CCDC97

Summary

CCDC97 (coiled-coil domain containing 97, HGNC:28289) is a protein-coding gene on chromosome 19q13.2, encoding Coiled-coil domain-containing protein 97 (Q96F63). May play a role pre-mRNA splicing through the association with the splicing factor SF3B complex which is involved in branch-site recognition.

Predicted to be located in nucleus.

Source: NCBI Gene 90324 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 74 total
• MANE Select transcript: NM_052848

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28289
Approved symbol	CCDC97
Name	coiled-coil domain containing 97
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40267, MGC20255
Ensembl gene	ENSG00000142039
Ensembl biotype	protein_coding
Entrez	90324

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000269967, ENST00000596882, ENST00000600918, ENST00000886246

RefSeq mRNA: 2 — MANE Select: NM_052848 NM_001346100, NM_052848

CCDS: CCDS12578

Canonical transcript exons

ENST00000269967 — 5 exons

Exon	Start	End
ENSE00000951937	41319574	41319852
ENSE00000951939	41320341	41320470
ENSE00001052851	41316384	41316839
ENSE00001052852	41310172	41310356
ENSE00001052853	41322595	41324873

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 90.63.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.8316 / max 271.3708, expressed in 1815 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176000	20.3015	1812
176001	2.7071	1214
176002	1.7103	993
176004	0.1126	46

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	90.63	gold quality
sural nerve	UBERON:0015488	89.74	gold quality
bone marrow cell	CL:0002092	89.46	gold quality
vena cava	UBERON:0004087	88.83	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.10	gold quality
left testis	UBERON:0004533	88.09	gold quality
right testis	UBERON:0004534	87.93	gold quality
apex of heart	UBERON:0002098	87.45	gold quality
gastrocnemius	UBERON:0001388	87.17	gold quality
blood	UBERON:0000178	87.12	gold quality
ectocervix	UBERON:0012249	87.08	gold quality
muscle of leg	UBERON:0001383	87.06	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	87.01	silver quality
upper arm skin	UBERON:0004263	86.90	silver quality
endocervix	UBERON:0000458	86.84	gold quality
right ovary	UBERON:0002118	86.83	gold quality
testis	UBERON:0000473	86.76	gold quality
left ovary	UBERON:0002119	86.49	gold quality
leukocyte	CL:0000738	86.47	gold quality
parotid gland	UBERON:0001831	86.41	silver quality
body of uterus	UBERON:0009853	86.36	gold quality
lymph node	UBERON:0000029	86.34	gold quality
vermiform appendix	UBERON:0001154	86.27	gold quality
ventricular zone	UBERON:0003053	86.20	gold quality
monocyte	CL:0000576	86.11	gold quality
caecum	UBERON:0001153	85.97	gold quality
kidney epithelium	UBERON:0004819	85.97	gold quality
esophagus mucosa	UBERON:0002469	85.89	gold quality
uterine cervix	UBERON:0000002	85.86	gold quality
left uterine tube	UBERON:0001303	85.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

149 targeting CCDC97, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-23A-5P	99.94	65.39	468
HSA-MIR-6721-5P	99.93	68.92	2981

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc97	ENSDARG00000074703
mus_musculus	Ccdc97	ENSMUSG00000002608
rattus_norvegicus	Ccdc97	ENSRNOG00000020675
drosophila_melanogaster	CG7810	FBGN0032017
caenorhabditis_elegans		WBGENE00011194

Protein

Protein identifiers

Coiled-coil domain-containing protein 97 — Q96F63 (reviewed: Q96F63)

All UniProt accessions (3): Q96F63, M0QXS4, M0QZY6

UniProt curated annotations — full annotation on UniProt →

Function. May play a role pre-mRNA splicing through the association with the splicing factor SF3B complex which is involved in branch-site recognition.

Subunit / interactions. Associates with splicing factor SF3B complex, involved in branch-site recognition.

Subcellular location. Nucleus.

RefSeq proteins (2): NP_001333029, NP_443080* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018613	Ccdc97-like	Family
IPR040233	CCD97-like_C	Domain

Pfam: PF09747

UniProt features (13 total): region of interest 4, modified residue 4, compositionally biased region 3, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96F63-F1	78.25	0.42

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 (4): 47, 275, 337, 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): TGCGCANK_UNKNOWN, FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN, LIAO_METASTASIS, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, LIAO_HAVE_SOX4_BINDING_SITES, ACACTCC_MIR122A, NAKAMURA_METASTASIS, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_UP, NRF1_Q6, CDC5L_TARGET_GENES, CHAF1B_TARGET_GENES, DIDO1_TARGET_GENES, DLX4_TARGET_GENES, DMRT1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

