CCDC107

Summary

CCDC107 (coiled-coil domain containing 107, HGNC:28465) is a protein-coding gene on chromosome 9p13.3, encoding Coiled-coil domain-containing protein 107 (Q8WV48). It is a selective cancer dependency (DepMap: 18.2% of cell lines).

This gene encodes a membrane protein which contains a coiled-coil domain in the central region. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 203260 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 25 total
• Cancer dependency (DepMap): dependent in 18.2% of screened cell lines
• MANE Select transcript: NM_174923

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28465
Approved symbol	CCDC107
Name	coiled-coil domain containing 107
Location	9p13.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC31967
Ensembl gene	ENSG00000159884
Ensembl biotype	protein_coding
Entrez	203260

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000327351, ENST00000378406, ENST00000378407, ENST00000378409, ENST00000421582, ENST00000426546

RefSeq mRNA: 4 — MANE Select: NM_174923 NM_001195200, NM_001195201, NM_001195217, NM_174923

CCDS: CCDS56573, CCDS56574, CCDS56575, CCDS6583

Canonical transcript exons

ENST00000426546 — 5 exons

Exon	Start	End
ENSE00001048241	35660557	35660647
ENSE00001048254	35660401	35660461
ENSE00001150340	35658576	35658727
ENSE00001724372	35660746	35661511
ENSE00003845413	35658292	35658485

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 98.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.0886 / max 208.6752, expressed in 1815 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96609	21.5701	1814
96610	0.5184	274

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
popliteal artery	UBERON:0002250	98.14	gold quality
tibial artery	UBERON:0007610	98.14	gold quality
aorta	UBERON:0000947	97.97	gold quality
ascending aorta	UBERON:0001496	97.89	gold quality
thoracic aorta	UBERON:0001515	97.88	gold quality
left coronary artery	UBERON:0001626	97.81	gold quality
right coronary artery	UBERON:0001625	97.61	gold quality
coronary artery	UBERON:0001621	97.52	gold quality
descending thoracic aorta	UBERON:0002345	97.51	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.45	gold quality
lower esophagus	UBERON:0013473	97.41	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.23	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.05	gold quality
apex of heart	UBERON:0002098	96.70	gold quality
mucosa of stomach	UBERON:0001199	96.27	gold quality
right atrium auricular region	UBERON:0006631	95.51	gold quality
left uterine tube	UBERON:0001303	95.39	gold quality
left ventricle myocardium	UBERON:0006566	95.28	gold quality
body of stomach	UBERON:0001161	95.26	gold quality
cardiac atrium	UBERON:0002081	95.25	gold quality
kidney epithelium	UBERON:0004819	95.11	silver quality
omental fat pad	UBERON:0010414	95.09	gold quality
peritoneum	UBERON:0002358	95.06	gold quality
adipose tissue of abdominal region	UBERON:0007808	94.96	gold quality
heart left ventricle	UBERON:0002084	94.93	gold quality
body of uterus	UBERON:0009853	94.90	gold quality
subcutaneous adipose tissue	UBERON:0002190	94.70	gold quality
cardiac ventricle	UBERON:0002082	94.68	gold quality
adipose tissue	UBERON:0001013	94.44	gold quality
cardiac muscle of right atrium	UBERON:0003379	94.13	silver quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-11	yes	9.99
E-GEOD-134144	yes	8.55
E-ANND-3	yes	5.18
E-HCAD-13	no	3.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting CCDC107, 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-4455	100.00	65.48	1587
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-3177-5P	99.65	70.38	1174
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-19B-1-5P	99.36	67.07	1669
HSA-MIR-19B-2-5P	99.36	67.07	1669
HSA-MIR-6509-3P	98.32	67.33	1343
HSA-MIR-4423-3P	97.98	69.66	912
HSA-MIR-676-3P	97.86	65.70	668
HSA-MIR-6781-3P	97.44	66.85	970
HSA-MIR-2682-3P	97.10	66.16	840
HSA-MIR-6773-5P	97.04	64.30	595
HSA-MIR-2355-3P	96.84	68.54	909
HSA-MIR-6839-5P	96.74	68.29	1088
HSA-MIR-378J	96.44	66.20	1020
HSA-MIR-6724-5P	96.41	63.11	507

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 18.2% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• Differential expression analysis of CCDC107 and RMRP lncRNA as potential biomarkers in colorectal cancer diagnosis. (PMID:34669559)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc107	ENSMUSG00000028461
rattus_norvegicus	Ccdc107	ENSRNOG00000017253

Protein

Protein identifiers

Coiled-coil domain-containing protein 107 — Q8WV48 (reviewed: Q8WV48)

All UniProt accessions (2): Q8WV48, X6R9Y9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (5)

UniProt ID	Names	Canonical?
Q8WV48-1	1	yes
Q8WV48-2	2
Q8WV48-3	3
Q8WV48-4	4
Q8WV48-5	5

