CCDC24

Summary

CCDC24 (coiled-coil domain containing 24, HGNC:28688) is a protein-coding gene on chromosome 1p34.1, encoding Coiled-coil domain-containing protein 24 (Q8N4L8).

Predicted to act upstream of or within blastocyst hatching.

Source: NCBI Gene 149473 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 48 total
• MANE Select transcript: NM_152499

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28688
Approved symbol	CCDC24
Name	coiled-coil domain containing 24
Location	1p34.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC45441
Ensembl gene	ENSG00000159214
Ensembl biotype	protein_coding
Entrez	149473

Gene structure

Transcript identifiers

Ensembl transcripts: 43 — 34 protein_coding, 5 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000372318, ENST00000460543, ENST00000463846, ENST00000466180, ENST00000472562, ENST00000479055, ENST00000485811, ENST00000486064, ENST00000486504, ENST00000490064, ENST00000490563, ENST00000857675, ENST00000857676, ENST00000857677, ENST00000857678, ENST00000857679, ENST00000857680, ENST00000857681, ENST00000857682, ENST00000857683, ENST00000857684, ENST00000857685, ENST00000857686, ENST00000857687, ENST00000857688, ENST00000857689, ENST00000857690, ENST00000912584, ENST00000912585, ENST00000912586, ENST00000912587, ENST00000912588, ENST00000912589, ENST00000912590, ENST00000912591, ENST00000968710, ENST00000968711, ENST00000968712, ENST00000968713, ENST00000968714, ENST00000968715, ENST00000968716, ENST00000968717

RefSeq mRNA: 4 — MANE Select: NM_152499 NM_001349127, NM_001349128, NM_001349129, NM_152499

CCDS: CCDS507

Canonical transcript exons

ENST00000372318 — 9 exons

Exon	Start	End
ENSE00001187563	43992212	43992387
ENSE00001237118	43991599	43991746
ENSE00003468545	43993887	43993964
ENSE00003524624	43992523	43992639
ENSE00003558834	43995938	43996528
ENSE00003703037	43995601	43995670
ENSE00003703108	43995778	43995856
ENSE00003703876	43995108	43995162
ENSE00003709148	43991847	43992004

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 97.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.5312 / max 41.7298, expressed in 1300 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2583	2.5900	1204
2585	0.6881	336
2582	0.2206	72
2584	0.0325	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.34	gold quality
adenohypophysis	UBERON:0002196	93.28	gold quality
pituitary gland	UBERON:0000007	91.83	gold quality
left testis	UBERON:0004533	91.71	gold quality
right testis	UBERON:0004534	91.61	gold quality
pancreatic ductal cell	CL:0002079	90.67	silver quality
right lobe of thyroid gland	UBERON:0001119	90.28	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.14	gold quality
left lobe of thyroid gland	UBERON:0001120	89.60	gold quality
mucosa of transverse colon	UBERON:0004991	88.71	gold quality
thyroid gland	UBERON:0002046	88.64	gold quality
testis	UBERON:0000473	88.56	gold quality
metanephros cortex	UBERON:0010533	88.18	gold quality
right frontal lobe	UBERON:0002810	87.90	gold quality
anterior cingulate cortex	UBERON:0009835	87.55	gold quality
bronchial epithelial cell	CL:0002328	87.16	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.15	gold quality
bronchus	UBERON:0002185	86.28	gold quality
amygdala	UBERON:0001876	86.18	gold quality
hypothalamus	UBERON:0001898	85.98	gold quality
nucleus accumbens	UBERON:0001882	84.60	gold quality
endocervix	UBERON:0000458	84.45	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	84.33	gold quality
right adrenal gland cortex	UBERON:0035827	84.28	gold quality
right adrenal gland	UBERON:0001233	83.93	gold quality
body of pancreas	UBERON:0001150	83.53	gold quality
caudate nucleus	UBERON:0001873	82.84	gold quality
minor salivary gland	UBERON:0001830	82.80	gold quality
left adrenal gland cortex	UBERON:0035825	82.60	gold quality
prefrontal cortex	UBERON:0000451	82.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting CCDC24, 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-4482-3P	99.98	72.50	3147
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-6507-3P	99.35	67.32	1059
HSA-MIR-593-3P	99.22	67.28	1327
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-6731-3P	98.61	67.86	749
HSA-MIR-4421	97.99	64.89	701
HSA-MIR-5699-3P	97.81	65.00	861
HSA-MIR-3921	97.81	67.45	1431
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-4726-5P	97.24	65.67	1299
HSA-MIR-4653-5P	97.22	67.72	1429
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-7847-3P	96.63	64.58	952
HSA-MIR-6820-5P	94.04	61.13	161