758 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC97	ZNF581	Q9P0T4	593
CCDC97	SF3A2	Q15428	540
CCDC97	GPATCH11	Q8N954	528
CCDC97	U2SURP	O15042	505
CCDC97	CHERP	Q8IWX8	505
CCDC97	RWDD1	Q9H446	487
CCDC97	CCDC87	Q9NVE4	479
CCDC97	ZNF428	Q96B54	476
CCDC97	NUBP1	P53384	469
CCDC97	CTDP1	Q9Y5B0	453
CCDC97	GAGE10	A6NGK3	447
CCDC97	HNRNPUL1	Q9BUJ2	446
CCDC97	SF3B4	Q15427	444
CCDC97	ETFB	P38117	439
CCDC97	UBL7	Q96S82	438

IntAct

32 interactions, top by confidence:

A	B	Type	Score
CCDC97	SF3B1	psi-mi:“MI:0914”(association)	0.730
PHF5A	SF3B1	psi-mi:“MI:0914”(association)	0.730
COMMD4	VPS26C	psi-mi:“MI:0914”(association)	0.730
COMMD6	VPS26C	psi-mi:“MI:0914”(association)	0.640
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
SKIC8	PFDN6	psi-mi:“MI:0914”(association)	0.530
SNRPE	PRMT5	psi-mi:“MI:0914”(association)	0.530
SRPK2	CCDC97	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
Sf3a1	U2SURP	psi-mi:“MI:0915”(physical association)	0.400
PCNA	CCDC97	psi-mi:“MI:0915”(physical association)	0.370
TIGD6	ZRANB2	psi-mi:“MI:0914”(association)	0.350
COMMD2	PCBP2	psi-mi:“MI:0914”(association)	0.350
RSL1D1	KPNA3	psi-mi:“MI:0914”(association)	0.350
SF3A1	HSPA8	psi-mi:“MI:0914”(association)	0.350
SF3B3	ATXN7	psi-mi:“MI:0914”(association)	0.350
SF3B5	SUPT3H	psi-mi:“MI:0914”(association)	0.350
SF3B6	HTATSF1	psi-mi:“MI:0914”(association)	0.350
AKR7L	KIF2A	psi-mi:“MI:0914”(association)	0.350
PHF5A	VPS26C	psi-mi:“MI:0914”(association)	0.350
SERF2	WDR46	psi-mi:“MI:0914”(association)	0.350
LBH	DHX16	psi-mi:“MI:0914”(association)	0.350
TMC4	MARCHF6	psi-mi:“MI:0914”(association)	0.350
SNRPB2	U2SURP	psi-mi:“MI:0914”(association)	0.350
CCDC97	U2SURP	psi-mi:“MI:0914”(association)	0.350
SF3B1	RBM10	psi-mi:“MI:0914”(association)	0.350
SF3B1	FAM83G	psi-mi:“MI:0914”(association)	0.350

BioGRID (84): CCDC97 (Affinity Capture-RNA), CCDC97 (Affinity Capture-RNA), CCDC97 (Affinity Capture-MS), CCDC97 (Co-fractionation), CCDC97 (Co-fractionation), CCDC97 (Co-fractionation), SF3B3 (Co-fractionation), SF3B5 (Co-fractionation), CCDC97 (Affinity Capture-MS), PAXIP1 (Affinity Capture-MS), TTC33 (Affinity Capture-MS), SF3A2 (Affinity Capture-MS), SF3A3 (Affinity Capture-MS), SF3A1 (Affinity Capture-MS), SF3B1 (Affinity Capture-MS)

ESM2 similar proteins: A0JN53, A8MXQ7, C5IJB0, D3ZND0, F1MLB4, F1MX48, O60232, O95400, P56873, Q15527, Q17QX2, Q27J81, Q2KIJ6, Q2YD98, Q3SYU1, Q5FVK6, Q5PPF5, Q5T0F9, Q7T0L4, Q7TMX5, Q8BIY1, Q8BRN9, Q8C0R7, Q8CC12, Q8IWY9, Q8N5A5, Q8N9W5, Q8VDM1, Q8WVB6, Q8WVT3, Q91WR3, Q924T7, Q95K25, Q96EP0, Q96F63, Q96K21, Q99PL6, Q9BWH6, Q9BZV1, Q9D479

Diamond homologs: Q96F63, Q9DBT3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 41 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
CHD1 and CHD2 subfamily	11	37.4×	1e-13
mRNA Polyadenylation	13	35.7×	9e-16
mRNA Splicing - Minor Pathway	5	35.0×	7e-06
mRNA Splicing	10	34.3×	5e-12
Processing of Capped Intron-Containing Pre-mRNA	12	30.8×	8e-14
mRNA Splicing - Major Pathway	16	27.3×	9e-18
Dengue Virus-Host Interactions	13	18.6×	2e-12
Metabolism of RNA	13	16.9×	5e-12

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	10	178.3×	7e-19
mRNA splicing, via spliceosome	13	34.0×	3e-15
RNA splicing	7	17.6×	8e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

967 predictions. Top by Δscore:

