CCDC125

Summary

CCDC125 (coiled-coil domain containing 125, HGNC:28924) is a protein-coding gene on chromosome 5q13.2, encoding Coiled-coil domain-containing protein 125 (Q86Z20). May be involved in the regulation of cell migration.

Enables identical protein binding activity. Involved in activation of GTPase activity; negative regulation of Rho protein signal transduction; and negative regulation of cell motility. Located in cytoplasm.

Source: NCBI Gene 202243 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 88 total — 1 likely-pathogenic
• MANE Select transcript: NM_176816

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28924
Approved symbol	CCDC125
Name	coiled-coil domain containing 125
Location	5q13.2
Locus type	gene with protein product
Status	Approved
Aliases	KENAE
Ensembl gene	ENSG00000183323
Ensembl biotype	protein_coding
OMIM	613781
Entrez	202243

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000383374, ENST00000396496, ENST00000396499, ENST00000460090, ENST00000511257, ENST00000512045, ENST00000513172, ENST00000877999, ENST00000878000, ENST00000878001

RefSeq mRNA: 3 — MANE Select: NM_176816 NM_001297696, NM_001297697, NM_176816

CCDS: CCDS4000, CCDS75255

Canonical transcript exons

ENST00000396496 — 12 exons

Exon	Start	End
ENSE00001293712	69292188	69292362
ENSE00001496533	69332649	69332801
ENSE00001648227	69303847	69303929
ENSE00001658612	69307951	69308028
ENSE00001746787	69306817	69306902
ENSE00002021812	69280175	69283034
ENSE00003533595	69294793	69294900
ENSE00003572217	69285337	69285467
ENSE00003574552	69313985	69314046
ENSE00003579767	69300012	69300127
ENSE00003598255	69320237	69320580
ENSE00003625936	69311118	69311204

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 87.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.0120 / max 54.2742, expressed in 1241 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
62015	3.0120	1241

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	87.78	gold quality
oviduct epithelium	UBERON:0004804	83.36	gold quality
right uterine tube	UBERON:0001302	83.30	gold quality
right lobe of liver	UBERON:0001114	82.52	gold quality
bone marrow	UBERON:0002371	81.14	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	80.88	gold quality
bronchial epithelial cell	CL:0002328	80.72	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.58	gold quality
monocyte	CL:0000576	80.50	gold quality
rectum	UBERON:0001052	80.36	gold quality
leukocyte	CL:0000738	80.20	gold quality
buccal mucosa cell	CL:0002336	80.15	silver quality
calcaneal tendon	UBERON:0003701	79.45	gold quality
bronchus	UBERON:0002185	79.08	gold quality
islet of Langerhans	UBERON:0000006	78.62	gold quality
tendon	UBERON:0000043	78.19	gold quality
mucosa of transverse colon	UBERON:0004991	77.58	gold quality
liver	UBERON:0002107	77.52	gold quality
blood	UBERON:0000178	77.26	gold quality
stromal cell of endometrium	CL:0002255	77.15	gold quality
tendon of biceps brachii	UBERON:0008188	77.12	gold quality
gall bladder	UBERON:0002110	77.09	gold quality
minor salivary gland	UBERON:0001830	76.63	gold quality
lower esophagus mucosa	UBERON:0035834	76.20	gold quality
body of pancreas	UBERON:0001150	76.05	gold quality
fallopian tube	UBERON:0003889	75.92	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.81	gold quality
prostate gland	UBERON:0002367	75.74	gold quality
pancreas	UBERON:0001264	75.72	gold quality
right adrenal gland	UBERON:0001233	75.18	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

60 targeting CCDC125, 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-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-106A-3P	99.53	67.58	995

Literature-anchored findings (GeneRIF, showing 1)

• These results suggest that the novel gene, Kenae/CCDC125, acts as a regulator of cell motility through RhoA, Rac1 and cdc42. (PMID:19787194)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc125	ENSMUSG00000048924
rattus_norvegicus	Ccdc125	ENSRNOG00000027410

Protein

Protein identifiers

Coiled-coil domain-containing protein 125 — Q86Z20 (reviewed: Q86Z20)

Alternative names: Protein kenae

All UniProt accessions (2): Q86Z20, F8W912

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the regulation of cell migration.

