CCDC124

Summary

CCDC124 (coiled-coil domain containing 124, HGNC:25171) is a protein-coding gene on chromosome 19p13.11, encoding Coiled-coil domain-containing protein 124 (Q96CT7). Ribosome-binding protein involved in ribosome hibernation: associates with translationally inactive ribosomes and stabilizes the nonrotated conformation of the 80S ribosome, thereby promoting ribosome preservation and storage.

Enables RNA binding activity. Predicted to be involved in transcription by RNA polymerase II. Located in cytosol and plasma membrane.

Source: NCBI Gene 115098 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_001136203

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25171
Approved symbol	CCDC124
Name	coiled-coil domain containing 124
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	Lso2, oxs1
Ensembl gene	ENSG00000007080
Ensembl biotype	protein_coding
OMIM	621286
Entrez	115098

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 21 protein_coding, 1 retained_intron

ENST00000445755, ENST00000596123, ENST00000597436, ENST00000602080, ENST00000873323, ENST00000873324, ENST00000873325, ENST00000873326, ENST00000873327, ENST00000926054, ENST00000926055, ENST00000926056, ENST00000926057, ENST00000926058, ENST00000926059, ENST00000926060, ENST00000926061, ENST00000926062, ENST00000926063, ENST00000926064, ENST00000926065, ENST00000944720

RefSeq mRNA: 2 — MANE Select: NM_001136203 NM_001136203, NM_138442

CCDS: CCDS12369

Canonical transcript exons

ENST00000445755 — 5 exons

Exon	Start	End
ENSE00000689900	17943261	17943375
ENSE00001056262	17942656	17942845
ENSE00001658662	17936410	17936579
ENSE00001765913	17933015	17933048
ENSE00003035563	17943508	17943985

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 97.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.4647 / max 209.8827, expressed in 1821 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174563	32.5623	1821
174564	1.9024	1081

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
anterior cingulate cortex	UBERON:0009835	97.45	gold quality
gastrocnemius	UBERON:0001388	97.35	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.27	gold quality
lower esophagus	UBERON:0013473	97.26	gold quality
right frontal lobe	UBERON:0002810	97.20	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	96.99	gold quality
apex of heart	UBERON:0002098	96.96	gold quality
muscle layer of sigmoid colon	UBERON:0035805	96.90	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.88	gold quality
right atrium auricular region	UBERON:0006631	96.78	gold quality
left coronary artery	UBERON:0001626	96.77	gold quality
lower esophagus mucosa	UBERON:0035834	96.77	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.76	gold quality
prefrontal cortex	UBERON:0000451	96.64	gold quality
muscle of leg	UBERON:0001383	96.60	gold quality
mucosa of transverse colon	UBERON:0004991	96.51	gold quality
popliteal artery	UBERON:0002250	96.50	gold quality
tibial artery	UBERON:0007610	96.49	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.47	gold quality
ascending aorta	UBERON:0001496	96.34	gold quality
aorta	UBERON:0000947	96.32	gold quality
thoracic aorta	UBERON:0001515	96.30	gold quality
coronary artery	UBERON:0001621	96.15	gold quality
amygdala	UBERON:0001876	96.10	gold quality
right coronary artery	UBERON:0001625	96.08	gold quality
skin of leg	UBERON:0001511	96.02	gold quality
hypothalamus	UBERON:0001898	95.90	gold quality
mucosa of stomach	UBERON:0001199	95.89	gold quality
ectocervix	UBERON:0012249	95.82	gold quality
esophagus	UBERON:0001043	95.79	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.17
E-MTAB-7303	no	492.84

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting CCDC124, 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-138-5P	98.43	70.49	1292
HSA-MIR-3661	97.83	67.30	705
HSA-MIR-10398-5P	97.12	64.94	1051

Literature-anchored findings (GeneRIF, showing 5)

• Ccdc124 is a novel factor operating both for proper progression of late cytokinetic stages in eukaryotes. (PMID:23894443)
• Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. (PMID:32687489)
• Coiled-coil domain-containing protein-124 (Ccdc124) is a novel RNA binding factor up-regulated in endometrial, ovarian, and urinary bladder cancers. (PMID:33896821)
• Dimerization underlies the aggregation propensity of intrinsically disordered coiled-coil domain-containing 124. (PMID:34369007)
• Live Cell Protein Imaging of Tandem Complemented-GFP11-Tagged Coiled-Coil Domain-Containing Protein-124 Identifies this Factor in G3BP1-Induced Stress-Granules. (PMID:39009911)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc124	ENSDARG00000043502
mus_musculus	Ccdc124	ENSMUSG00000007721
rattus_norvegicus	Ccdc124	ENSRNOG00000018932
drosophila_melanogaster	CG6013	FBGN0038675
caenorhabditis_elegans	Y73E7A.1	WBGENE00022268