Variant	Effect	Δscore
19:41310351:A:G	donor_gain	1.0000
19:41310355:GG:G	donor_gain	1.0000
19:41310356:GG:G	donor_gain	1.0000
19:41316380:TCA:T	acceptor_loss	1.0000
19:41316382:A:AG	acceptor_gain	1.0000
19:41316383:G:GG	acceptor_gain	1.0000
19:41316835:CCAAG:C	donor_loss	1.0000
19:41316836:CAAGG:C	donor_loss	1.0000
19:41316838:AGGTG:A	donor_loss	1.0000
19:41316839:GGTG:G	donor_loss	1.0000
19:41316840:GTGT:G	donor_loss	1.0000
19:41319572:A:AG	acceptor_gain	1.0000
19:41319572:AG:A	acceptor_gain	1.0000
19:41319572:AGGG:A	acceptor_gain	1.0000
19:41319572:AGGGG:A	acceptor_gain	1.0000
19:41319573:G:GG	acceptor_gain	1.0000
19:41319573:GG:G	acceptor_gain	1.0000
19:41319573:GGGG:G	acceptor_gain	1.0000
19:41319573:GGGGG:G	acceptor_gain	1.0000
19:41319825:G:GT	donor_gain	1.0000
19:41319848:GGAAG:G	donor_gain	1.0000
19:41319849:G:GT	donor_gain	1.0000
19:41319849:GAAG:G	donor_gain	1.0000
19:41319850:A:T	donor_gain	1.0000
19:41319851:AGG:A	donor_loss	1.0000
19:41319852:GGTG:G	donor_loss	1.0000
19:41319853:G:GG	donor_gain	1.0000
19:41319854:T:A	donor_loss	1.0000
19:41320336:TGCA:T	acceptor_loss	1.0000
19:41320337:GCA:G	acceptor_loss	1.0000

AlphaMissense

2244 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:41320437:T:C	F293S	0.999
19:41320436:T:C	F293L	0.998
19:41320438:C:A	F293L	0.998
19:41320438:C:G	F293L	0.998
19:41320413:T:C	F285S	0.997
19:41322662:T:C	F327L	0.997
19:41322664:T:A	F327L	0.997
19:41322664:T:G	F327L	0.997
19:41316657:T:C	F107S	0.996
19:41316668:T:C	F111L	0.996
19:41316670:C:A	F111L	0.996
19:41316670:C:G	F111L	0.996
19:41316809:C:A	R158S	0.996
19:41319585:T:C	F172L	0.996
19:41319586:T:C	F172S	0.996
19:41319587:C:A	F172L	0.996
19:41319587:C:G	F172L	0.996
19:41319601:T:C	M177T	0.996
19:41320437:T:G	F293C	0.995
19:41316656:T:C	F107L	0.993
19:41316658:C:A	F107L	0.993
19:41316658:C:G	F107L	0.993
19:41316831:T:C	L165P	0.993
19:41320446:G:T	G296V	0.993
19:41320466:T:C	Y303H	0.993
19:41316822:T:C	L162P	0.992
19:41319610:G:C	R180P	0.991
19:41316818:G:C	A161P	0.990
19:41319586:T:G	F172C	0.990
19:41316669:T:C	F111S	0.989

dbSNP variants (sampled 300 via entrez): RS1000226840 (19:41323608 A>C,G), RS1000263906 (19:41320887 C>G,T), RS1000317775 (19:41309546 G>A), RS1000491727 (19:41315920 C>A,T), RS1000558823 (19:41317272 A>G), RS1000599804 (19:41319765 G>T), RS1000778400 (19:41314690 C>G), RS1000839594 (19:41316116 T>G), RS1001230393 (19:41314370 G>A,C), RS1001268256 (19:41322252 G>A), RS1001269378 (19:41310596 A>G), RS1001303720 (19:41321074 T>C), RS1001331521 (19:41310956 A>C), RS1001442107 (19:41317236 A>G), RS1001490892 (19:41325203 C>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

6 associations (top):

Study	Trait	p-value
GCST005194_184	Coronary artery disease	1.000000e-14
GCST005196_237	Coronary artery disease	7.000000e-15
GCST009640_55	Urinary albumin-to-creatinine ratio	8.000000e-10
GCST011365_76	Myocardial infarction	5.000000e-10
GCST90002402_563	Platelet count	2.000000e-11
GCST90013407_99	Liver enzyme levels (gamma-glutamyl transferase)	3.000000e-47

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007778	urinary albumin to creatinine ratio
EFO:0004309	platelet count
EFO:0004532	serum gamma-glutamyl transferase measurement

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
Cadmium	increases expression, decreases expression, increases abundance	2
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
ginger extract	increases abundance, increases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
corosolic acid	increases expression	1
abrine	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	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Doxorubicin	decreases expression	1
Lead	affects expression	1
Methyl Methanesulfonate	increases expression	1
Oils, Volatile	increases abundance, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1
Valproic Acid	affects expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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