Subcellular location. Cytoplasm.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86Z20-1	1, Kenae-1	yes
Q86Z20-2	2, Kenae-2

RefSeq proteins (3): NP_001284625, NP_001284626, NP_789786* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR034608	CCDC125	Family

UniProt features (10 total): compositionally biased region 3, coiled-coil region 2, chain 1, region of interest 1, modified residue 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86Z20-F1	67.24	0.32

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 (1): 504

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 100 (showing top): GOBP_ACTIVATION_OF_GTPASE_ACTIVITY, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, TAL1ALPHAE47_01, GOBP_NEGATIVE_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, GOBP_NEGATIVE_REGULATION_OF_RHO_PROTEIN_SIGNAL_TRANSDUCTION, GOBP_REGULATION_OF_RHO_PROTEIN_SIGNAL_TRANSDUCTION, BROWN_MYELOID_CELL_DEVELOPMENT_UP, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, ZHAN_MULTIPLE_MYELOMA_CD1_DN

GO Biological Process (4): negative regulation of Rho protein signal transduction (GO:0035024), activation of GTPase activity (GO:0090630), negative regulation of cell motility (GO:2000146), regulation of cell motility (GO:2000145)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell motility	2
Rho protein signal transduction	1
regulation of Rho protein signal transduction	1
negative regulation of small GTPase mediated signal transduction	1
positive regulation of GTPase activity	1
negative regulation of locomotion	1
negative regulation of cellular process	1
regulation of cell motility	1
regulation of locomotion	1
regulation of cellular process	1
protein binding	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC125	CCDC74B	Q96LY2	624
CCDC125	CFAP184	Q2M329	614
CCDC125	CFAP263	Q9H0I3	540
CCDC125	CCDC70	Q6NSX1	537
CCDC125	CCDC92	Q53HC0	526
CCDC125	C9orf153	Q5TBE3	514
CCDC125	BICDL1	Q6ZP65	485
CCDC125	RASL11B	Q9BPW5	454
CCDC125	TACC1	O75410	443
CCDC125	CCDC169	A6NNP5	435
CCDC125	CCDC190	Q86UF4	431
CCDC125	POLR2B	P30876	421
CCDC125	TLCD2	A6NGC4	415
CCDC125	CCDC42	Q96M95	412
CCDC125	TXNDC15	Q96J42	408

IntAct

198 interactions, top by confidence:

A	B	Type	Score
CCDC125	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	CDC23	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	OTOS	psi-mi:“MI:0915”(physical association)	0.560
ATOSB	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	FAM161B	psi-mi:“MI:0915”(physical association)	0.560
RAB2A	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
ZNF165	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
NEBL	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	ZNF337	psi-mi:“MI:0915”(physical association)	0.560
EIF3D	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
TRIM14	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	ZNF837	psi-mi:“MI:0915”(physical association)	0.560
C21orf58	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	KAT5	psi-mi:“MI:0915”(physical association)	0.560
GEM	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
TSGA10IP	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
ZNF792	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	ZNF587	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	ZNF764	psi-mi:“MI:0915”(physical association)	0.560
TEAD4	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	AIRIM	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	CEP95	psi-mi:“MI:0915”(physical association)	0.560
ZNF883	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	ZNF564	psi-mi:“MI:0915”(physical association)	0.560
CDK18	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
MYH1	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
ZFP1	CCDC125	psi-mi:“MI:0915”(physical association)	0.560
NSMF	CCDC125	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (68): CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid), CCDC125 (Two-hybrid)

ESM2 similar proteins: A0A1W2P884, A2AM05, A2AUM9, A2BGP7, E1U8D0, O94964, P60853, Q05D60, Q0KK56, Q2M243, Q32LC2, Q3UPP8, Q3V036, Q5PQQ9, Q5PQS2, Q5R9L2, Q5SZL2, Q5U3Z6, Q5U465, Q5U4W1, Q5XJA2, Q6AXZ4, Q6AYB8, Q6DIS8, Q6IPM2, Q6NRK1, Q6NRX3, Q6P2H3, Q6P402, Q6PCQ0, Q70YC5, Q7M6Y5, Q86YF9, Q86Z20, Q8BG89, Q8BMD2, Q8BMK0, Q8BVC4, Q8CFC9, Q8CGZ2

Diamond homologs: A2BGP7, Q5U465, Q86Z20

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 66 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
Activation of BAD and translocation to mitochondria	5	100.2×	7e-08
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	5	88.4×	9e-08
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	5	88.4×	9e-08
Activation of BH3-only proteins	5	65.3×	3e-07
RHO GTPases activate PKNs	5	41.7×	3e-06
Intrinsic Pathway for Apoptosis	5	38.5×	4e-06
SARS-CoV-1-host interactions	5	23.1×	4e-05
Apoptosis	5	22.1×	4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	64
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
563075	GRCh37/hg19 5q12.3-13.2(chr5:65315606-68755816)x1	Likely pathogenic

SpliceAI

3018 predictions. Top by Δscore:

Variant	Effect	Δscore
5:69282889:CG:C	donor_gain	1.0000
5:69283030:TTAAG:T	acceptor_gain	1.0000
5:69283031:TAAG:T	acceptor_gain	1.0000
5:69283032:AAG:A	acceptor_gain	1.0000
5:69283033:AG:A	acceptor_gain	1.0000
5:69283034:GC:G	acceptor_loss	1.0000
5:69283035:C:A	acceptor_loss	1.0000
5:69283035:C:CC	acceptor_gain	1.0000
5:69283036:T:G	acceptor_loss	1.0000
5:69283038:CA:C	acceptor_gain	1.0000
5:69283039:A:AC	acceptor_gain	1.0000
5:69283039:A:C	acceptor_gain	1.0000
5:69283044:C:CT	acceptor_gain	1.0000
5:69283045:A:T	acceptor_gain	1.0000
5:69300123:CAAAA:C	acceptor_gain	1.0000
5:69300128:C:CC	acceptor_gain	1.0000
5:69313878:C:CT	acceptor_gain	1.0000
5:69320577:CTGT:C	acceptor_gain	1.0000
5:69320581:C:CC	acceptor_gain	1.0000
5:69282888:A:AC	donor_gain	0.9900
5:69282888:ACG:A	donor_gain	0.9900
5:69282889:C:CC	donor_gain	0.9900
5:69282889:CGC:C	donor_gain	0.9900
5:69283042:C:CT	acceptor_gain	0.9900
5:69292369:T:C	acceptor_gain	0.9900
5:69292369:T:TC	acceptor_gain	0.9900
5:69294794:T:TA	donor_gain	0.9900
5:69300008:CTA:C	donor_loss	0.9900
5:69300010:A:AG	donor_loss	0.9900
5:69300011:CCTC:C	donor_loss	0.9900

AlphaMissense

3430 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:69292309:G:C	F326L	0.990
5:69292309:G:T	F326L	0.990
5:69292311:A:G	F326L	0.990
5:69282990:G:C	S425R	0.989
5:69282990:G:T	S425R	0.989
5:69282992:T:G	S425R	0.989
5:69292297:A:C	F330L	0.986
5:69292297:A:T	F330L	0.986
5:69292299:A:G	F330L	0.986
5:69292332:C:G	A319P	0.985
5:69283016:C:G	A417P	0.983
5:69292314:C:G	A325P	0.983
5:69294852:A:G	C289R	0.982
5:69282999:T:A	R422S	0.981
5:69282999:T:G	R422S	0.981
5:69294850:A:C	C289W	0.980
5:69311141:C:G	A144P	0.980
5:69311179:A:G	L131P	0.980
5:69282980:C:G	A429P	0.979
5:69292320:C:G	A323P	0.979
5:69282982:A:G	L428P	0.978
5:69294882:A:G	C279R	0.978
5:69283003:T:G	Q421P	0.977
5:69283007:G:C	H420D	0.975
5:69306884:A:G	W184R	0.975
5:69306884:A:T	W184R	0.975
5:69311128:A:G	L148P	0.975
5:69311158:A:G	L138P	0.975
5:69294880:G:C	C279W	0.974
5:69292306:T:A	R327S	0.973

dbSNP variants (sampled 300 via entrez): RS1000025282 (5:69316765 G>A), RS1000066371 (5:69295015 CA>C,CAA), RS1000093550 (5:69334054 G>A,T), RS1000125340 (5:69317172 C>A,T), RS1000221720 (5:69315282 G>A), RS1000270662 (5:69333086 G>T), RS1000308433 (5:69289080 G>A,C), RS1000327476 (5:69308287 C>G), RS1000327949 (5:69300658 A>G), RS1000537827 (5:69288295 A>G), RS1000611255 (5:69290900 G>C), RS1000657960 (5:69334416 A>G), RS1000663079 (5:69302703 G>A), RS1000822759 (5:69296699 T>C), RS1000836867 (5:69334342 G>T)

Disease associations

OMIM: gene MIM:613781 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST004608_13	Granulocyte percentage of myeloid white cells	3.000000e-12
GCST004610_74	White blood cell count	3.000000e-12
GCST004613_138	Sum neutrophil eosinophil counts	4.000000e-15
GCST004614_155	Granulocyte count	2.000000e-15
GCST004620_151	Sum basophil neutrophil counts	1.000000e-15
GCST004626_45	Myeloid white cell count	9.000000e-14
GCST004629_66	Neutrophil count	2.000000e-15
GCST004633_54	Neutrophil percentage of white cells	1.000000e-09
GCST90002389_204	Lymphocyte percentage of white cells	1.000000e-13
GCST90002394_69	Monocyte percentage of white cells	1.000000e-10
GCST90002398_467	Neutrophil count	2.000000e-31
GCST90002399_392	Neutrophil percentage of white cells	9.000000e-20
GCST90002407_458	White blood cell count	9.000000e-22

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007997	granulocyte percentage of myeloid white cells
EFO:0004833	neutrophil count
EFO:0004842	eosinophil count
EFO:0007987	granulocyte count
EFO:0005090	basophil count
EFO:0007990	neutrophil percentage of leukocytes
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0007989	monocyte percentage of leukocytes

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
potassium chromate(VI)	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
beta-lapachone	increases expression	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression	1
CGP 52608	affects binding, increases reaction	1
ICG 001	increases expression	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
Temozolomide	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Smoke	increases abundance, increases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases methylation	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Vitamin K 3	affects expression	1

Clinical trials (associated diseases)

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