CCDC43

Summary

CCDC43 (coiled-coil domain containing 43, HGNC:26472) is a protein-coding gene on chromosome 17q21.31, encoding Coiled-coil domain-containing protein 43 (Q96MW1).

Located in cytosol.

Source: NCBI Gene 124808 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_144609

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26472
Approved symbol	CCDC43
Name	coiled-coil domain containing 43
Location	17q21.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31795
Ensembl gene	ENSG00000180329
Ensembl biotype	protein_coding
Entrez	124808

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 retained_intron

ENST00000315286, ENST00000457422, ENST00000588210, ENST00000588687, ENST00000592333, ENST00000938683, ENST00000946236

RefSeq mRNA: 2 — MANE Select: NM_144609 NM_001099225, NM_144609

CCDS: CCDS45704, CCDS45705

Canonical transcript exons

ENST00000315286 — 5 exons

Exon	Start	End
ENSE00001253871	44680585	44680643
ENSE00001253878	44682003	44682138
ENSE00002946779	44689550	44689776
ENSE00002963874	44677440	44679043
ENSE00003513018	44683872	44683959

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 95.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.0653 / max 178.4977, expressed in 1820 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
166389	23.7694	1820
166388	0.1780	58
166390	0.1179	45

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
deltoid	UBERON:0001476	95.29	gold quality
tibialis anterior	UBERON:0001385	94.06	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.41	gold quality
buccal mucosa cell	CL:0002336	93.28	gold quality
skeletal muscle tissue	UBERON:0001134	92.91	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	92.84	gold quality
quadriceps femoris	UBERON:0001377	92.68	gold quality
skeletal muscle organ	UBERON:0014892	92.68	gold quality
muscle of leg	UBERON:0001383	92.65	gold quality
vastus lateralis	UBERON:0001379	92.58	gold quality
gastrocnemius	UBERON:0001388	92.50	gold quality
biceps brachii	UBERON:0001507	91.21	gold quality
muscle tissue	UBERON:0002385	90.70	gold quality
secondary oocyte	CL:0000655	89.38	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	88.95	gold quality
pancreatic ductal cell	CL:0002079	88.46	silver quality
calcaneal tendon	UBERON:0003701	88.42	gold quality
monocyte	CL:0000576	88.11	gold quality
ileal mucosa	UBERON:0000331	87.83	gold quality
leukocyte	CL:0000738	87.78	gold quality
body of tongue	UBERON:0011876	87.60	gold quality
adrenal tissue	UBERON:0018303	86.63	gold quality
rectum	UBERON:0001052	86.61	gold quality
palpebral conjunctiva	UBERON:0001812	86.61	gold quality
tendon	UBERON:0000043	86.23	gold quality
esophagus squamous epithelium	UBERON:0006920	85.95	gold quality
prefrontal cortex	UBERON:0000451	85.90	gold quality
tongue	UBERON:0001723	85.86	gold quality
ventricular zone	UBERON:0003053	85.79	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.02

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): YY1

miRNA regulators (miRDB)

102 targeting CCDC43, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-129-5P	99.88	70.26	3273

Literature-anchored findings (GeneRIF, showing 3)

• This work identified that CCDC43 promoted epithelial-mesenchymal transition and was a direct transcriptional target of FOXK1 in colorectal cancer cells. (PMID:30562730)
• The CCDC43-ADRM1 axis regulated by YY1, promotes proliferation and metastasis of gastric cancer. (PMID:32278016)
• HMGA1 promotes gastric cancer growth and metastasis by transactivating SUZ12 and CCDC43 expression. (PMID:34167089)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc43	ENSDARG00000054446
mus_musculus	Ccdc43	ENSMUSG00000020925
rattus_norvegicus	Ccdc43	ENSRNOG00000002748
drosophila_melanogaster	CG9586	FBGN0032101

Protein

Protein identifiers

Coiled-coil domain-containing protein 43 — Q96MW1 (reviewed: Q96MW1)

All UniProt accessions (3): Q96MW1, K7ER24, Q86WV7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CCDC43 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96MW1-1	1	yes
Q96MW1-2	2

RefSeq proteins (2): NP_001092695, NP_653210* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037666	CCDC43	Family
IPR058771	PWI_CCDC43	Domain

Pfam: PF26091

UniProt features (12 total): compositionally biased region 3, region of interest 2, coiled-coil region 2, chain 1, splice variant 1, sequence conflict 1, modified residue 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96MW1-F1	77.30	0.38

