus_norvegicus	Ccdc42	ENSRNOG00000004075

Paralogs (3): CFAP100 (ENSG00000163885), CCDC38 (ENSG00000165972), CFAP73 (ENSG00000186710)

Protein

Protein identifiers

Coiled-coil domain-containing protein 42 — Q96M95 (reviewed: Q96M95)

All UniProt accessions (2): Q96M95, J3KSK0

UniProt curated annotations — full annotation on UniProt →

Function. Essential for male fertility. Required for sperm development.

Subunit / interactions. Interacts with ODF1 and ODF2. Interacts with CCDC38. Interacts with CCDC146. Interacts with CFAP53.

Subcellular location. Cytoplasm. Perinuclear region. Cytoskeleton. Cell projection. Cilium. Flagellum. Microtubule organizing center. Centrosome.

Similarity. Belongs to the CFAP73 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96M95-1	1	yes
Q96M95-2	2

RefSeq proteins (2): NP_001151733, NP_653282* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025252	DUF4200	Domain
IPR051147	CFAP_domain-containing	Family

Pfam: PF13863

UniProt features (8 total): sequence variant 3, coiled-coil region 2, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96M95-F1	87.54	0.67

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): GOBP_VESICLE_ORGANIZATION, GOBP_MALE_GAMETE_GENERATION, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_SECRETORY_GRANULE_ORGANIZATION, GOBP_CELLULAR_COMPONENT_ASSEMBLY_INVOLVED_IN_MORPHOGENESIS, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, GOBP_ACROSOME_ASSEMBLY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_CELL_PROJECTION_ORGANIZATION, GOCC_MOTILE_CILIUM, GOCC_SPERM_PRINCIPAL_PIECE

GO Biological Process (6): acrosome assembly (GO:0001675), centrosome cycle (GO:0007098), spermatid development (GO:0007286), cilium assembly (GO:0060271), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

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

GO Cellular Component (10): manchette (GO:0002177), centrosome (GO:0005813), perinuclear region of cytoplasm (GO:0048471), sperm principal piece (GO:0097228), sperm head-tail coupling apparatus (GO:0120212), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
developmental process involved in reproduction	2
organelle assembly	2
spermatid development	1
cellular component assembly involved in morphogenesis	1
cellular process involved in reproduction in multicellular organism	1
secretory granule organization	1
cell cycle process	1
microtubule organizing center organization	1
germ cell development	1
spermatid differentiation	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
male gamete generation	1
cellular developmental process	1
binding	1
microtubule cytoskeleton	1
centriole	1
microtubule organizing center	1
cytoplasm	1
sperm flagellum	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

532 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC42	CCDC38	Q502W7	791
CCDC42	ODF1	Q14990	770
CCDC42	CNTROB	Q8N137	641
CCDC42	ODF2	Q5BJF6	598
CCDC42	OAZ3	Q9UMX2	593
CCDC42	IFT88	Q13099	572
CCDC42	CEP131	Q9UPN4	560
CCDC42	SUN5	Q8TC36	552
CCDC42	CFAP100	Q494V2	518
CCDC42	TENT5C	Q5VWP2	500
CCDC42	CCDC40	Q4G0X9	493
CCDC42	CCDC39	Q9UFE4	485
CCDC42	TSSK6	Q9BXA6	464
CCDC42	CCDC70	Q6NSX1	455
CCDC42	CCDC182	A6NF36	439

IntAct

15 interactions, top by confidence:

A	B	Type	Score
CCDC42	TFIP11	psi-mi:“MI:0915”(physical association)	0.670
TFIP11	CCDC42	psi-mi:“MI:0915”(physical association)	0.670
MID2	CCDC42	psi-mi:“MI:0915”(physical association)	0.560
CCDC42	MID2	psi-mi:“MI:0915”(physical association)	0.560
CCDC42	KRT18	psi-mi:“MI:0915”(physical association)	0.400
CCDC42	MYH9	psi-mi:“MI:0915”(physical association)	0.400
MID2	CCDC42	psi-mi:“MI:0915”(physical association)	0.370
TSC22D4	CCDC42	psi-mi:“MI:0915”(physical association)	0.370
TTI1	HERC1	psi-mi:“MI:0914”(association)	0.350
TTI1	POTEF	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): CCDC42 (Two-hybrid), CCDC42 (Two-hybrid), CCDC42 (Two-hybrid), TFIP11 (Two-hybrid), CCDC42 (Two-hybrid), CCDC42 (Two-hybrid), CCDC42 (Proximity Label-MS), CCDC42 (Proximity Label-MS), CCDC42 (Affinity Capture-MS), CCDC42 (Affinity Capture-MS), CCDC42 (Proximity Label-MS), MYH9 (Cross-Linking-MS (XL-MS)), EEA1 (Cross-Linking-MS (XL-MS)), CCDC42 (Affinity Capture-MS)