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc24	ENSDARG00000038793
mus_musculus	Ccdc24	ENSMUSG00000078588
rattus_norvegicus	Ccdc24	ENSRNOG00000019586

Protein

Protein identifiers

Coiled-coil domain-containing protein 24 — Q8N4L8 (reviewed: Q8N4L8)

All UniProt accessions (5): Q8N4L8, V9GY72, V9GYB9, V9GYE2, V9GYM6

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N4L8-1	1	yes
Q8N4L8-2	2

RefSeq proteins (4): NP_001336056, NP_001336057, NP_001336058, NP_689712* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031367	CCDC24	Family

Pfam: PF15669

UniProt features (7 total): region of interest 2, chain 1, coiled-coil region 1, compositionally biased region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4L8-F1	67.31	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 41 (showing top): MAZ_Q6, SREBP1_02, PAX8_B, chr1p34, E4F1_Q6, DELASERNA_MYOD_TARGETS_DN, AP2GAMMA_01, AAGCACA_MIR218, MZF1_02, AP2ALPHA_01, HOXB4_TARGET_GENES, ZNF407_TARGET_GENES, ZNF667_TARGET_GENES, PAX8_01, MIR6507_3P

GO Biological Process (1): blastocyst hatching (GO:0001835)

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
blastocyst development	1
hatching	1
binding	1

Protein interactions and networks

STRING

406 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC24	ERI3	O43414	526
CCDC24	C5orf52	A6NGY3	515
CCDC24	ISCA1	Q9BUE6	503
CCDC24	ZNF644	Q9H582	500
CCDC24	WDR89	Q96FK6	499
CCDC24	RNF220	Q5VTB9	497
CCDC24	CFAP97D1	B2RV13	478
CCDC24	TIGD5	Q53EQ6	478
CCDC24	B4GALT2	O60909	471
CCDC24	KLF18	A0A0U1RQI7	451
CCDC24	ANKRD7	Q92527	431
CCDC24	SMIM14	Q96QK8	427
CCDC24	LRRIQ3	A6PVS8	414
CCDC24	ZFP14	Q9HCL3	409
CCDC24	IFT22	Q9H7X7	407

IntAct

124 interactions, top by confidence:

A	B	Type	Score
USHBP1	CCDC24	psi-mi:“MI:0915”(physical association)	0.720
CCDC24	USHBP1	psi-mi:“MI:0915”(physical association)	0.720
CCDC24	GATA1	psi-mi:“MI:0915”(physical association)	0.560
CCDC24	RNF31	psi-mi:“MI:0915”(physical association)	0.560
CDC23	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
GATA1	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
RNF31	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
CCDC24	CDC23	psi-mi:“MI:0915”(physical association)	0.560
CCDC24	KRTAP6-1	psi-mi:“MI:0915”(physical association)	0.560
CCDC24	KRTAP19-7	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-3	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
KRT34	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
MAGEA6	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
TRIP6	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
USP54	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
CCDC24	AKAP8L	psi-mi:“MI:0915”(physical association)	0.560
OIP5	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
TRIM42	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
KRT33B	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
KRTAP19-6	CCDC24	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (40): CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), REN (Two-hybrid), CCDC24 (Affinity Capture-MS), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid), CCDC24 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVZ6, A0A1W2PR82, A0A286YDK6, A2A9F4, A2VE02, A5D7I0, A6H7B4, A6NE82, A6NEV1, A6NJB7, A6NJI1, A6NJJ6, A6QP24, A6QPM6, A8MZG2, D3ZAQ5, D4AAA5, O94850, O95873, P0C7X2, P50617, P70339, Q0P5M0, Q2KIL8, Q2KIS6, Q3UN58, Q3ZCQ2, Q5JPB2, Q5M844, Q5VZ46, Q6AY88, Q6GQX2, Q6NZ36, Q6ZW13, Q76NI1, Q7TNS8, Q80TS7, Q86YN6, Q8C1M2, Q8K2F3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 36 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	9	22.8×	8e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1449 predictions. Top by Δscore:

Variant	Effect	Δscore
1:43991691:G:GT	donor_gain	0.9900
1:43991706:A:T	donor_gain	0.9900
1:43991727:G:T	donor_gain	0.9900
1:43991945:G:GT	donor_gain	0.9900
1:43991956:G:GT	donor_gain	0.9900
1:43992016:G:T	donor_gain	0.9900
1:43995083:T:TA	acceptor_gain	0.9900
1:43995599:A:AG	acceptor_gain	0.9900
1:43995600:G:GG	acceptor_gain	0.9900
1:43995600:GC:G	acceptor_gain	0.9900
1:43995600:GCGCT:G	acceptor_gain	0.9900
1:43995776:A:AG	acceptor_gain	0.9900
1:43995777:G:GG	acceptor_gain	0.9900
1:43995777:GA:G	acceptor_gain	0.9900
1:43995852:CACAG:C	donor_loss	0.9900
1:43995853:ACAG:A	donor_loss	0.9900
1:43995854:CAGG:C	donor_loss	0.9900
1:43995855:AGG:A	donor_loss	0.9900
1:43995856:GGTA:G	donor_loss	0.9900
1:43995857:G:T	donor_loss	0.9900
1:43995858:T:A	donor_loss	0.9900
1:43991950:G:GT	donor_gain	0.9800
1:43991966:G:GT	donor_gain	0.9800
1:43991966:G:T	donor_gain	0.9800
1:43993793:T:TA	acceptor_gain	0.9800
1:43993795:T:TA	acceptor_gain	0.9800
1:43995076:C:A	acceptor_gain	0.9800
1:43995077:G:A	acceptor_gain	0.9800
1:43995668:CAGGT:C	donor_loss	0.9800
1:43995669:AG:A	donor_loss	0.9800

AlphaMissense

1962 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:43992339:T:C	L85P	0.978
1:43992569:T:C	F117L	0.976
1:43992571:T:A	F117L	0.976
1:43992571:T:G	F117L	0.976
1:43991905:G:C	W9C	0.973
1:43991905:G:T	W9C	0.973
1:43992573:C:A	A118D	0.973
1:43991903:T:A	W9R	0.971
1:43991903:T:C	W9R	0.971
1:43991984:A:C	S36R	0.971
1:43991986:C:A	S36R	0.971
1:43991986:C:G	S36R	0.971
1:43995781:T:C	L209P	0.969
1:43995794:G:C	K213N	0.958
1:43995794:G:T	K213N	0.958
1:43993961:T:C	L165P	0.956
1:43991953:G:C	K25N	0.949
1:43991953:G:T	K25N	0.949
1:43992371:G:C	A96P	0.949
1:43992339:T:A	L85H	0.945
1:43992370:A:C	K95N	0.945
1:43992370:A:T	K95N	0.945
1:43992539:T:A	W107R	0.945
1:43992539:T:C	W107R	0.945
1:43991994:T:C	L39P	0.943
1:43992351:T:C	L89P	0.941
1:43992570:T:C	F117S	0.938
1:43991963:G:T	G29W	0.933
1:43991964:G:T	G29V	0.930
1:43992561:T:A	V114D	0.926

dbSNP variants (sampled 300 via entrez): RS1000535126 (1:43995182 C>G), RS1000661808 (1:43989698 C>T), RS1000913421 (1:43992898 A>T), RS1001245835 (1:43992963 T>C), RS1001475089 (1:43994563 C>G,T), RS1001940026 (1:43990585 T>A), RS1002832901 (1:43993293 A>G,T), RS1002992394 (1:43991337 G>A), RS1003350691 (1:43991520 C>A,G,T), RS1003454575 (1:43994819 G>A), RS1005219902 (1:43993728 GGCAGAGCTCATTT>G), RS1005235205 (1:43995103 C>A,T), RS1005484438 (1:43994870 G>A), RS1005822864 (1:43989716 C>T), RS1005830463 (1:43996374 A>G)

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

1 associations (top):

Study	Trait	p-value
GCST004521_235	Autism spectrum disorder or schizophrenia	4.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tunicamycin	decreases expression, increases expression	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment, increases expression	2
triphenyl phosphate	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
ICG 001	affects expression	1
jinfukang	increases expression, affects cotreatment	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Calcitriol	increases expression, affects cotreatment	1
Cisplatin	increases expression, affects cotreatment	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1

Clinical trials (associated diseases)

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