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): 139, 95

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 81 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, CAGCTG_AP4_Q5, MARTINEZ_RB1_TARGETS_DN, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, ACACTGG_MIR199A_MIR199B, JOHNSTONE_PARVB_TARGETS_3_DN, CIITA_TARGET_GENES, GUCY1B1_TARGET_GENES, NFE2L1_TARGET_GENES, ZSCAN2_TARGET_GENES, MIR153_5P, MIR30B_5P_MIR30C_5P

GO Biological Process (0):

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

GO Cellular Component (1): cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

746 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC43	WASHC3	Q9Y3C0	464
CCDC43	FOXK1	P85037	462
CCDC43	GOSR2	O14653	442
CCDC43	CCDC34	Q96HJ3	440
CCDC43	EFTUD2	Q15029	424
CCDC43	IGSF22	Q8N9C0	400
CCDC43	CCDC68	Q9H2F9	395
CCDC43	ANKRD31	Q8N7Z5	393
CCDC43	ZNF28	P17035	376
CCDC43	ZNF781	Q8N8C0	369
CCDC43	WASHC5	Q12768	364
CCDC43	CCDC8	Q9H0W5	363
CCDC43	RUNDC1	Q96C34	352
CCDC43	TMEM101	Q96IK0	350
CCDC43	CCDC171	Q6TFL3	337

IntAct

41 interactions, top by confidence:

A	B	Type	Score
MED17	MED19	psi-mi:“MI:0914”(association)	0.840
CCDC43	PNKP	psi-mi:“MI:0914”(association)	0.640
CCDC43	KLHL2	psi-mi:“MI:0915”(physical association)	0.560
CCDC43	TINF2	psi-mi:“MI:0915”(physical association)	0.510
CCDC43	MFHAS1	psi-mi:“MI:0407”(direct interaction)	0.440
CCDC43	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
SCNM1	CCDC43	psi-mi:“MI:0915”(physical association)	0.400
CCDC43	TK1	psi-mi:“MI:0915”(physical association)	0.400
RAN	NUP214	psi-mi:“MI:0914”(association)	0.350
TXNDC9	TUBAL3	psi-mi:“MI:0914”(association)	0.350
CLRN3	TXNDC9	psi-mi:“MI:0914”(association)	0.350
BBS1	SHTN1	psi-mi:“MI:0914”(association)	0.350
DOK4	SHTN1	psi-mi:“MI:0914”(association)	0.350
AHR	SHTN1	psi-mi:“MI:0914”(association)	0.350
ZBTB2	SHTN1	psi-mi:“MI:0914”(association)	0.350
MRPS18C	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
ATP5PB	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
SMAD4	SBNO1	psi-mi:“MI:0914”(association)	0.350
ANAPC16	METTL15	psi-mi:“MI:0914”(association)	0.350
PHKA2	STK25	psi-mi:“MI:0914”(association)	0.350
UNC45A	SLC27A2	psi-mi:“MI:0914”(association)	0.350
SPRTN	ROCK2	psi-mi:“MI:0914”(association)	0.350
FCGRT	WBP4	psi-mi:“MI:0914”(association)	0.350
TAGAP	METTL18	psi-mi:“MI:0914”(association)	0.350
CCDC43	APTX	psi-mi:“MI:0914”(association)	0.350
CDH1	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
MST1R	SHTN1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (62): CCDC43 (Two-hybrid), GOPC (Affinity Capture-MS), SCML1 (Affinity Capture-MS), PNKP (Affinity Capture-MS), CCDC43 (Proximity Label-MS), CCDC43 (Proximity Label-MS), SCML1 (Affinity Capture-MS), PNKP (Affinity Capture-MS), GOPC (Affinity Capture-MS), CCDC43 (Reconstituted Complex), CCDC43 (Reconstituted Complex), CCDC43 (Affinity Capture-MS), CCDC43 (Proximity Label-MS), CCDC43 (Two-hybrid), ADRM1 (Affinity Capture-Western)

ESM2 similar proteins: A0JPM9, A2AQ19, O43395, O75391, O75822, P04973, P09496, P29084, P29540, Q02614, Q0VCU8, Q13123, Q15650, Q2HJ41, Q2KIA6, Q2KJF9, Q3MHJ0, Q3UGC7, Q5BK07, Q5I0B5, Q5NVI3, Q5R5F1, Q5R8D1, Q5RAD5, Q5RE03, Q5ZJ85, Q5ZJ97, Q5ZK25, Q5ZKA4, Q66HG8, Q66JS6, Q6GMH0, Q6INR1, Q6P320, Q7SXU0, Q7SYJ9, Q7TNE3, Q8BM39, Q91WE2, Q922U1