ESM2 similar proteins: A2AJB1, A5D8V7, A6QQM8, A7MBH5, A7S8T5, A8E4X8, B0BMJ2, B1H228, D3Z5T1, D6REC4, O60826, P86182, Q1RMI8, Q2M329, Q32KY1, Q32LK9, Q3UX62, Q494V2, Q4R8V8, Q4V8F7, Q4V909, Q571B6, Q5JU67, Q5SPX1, Q5SV66, Q5T5N4, Q5T5S1, Q5XI03, Q5XI65, Q62036, Q6NTM6, Q6NVC9, Q7T0Y4, Q80VN0, Q8BSN3, Q8BVV7, Q8CDV6, Q8N9B5, Q8NA47, Q8TF30

Diamond homologs: A6NFT4, A6QQM8, A7S8T5, A9UQN0, B0BMJ2, J3QPZ5, Q5SV66, Q6NTM6, Q96M95, Q3KPZ2, M1V4Y8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

880 predictions. Top by Δscore:

Variant	Effect	Δscore
17:8735090:TCCTA:T	donor_loss	1.0000
17:8735092:CTAC:C	donor_loss	1.0000
17:8735093:TACC:T	donor_loss	1.0000
17:8735094:A:AC	donor_gain	1.0000
17:8735094:ACCAT:A	donor_loss	1.0000
17:8735095:C:CC	donor_gain	1.0000
17:8735095:CCA:C	donor_loss	1.0000
17:8735142:T:TA	donor_gain	1.0000
17:8741470:TCA:T	donor_loss	1.0000
17:8741471:CACC:C	donor_loss	1.0000
17:8741472:ACCTC:A	donor_loss	1.0000
17:8741473:C:CG	donor_loss	1.0000
17:8741473:CCT:C	donor_gain	1.0000
17:8741669:CTC:C	acceptor_gain	1.0000
17:8741671:CCTG:C	acceptor_loss	1.0000
17:8741672:C:CC	acceptor_gain	1.0000
17:8741672:CTGGG:C	acceptor_loss	1.0000
17:8741673:T:G	acceptor_loss	1.0000
17:8741680:C:CT	acceptor_gain	1.0000
17:8741680:C:T	acceptor_gain	1.0000
17:8743646:T:TA	donor_gain	1.0000
17:8743728:CAT:C	acceptor_gain	1.0000
17:8743731:C:CC	acceptor_gain	1.0000
17:8743732:T:C	acceptor_gain	1.0000
17:8743733:T:C	acceptor_gain	1.0000
17:8743738:G:C	acceptor_gain	1.0000
17:8743738:G:GC	acceptor_gain	1.0000
17:8744519:ACACT:A	donor_loss	1.0000
17:8744520:CACTC:C	donor_loss	1.0000
17:8744521:ACTC:A	donor_loss	1.0000

AlphaMissense

2113 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:8735609:G:C	F165L	0.962
17:8735609:G:T	F165L	0.962
17:8735611:A:G	F165L	0.962
17:8735185:C:G	A262P	0.944
17:8735413:C:G	A231P	0.938
17:8735224:C:G	A249P	0.926
17:8735172:A:G	L266P	0.924
17:8735168:G:C	F267L	0.916
17:8735168:G:T	F267L	0.916
17:8735170:A:G	F267L	0.916
17:8741510:G:C	F152L	0.916
17:8741510:G:T	F152L	0.916
17:8741512:A:G	F152L	0.916
17:8735245:A:G	W242R	0.911
17:8735245:A:T	W242R	0.911
17:8735433:A:G	L224P	0.911
17:8735583:C:G	R174P	0.911
17:8735221:C:G	A250P	0.907
17:8730196:A:C	F295L	0.903
17:8730196:A:T	F295L	0.903
17:8730198:A:G	F295L	0.903
17:8735550:A:G	L185P	0.893
17:8735251:A:G	S240P	0.879
17:8735103:A:G	L289P	0.875
17:8741499:A:G	L156P	0.868
17:8735105:C:A	Q288H	0.863
17:8735105:C:G	Q288H	0.863
17:8735232:T:G	Q246P	0.858
17:8735243:C:A	W242C	0.857
17:8735243:C:G	W242C	0.857

dbSNP variants (sampled 300 via entrez): RS1000518264 (17:8731993 T>C), RS1001103404 (17:8736868 G>A), RS1001270575 (17:8742260 G>A), RS1001317078 (17:8730631 C>T), RS1001516177 (17:8734997 G>T), RS1002201615 (17:8745006 G>C), RS1002548265 (17:8729885 C>A), RS1002621730 (17:8730151 T>C), RS1002637952 (17:8745391 G>T), RS1002654630 (17:8730381 C>G,T), RS1002919963 (17:8733599 T>C), RS1002927762 (17:8736171 C>T), RS1003026976 (17:8742065 A>C), RS1003248561 (17:8746285 C>G,T), RS1003261018 (17:8740380 C>A,G,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

2 associations (top):

Study	Trait	p-value
GCST003878_5	Heroin dependence	3.000000e-07
GCST006484_16	Type 2 diabetes	6.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
benzo(e)pyrene	increases methylation	1
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Methapyrilene	increases methylation	1
Silicon Dioxide	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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