Protein

Protein identifiers

Coiled-coil domain-containing protein 124 — Q96CT7 (reviewed: Q96CT7)

All UniProt accessions (2): Q96CT7, M0R2F5

UniProt curated annotations — full annotation on UniProt →

Function. Ribosome-binding protein involved in ribosome hibernation: associates with translationally inactive ribosomes and stabilizes the nonrotated conformation of the 80S ribosome, thereby promoting ribosome preservation and storage. Also required for proper progression of late cytokinetic stages.

Subunit / interactions. Associates with translationally inactive ribosomes in the nonrotated state. Interacts with RASGEF1B.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Midbody.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the CCDC124 family.

RefSeq proteins (2): NP_001129675, NP_612451 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010422	Ccdc124/Oxs1	Family
IPR054414	Ccdc124/Oxs1_C	Domain

Pfam: PF06244

UniProt features (9 total): region of interest 2, compositionally biased region 2, modified residue 2, chain 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

7 structures.

PDB	Method	Resolution (Å)
8K2C	ELECTRON MICROSCOPY	2.4
6ZM7	ELECTRON MICROSCOPY	2.7
9P9H	ELECTRON MICROSCOPY	2.84
6Z6L	ELECTRON MICROSCOPY	3
6ZME	ELECTRON MICROSCOPY	3
8XSY	ELECTRON MICROSCOPY	3
9B0J

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96CT7-F1	80.59	0.33

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 141, 194

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): GOCC_MICROTUBULE_ORGANIZING_CENTER, GOCC_CENTROSOME, GOBP_CELL_DIVISION, GOCC_MIDBODY, chr19p13, GOMF_TRANSCRIPTION_COACTIVATOR_ACTIVITY, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, BRUINS_UVC_RESPONSE_EARLY_LATE, DELACROIX_RARG_BOUND_MEF, GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY, MYC_UP.V1_UP, CAMP_UP.V1_UP, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GSE14415_ACT_TCONV_VS_ACT_NATURAL_TREG_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY

GO Biological Process (3): transcription by RNA polymerase II (GO:0006366), cell division (GO:0051301), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (3): transcription coactivator activity (GO:0003713), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (7): nucleus (GO:0005634), centrosome (GO:0005813), cytosol (GO:0005829), plasma membrane (GO:0005886), midbody (GO:0030496), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
DNA-templated transcription	2
cellular process	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
transcription coregulator activity	1
positive regulation of DNA-templated transcription	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
centriole	1
microtubule organizing center	1
cytoplasm	1
membrane	1
cell periphery	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1381 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC124	C5orf34	Q96MH7	749
CCDC124	HAAO	P46952	669
CCDC124	COPS8	Q99627	665
CCDC124	IFRD2	Q12894	508
CCDC124	RDH12	Q96NR8	506
CCDC124	SERBP1	Q8NC51	490
CCDC124	C19orf53	Q9UNZ5	481
CCDC124	PPIAL4D	F5H284	466
CCDC124	EML3	Q32P44	459
CCDC124	PIK3R5	Q8WYR1	449
CCDC124	CCDC77	Q9BR77	441
CCDC124	TRIM64B	A6NI03	434
CCDC124	AURKAIP1	Q9NWT8	432
CCDC124	P4HB	P07237	428
CCDC124	EIF3J	O75822	426

IntAct

92 interactions, top by confidence:

A	B	Type	Score
NPM1	CCDC124	psi-mi:“MI:0403”(colocalization)	0.650
CCDC124	NPM1	psi-mi:“MI:0914”(association)	0.650
NPM1	CCDC124	psi-mi:“MI:0915”(physical association)	0.650
ABCE1	EIF3H	psi-mi:“MI:0914”(association)	0.530
CHLSN	RPL14	psi-mi:“MI:0914”(association)	0.530
CCDC124	MYH9	psi-mi:“MI:0915”(physical association)	0.400
CCDC124	H1-1	psi-mi:“MI:0915”(physical association)	0.400
CCDC124	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
CD81	HIP1R	psi-mi:“MI:0914”(association)	0.350
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
Bcas2	PEX10	psi-mi:“MI:0914”(association)	0.350
Pcgf1	SCAMP3	psi-mi:“MI:0914”(association)	0.350
RPL10	RPS6	psi-mi:“MI:0914”(association)	0.350
BCOR	HSPD1	psi-mi:“MI:0914”(association)	0.350
Srp72		psi-mi:“MI:0914”(association)	0.350
Rrbp1	PIPSL	psi-mi:“MI:0914”(association)	0.350
NOP56	C12orf43	psi-mi:“MI:0914”(association)	0.350
XRCC3	DERL1	psi-mi:“MI:0914”(association)	0.350
EMC2	TBL2	psi-mi:“MI:0914”(association)	0.350
MMGT1	DERL1	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
NP	HNRNPAB	psi-mi:“MI:0914”(association)	0.350
BCAR1	MYO1C	psi-mi:“MI:0914”(association)	0.350
DLD	NFKBIE	psi-mi:“MI:0914”(association)	0.350
MAPT	MEX3A	psi-mi:“MI:0914”(association)	0.350
MAPT	C11orf98	psi-mi:“MI:0914”(association)	0.350
MAPT	POTEF	psi-mi:“MI:0914”(association)	0.350

BioGRID (148): CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Proximity Label-MS), CCDC124 (Proximity Label-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS), CCDC124 (Affinity Capture-MS)

ESM2 similar proteins: A5JSS4, B1MTI8, O88892, P02641, P06398, P09739, P0C0A9, P12620, P45378, P84101, P84102, Q05310, Q0UVD1, Q148I0, Q1E554, Q28HN4, Q28IN9, Q2KIT1, Q2TBR9, Q2TBV6, Q32P76, Q3E7B7, Q4I5Z5, Q5R5J3, Q5R6N0, Q5R7C4, Q5R8X8, Q5REM2, Q5ZHK9, Q68EY7, Q6DD17, Q6GNG8, Q6NVR5, Q6PHE8, Q75NG9, Q7SDA6, Q7ZY35, Q8MKI3, Q8NHG7, Q8R1F0

Diamond homologs: O94389, Q28HN4, Q2TBV6, Q54GW3, Q5R8X8, Q68EY7, Q6DD17, Q6PHE8, Q96CT7, Q9D8X2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 117 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
SRP-dependent cotranslational protein targeting to membrane	16	19.1×	6e-14
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	12	17.9×	2e-10
Formation of a pool of free 40S subunits	13	17.3×	1e-10
Peptide chain elongation	11	16.6×	3e-09
Viral mRNA Translation	11	16.6×	3e-09
Selenocysteine synthesis	11	15.7×	4e-09
Eukaryotic Translation Termination	11	15.7×	4e-09
L13a-mediated translational silencing of Ceruloplasmin expression	13	15.6×	2e-10

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	13	23.8×	6e-12
translational initiation	5	17.8×	1e-03
ribosomal small subunit biogenesis	7	15.8×	8e-05
translation	13	13.2×	7e-09
rRNA processing	7	9.8×	1e-03

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	43
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

863 predictions. Top by Δscore:

Variant	Effect	Δscore
19:17936408:A:AG	acceptor_gain	1.0000
19:17936409:G:GG	acceptor_gain	1.0000
19:17936409:GCCT:G	acceptor_gain	1.0000
19:17936564:G:GT	donor_gain	1.0000
19:17936580:G:GG	donor_gain	1.0000
19:17942654:A:AG	acceptor_gain	1.0000
19:17942654:AGGAG:A	acceptor_gain	1.0000
19:17942655:G:GT	acceptor_gain	1.0000
19:17942655:GGA:G	acceptor_gain	1.0000
19:17942655:GGAGG:G	acceptor_gain	1.0000
19:17942824:C:G	donor_gain	1.0000
19:17942829:G:GT	donor_gain	1.0000
19:17942830:G:GT	donor_gain	1.0000
19:17942830:G:T	donor_gain	1.0000
19:17942899:GACCT:G	donor_gain	1.0000
19:17943233:T:TA	acceptor_gain	1.0000
19:17943239:T:TA	acceptor_gain	1.0000
19:17943243:A:AG	acceptor_gain	1.0000
19:17943244:C:G	acceptor_gain	1.0000
19:17943247:A:AG	acceptor_gain	1.0000
19:17943248:C:G	acceptor_gain	1.0000
19:17943251:A:AG	acceptor_gain	1.0000
19:17943251:ACCC:A	acceptor_gain	1.0000
19:17943252:C:G	acceptor_gain	1.0000
19:17943254:C:CA	acceptor_gain	1.0000
19:17943256:CCCA:C	acceptor_loss	1.0000
19:17943258:CA:C	acceptor_loss	1.0000
19:17943259:A:AC	acceptor_loss	1.0000
19:17943259:A:AG	acceptor_gain	1.0000
19:17943259:AGCC:A	acceptor_gain	1.0000