RefSeq proteins (4): NP_001182129, NP_001182130, NP_001182146, NP_777583* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038779	CCDC107	Family

UniProt features (19 total): splice variant 7, sequence variant 3, region of interest 3, compositionally biased region 2, signal peptide 1, chain 1, transmembrane region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WV48-F1	61.31	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): CREL_01, NFKB_Q6, NFKB_C, chr9p13, GGGNNTTTCC_NFKB_Q6_01, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, POU3F2_02, YGCGYRCGC_UNKNOWN, YATGNWAAT_OCT_C, WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP, LU_EZH2_TARGETS_UP, OCT_Q6, NFKAPPAB65_01, KRIEG_HYPOXIA_NOT_VIA_KDM3A, NFKB_Q6_01

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

983 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC107	TBC1D12	O60347	513
CCDC107	CENATAC	Q86UT8	489
CCDC107	DXO	O77932	467
CCDC107	WDR54	Q9H977	428
CCDC107	LEPROTL1	O95214	419
CCDC107	TEDC2	Q7L2K0	418
CCDC107	ARHGEF39	Q8N4T4	403
CCDC107	HBB	P02023	396
CCDC107	WDR74	Q6RFH5	371
CCDC107	NUDCD3	Q8IVD9	370
CCDC107	VPS50	Q96JG6	364
CCDC107	PLEKHS1	Q5SXH7	358
CCDC107	DBF4B	Q8NFT6	356
CCDC107	PDZD4	Q76G19	345
CCDC107	PVRIG	Q6DKI7	319

IntAct

27 interactions, top by confidence:

A	B	Type	Score
ADIPOQ	CCDC107	psi-mi:“MI:0915”(physical association)	0.560
CCDC107	ADGRE2	psi-mi:“MI:0915”(physical association)	0.560
GRM2	CCDC107	psi-mi:“MI:0915”(physical association)	0.560
SLC35B1	CCDC107	psi-mi:“MI:0915”(physical association)	0.560
TNF	CCDC107	psi-mi:“MI:0915”(physical association)	0.560
CCDC107	UNC93B1	psi-mi:“MI:0915”(physical association)	0.560
CCDC107	PLD2	psi-mi:“MI:0914”(association)	0.530
PARP2	CCDC107	psi-mi:“MI:0557”(adp ribosylation reaction)	0.440
CCDC107	KPNA2	psi-mi:“MI:0915”(physical association)	0.370
CCDC107	TMEM131L	psi-mi:“MI:0914”(association)	0.350
SPRY4	HAL	psi-mi:“MI:0914”(association)	0.350
ADGRE2	CCDC107	psi-mi:“MI:0915”(physical association)	0.000
GRM2	CCDC107	psi-mi:“MI:0915”(physical association)	0.000
UNC93B1	CCDC107	psi-mi:“MI:0915”(physical association)	0.000
ADIPOQ	CCDC107	psi-mi:“MI:0915”(physical association)	0.000
SLC35B1	CCDC107	psi-mi:“MI:0915”(physical association)	0.000
TNF	CCDC107	psi-mi:“MI:0915”(physical association)	0.000
UBQLN4	CCDC107	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (83): TRPM4 (Affinity Capture-MS), GCC2 (Affinity Capture-MS), STX18 (Affinity Capture-MS), BNIP1 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), SLC9A1 (Affinity Capture-MS), TMEM214 (Affinity Capture-MS), GOLGA5 (Affinity Capture-MS), CENPH (Affinity Capture-MS), ALG8 (Affinity Capture-MS), PIGA (Affinity Capture-MS), STX5 (Affinity Capture-MS), PLD2 (Affinity Capture-MS), CTDNEP1 (Affinity Capture-MS), CXCR4 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GU29, A6NLX4, A6QNY1, A9CBA0, B7ZWI3, O14669, O88472, P14784, P16297, P25918, P26896, Q0VFL4, Q13651, Q32M26, Q38J84, Q38J85, Q3SYS8, Q58CT8, Q5BK39, Q5EAA5, Q5HZE8, Q5NCP0, Q5RCL0, Q64322, Q68DV7, Q6AXS2, Q6AXU5, Q6NUJ2, Q6UWV7, Q86UW2, Q8BHB3, Q8BLR5, Q8BSU2, Q8C353, Q8C708, Q8K1T1, Q8MII8, Q8N6P7, Q8NET5, Q8R182

Diamond homologs: Q2NL23, Q8WV48, Q9DCC3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

867 predictions. Top by Δscore:

Variant	Effect	Δscore
9:35658571:C:A	acceptor_gain	1.0000
9:35658574:A:AG	acceptor_gain	1.0000
9:35658574:AG:A	acceptor_gain	1.0000
9:35658574:AGG:A	acceptor_gain	1.0000
9:35658575:G:GG	acceptor_gain	1.0000
9:35658575:GG:G	acceptor_gain	1.0000
9:35658575:GGG:G	acceptor_gain	1.0000
9:35658713:TAC:T	donor_gain	1.0000
9:35658714:ACA:A	donor_gain	1.0000
9:35658726:AGG:A	donor_loss	1.0000
9:35658727:GGTAC:G	donor_loss	1.0000
9:35658728:G:GA	donor_loss	1.0000
9:35660396:A:AG	acceptor_gain	1.0000
9:35660396:AACAG:A	acceptor_gain	1.0000
9:35660397:A:G	acceptor_gain	1.0000
9:35660398:CAGG:C	acceptor_loss	1.0000
9:35660399:A:AG	acceptor_gain	1.0000
9:35660399:A:C	acceptor_loss	1.0000
9:35660399:AG:A	acceptor_gain	1.0000
9:35660399:AGG:A	acceptor_gain	1.0000
9:35660399:AGGG:A	acceptor_gain	1.0000
9:35660400:G:GC	acceptor_loss	1.0000
9:35660400:G:GG	acceptor_gain	1.0000
9:35660400:GG:G	acceptor_gain	1.0000
9:35660400:GGG:G	acceptor_gain	1.0000
9:35660400:GGGG:G	acceptor_gain	1.0000
9:35660457:GTCAG:G	donor_gain	1.0000
9:35660461:GG:G	donor_loss	1.0000
9:35660462:G:A	donor_loss	1.0000
9:35660549:A:AG	acceptor_gain	1.0000

AlphaMissense

1797 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:35660608:T:C	L124P	0.984
9:35660617:T:C	L127P	0.977
9:35658704:T:C	F79L	0.976
9:35658706:T:A	F79L	0.976
9:35658706:T:G	F79L	0.976
9:35658702:C:A	A78D	0.973
9:35658693:C:A	A75D	0.968
9:35660640:T:C	F135L	0.968
9:35660642:T:A	F135L	0.968
9:35660642:T:G	F135L	0.968
9:35658696:T:A	V76D	0.961
9:35660629:T:C	L131P	0.956
9:35658708:T:A	V80E	0.951
9:35660587:T:C	L117P	0.947
9:35660575:T:C	L113S	0.944
9:35658718:G:C	K83N	0.941
9:35658718:G:T	K83N	0.941
9:35658690:C:A	A74E	0.940
9:35660793:T:C	L153P	0.936
9:35658683:T:G	Y72D	0.928
9:35658705:T:C	F79S	0.923
9:35660811:T:C	L159P	0.923
9:35660781:T:C	L149P	0.921
9:35660596:C:T	T120I	0.915
9:35658701:G:C	A78P	0.910
9:35660641:T:G	F135C	0.910
9:35660802:T:C	I156T	0.905
9:35658692:G:C	A75P	0.899
9:35660778:T:C	L148P	0.897
9:35658705:T:G	F79C	0.895

dbSNP variants (sampled 300 via entrez): RS1000137459 (9:35657303 G>A), RS1000190119 (9:35657026 G>A,C), RS1000308916 (9:35661853 G>A,T), RS1000348471 (9:35657487 T>C), RS1000379566 (9:35657173 A>T), RS1000522852 (9:35657861 A>G), RS1000727643 (9:35661483 A>G,T), RS1001076608 (9:35661759 C>G), RS1001319150 (9:35656431 G>A), RS1001978453 (9:35659803 A>G), RS1002317041 (9:35659007 C>T), RS1002409010 (9:35657784 G>A,C), RS1002466740 (9:35659249 G>A,C), RS1002941043 (9:35658672 T>C), RS1004469515 (9:35657838 C>A,G,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:250250, MIM:250460, MIM:607095

GenCC curated gene-disease

Mondo (4): cartilage-hair hypoplasia (MONDO:0009595), metaphyseal dysplasia without hypotrichosis (MONDO:0009601), anauxetic dysplasia (MONDO:0011773), anauxetic dysplasia 1 (MONDO:0054560)

Orphanet (3): Cartilage-hair hypoplasia (Orphanet:175), Anauxetic dysplasia (Orphanet:93347), Metaphyseal dysplasia without hypotrichosis (Orphanet:1838)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90026413_8	Severe insulin-deficient type 2 diabetes	7.000000e-06

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
C538256	Anauxetic dysplasia (supp.)
C535916	Cartilage-hair hypoplasia (supp.)
C563574	Metaphyseal Dysplasia without Hypotrichosis (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Dexamethasone	affects cotreatment, increases expression	2
bisphenol A	affects cotreatment, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
K 7174	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
bisphenol S	increases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Cadmium	increases abundance, increases expression	1
Catechin	affects cotreatment, decreases expression	1
Cisplatin	decreases expression	1
Diazinon	increases methylation	1
Indomethacin	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Copper Sulfate	affects expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02383797	PHASE4	UNKNOWN	Immunodeficiency in Cartilage-hair Hypoplasia: Sub-project on Safety of Vaccination Against Chickenpox
NCT05058781	Not specified	RECRUITING	Minipuberty in Infants Born With Potential Hypogonadism Hypogonadotrope