Diamond homologs: Q5BK07, Q5ZK95, Q6PFL6, Q96MW1, Q9CR29

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1080 predictions. Top by Δscore:

Variant	Effect	Δscore
17:44673516:C:T	donor_gain	1.0000
17:44673542:CAGAG:C	donor_loss	1.0000
17:44673543:AGAGG:A	donor_loss	1.0000
17:44673544:GAG:G	donor_gain	1.0000
17:44673545:AG:A	donor_loss	1.0000
17:44673546:GG:G	donor_loss	1.0000
17:44673547:G:GA	donor_loss	1.0000
17:44673548:T:A	donor_loss	1.0000
17:44673971:TACA:T	acceptor_loss	1.0000
17:44673972:ACAG:A	acceptor_loss	1.0000
17:44673973:CA:C	acceptor_loss	1.0000
17:44673974:A:AG	acceptor_gain	1.0000
17:44673974:AG:A	acceptor_loss	1.0000
17:44673974:AGAT:A	acceptor_gain	1.0000
17:44673975:G:GA	acceptor_gain	1.0000
17:44673975:GA:G	acceptor_gain	1.0000
17:44673975:GAT:G	acceptor_gain	1.0000
17:44673975:GATG:G	acceptor_gain	1.0000
17:44673975:GATGT:G	acceptor_gain	1.0000
17:44679039:CAGAA:C	acceptor_gain	1.0000
17:44679044:C:CC	acceptor_gain	1.0000
17:44682003:T:TA	donor_gain	1.0000
17:44689544:ACT:A	donor_loss	1.0000
17:44689547:CA:C	donor_loss	1.0000
17:44689548:A:AC	donor_gain	1.0000
17:44689548:A:C	donor_loss	1.0000
17:44689548:AC:A	donor_gain	1.0000
17:44689549:C:CA	donor_gain	1.0000
17:44689549:CC:C	donor_gain	1.0000
17:44689549:CCA:C	donor_gain	1.0000

AlphaMissense

1445 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:44678883:C:A	R216S	0.994
17:44678883:C:G	R216S	0.994
17:44678906:G:T	R209S	0.993
17:44678905:C:G	R209P	0.992
17:44678884:C:G	R216T	0.983
17:44678934:C:A	R199S	0.983
17:44678934:C:G	R199S	0.983
17:44678989:C:G	R181P	0.982
17:44678901:C:A	K210N	0.981
17:44678901:C:G	K210N	0.981
17:44678958:C:A	K191N	0.981
17:44678958:C:G	K191N	0.981
17:44682034:C:G	A133P	0.980
17:44679030:G:C	N167K	0.979
17:44679030:G:T	N167K	0.979
17:44682039:A:G	L131P	0.978
17:44682047:T:A	K128N	0.976
17:44682047:T:G	K128N	0.976
17:44678866:C:G	R222P	0.975
17:44682100:C:G	A111P	0.975
17:44678862:C:A	K223N	0.974
17:44678862:C:G	K223N	0.974
17:44682036:A:G	L132P	0.974
17:44682123:A:T	I103N	0.974
17:44678889:T:A	K214N	0.973
17:44678889:T:G	K214N	0.973
17:44682114:A:G	L106P	0.973
17:44678884:C:A	R216M	0.972
17:44678955:C:A	K192N	0.972
17:44678955:C:G	K192N	0.972

dbSNP variants (sampled 300 via entrez): RS1000313568 (17:44677227 T>C), RS1000337000 (17:44685391 C>T), RS1000522005 (17:44691757 A>C), RS1000527796 (17:44688353 A>C,G), RS1000601804 (17:44677548 G>GC), RS1001102970 (17:44681435 C>A,T), RS1001399653 (17:44684638 G>A), RS1001424864 (17:44677214 G>A), RS1001497738 (17:44684704 A>AG,AT), RS1001517701 (17:44677652 T>C), RS1001654759 (17:44684355 G>A), RS1001769108 (17:44677156 A>G), RS1001769246 (17:44684958 T>C,G), RS1002125302 (17:44690393 C>G), RS1002198829 (17:44690075 T>C)

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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
Cadmium Chloride	increases expression	2
FR900359	affects phosphorylation	1
salinomycin	decreases expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
potassium chromate(VI)	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
cylindrospermopsin	increases expression	1
ICG 001	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	affects cotreatment, increases expression	1
Endosulfan	decreases expression	1
Ivermectin	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Vanadates	decreases expression	1

Clinical trials (associated diseases)

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