AlphaMissense

1461 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:17943630:T:C	L196P	0.999
19:17943653:T:A	W204R	0.999
19:17943653:T:C	W204R	0.999
19:17936453:G:C	K11N	0.998
19:17936453:G:T	K11N	0.998
19:17943359:G:C	A150P	0.998
19:17943598:A:C	K185N	0.998
19:17943598:A:T	K185N	0.998
19:17943655:G:C	W204C	0.998
19:17943655:G:T	W204C	0.998
19:17936575:G:C	R52P	0.997
19:17943360:C:A	A150D	0.997
19:17943363:T:A	I151N	0.997
19:17943569:T:C	F176L	0.997
19:17943571:T:A	F176L	0.997
19:17943571:T:G	F176L	0.997
19:17943642:T:C	L200P	0.997
19:17943654:G:C	W204S	0.997
19:17943673:C:A	N210K	0.997
19:17943673:C:G	N210K	0.997
19:17936447:C:A	N9K	0.996
19:17936447:C:G	N9K	0.996
19:17936451:A:G	K11E	0.996
19:17936464:C:A	A15D	0.996
19:17936469:G:C	A17P	0.996
19:17936535:T:A	W39R	0.996
19:17936535:T:C	W39R	0.996
19:17936537:G:C	W39C	0.996
19:17936537:G:T	W39C	0.996
19:17936574:C:A	R52S	0.996

dbSNP variants (sampled 300 via entrez): RS1000150866 (19:17933451 C>G,T), RS1000286032 (19:17939107 G>A), RS1000347128 (19:17943969 A>G), RS1000471513 (19:17934603 T>C), RS1000478939 (19:17943872 C>T), RS1000686330 (19:17942927 C>A,G), RS1001030424 (19:17938584 T>C), RS1001263430 (19:17935041 A>C), RS1001495123 (19:17940488 C>T), RS1001793598 (19:17938685 G>A,C), RS1001878351 (19:17934927 C>A,G,T), RS1002225188 (19:17932969 T>C), RS1002270708 (19:17933730 A>G), RS1002277506 (19:17933088 G>A,T), RS1002488638 (19:17941467 G>A)

Disease associations

OMIM: gene MIM:621286 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST90002385_505	High light scatter reticulocyte count	6.000000e-13
GCST90002385_506	High light scatter reticulocyte count	3.000000e-11
GCST90002386_201	High light scatter reticulocyte percentage of red cells	4.000000e-11
GCST90002386_75	High light scatter reticulocyte percentage of red cells	1.000000e-12
GCST90002387_48	Immature fraction of reticulocytes	1.000000e-14

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count

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
sodium arsenite	decreases expression, increases expression	3
bisphenol A	decreases methylation, increases expression	2
Caffeine	decreases phosphorylation, increases expression	2
Valproic Acid	increases expression, increases methylation	2
Particulate Matter	increases abundance, decreases expression, decreases reaction	2
aristolochic acid I	increases expression	1
bisphenol F	increases expression	1
beauvericin	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression, affects localization, increases expression	1
beta-lapachone	increases expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	decreases expression	1
bisphenol B	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, decreases reaction	1
bisphenol AF	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Vehicle Emissions	decreases expression, decreases reaction	1
Furaldehyde	increases expression, affects cotreatment, decreases expression, affects localization	1
Ivermectin	decreases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Sodium Chloride	affects localization, increases expression, affects cotreatment, decreases expression	1
Dronabinol	increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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