Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	83987
Gene name	Coiled-coil domain containing 8 subunit of 3M complex
Gene symbol	CCDC8
Synonyms (NCBI Gene)	3M3PPP1R20p90
Chromosome	19
Chromosome location	19q13.32
Summary	This gene encodes a coiled-coil domain-containing protein. The encoded protein functions as a cofactor required for p53-mediated apoptosis following DNA damage, and may also play a role in growth through interactions with the cytoskeletal adaptor protein

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs752254407	->C	Pathogenic	Frameshift variant, coding sequence variant
rs1568590155	->A	Pathogenic	Coding sequence variant, stop gained

Show/Hide all (98)

miRTarBase ID	miRNA	Experiments	Reference
MIRT044884	hsa-miR-193a-3p	CLASH	23622248
MIRT869892	hsa-miR-10a	CLIP-seq
MIRT869893	hsa-miR-10b	CLIP-seq
MIRT869894	hsa-miR-1285	CLIP-seq
MIRT869895	hsa-miR-1304	CLIP-seq
MIRT869896	hsa-miR-147	CLIP-seq
MIRT869897	hsa-miR-1827	CLIP-seq
MIRT869898	hsa-miR-24	CLIP-seq
MIRT869899	hsa-miR-338-3p	CLIP-seq
MIRT869900	hsa-miR-339-5p	CLIP-seq
MIRT869901	hsa-miR-3607-3p	CLIP-seq
MIRT869902	hsa-miR-3614-5p	CLIP-seq
MIRT869903	hsa-miR-3686	CLIP-seq
MIRT869904	hsa-miR-3911	CLIP-seq
MIRT869905	hsa-miR-4284	CLIP-seq
MIRT869906	hsa-miR-4421	CLIP-seq
MIRT869907	hsa-miR-4459	CLIP-seq
MIRT869908	hsa-miR-4722-5p	CLIP-seq
MIRT869909	hsa-miR-504	CLIP-seq
MIRT869910	hsa-miR-593	CLIP-seq
MIRT869911	hsa-miR-644	CLIP-seq
MIRT869912	hsa-miR-766	CLIP-seq
MIRT869913	hsa-miR-940	CLIP-seq
MIRT1958118	hsa-miR-1224-5p	CLIP-seq
MIRT869895	hsa-miR-1304	CLIP-seq
MIRT1958119	hsa-miR-219-1-3p	CLIP-seq
MIRT1958120	hsa-miR-33a	CLIP-seq
MIRT1958121	hsa-miR-33b	CLIP-seq
MIRT1958122	hsa-miR-3646	CLIP-seq
MIRT1958123	hsa-miR-3915	CLIP-seq
MIRT1958124	hsa-miR-3928	CLIP-seq
MIRT1958125	hsa-miR-4689	CLIP-seq
MIRT1958126	hsa-miR-571	CLIP-seq
MIRT869895	hsa-miR-1304	CLIP-seq
MIRT869897	hsa-miR-1827	CLIP-seq
MIRT869902	hsa-miR-3614-5p	CLIP-seq
MIRT2195068	hsa-miR-3616-5p	CLIP-seq
MIRT2195069	hsa-miR-3647-5p	CLIP-seq
MIRT2195070	hsa-miR-4257	CLIP-seq
MIRT869907	hsa-miR-4459	CLIP-seq
MIRT2195071	hsa-miR-4670-3p	CLIP-seq
MIRT869908	hsa-miR-4722-5p	CLIP-seq
MIRT2195072	hsa-miR-573	CLIP-seq
MIRT869913	hsa-miR-940	CLIP-seq
MIRT869895	hsa-miR-1304	CLIP-seq
MIRT869892	hsa-miR-10a	CLIP-seq
MIRT869893	hsa-miR-10b	CLIP-seq
MIRT869894	hsa-miR-1285	CLIP-seq
MIRT869895	hsa-miR-1304	CLIP-seq
MIRT2498400	hsa-miR-1323	CLIP-seq
MIRT869897	hsa-miR-1827	CLIP-seq
MIRT2498401	hsa-miR-3122	CLIP-seq
MIRT2498402	hsa-miR-330-3p	CLIP-seq
MIRT869899	hsa-miR-338-3p	CLIP-seq
MIRT869900	hsa-miR-339-5p	CLIP-seq
MIRT869901	hsa-miR-3607-3p	CLIP-seq
MIRT869902	hsa-miR-3614-5p	CLIP-seq
MIRT869903	hsa-miR-3686	CLIP-seq
MIRT2498403	hsa-miR-3689a-3p	CLIP-seq
MIRT2498404	hsa-miR-3689c	CLIP-seq
MIRT2498405	hsa-miR-3913-5p	CLIP-seq
MIRT2498406	hsa-miR-4282	CLIP-seq
MIRT2498407	hsa-miR-4310	CLIP-seq
MIRT869906	hsa-miR-4421	CLIP-seq
MIRT2498408	hsa-miR-4422	CLIP-seq
MIRT869907	hsa-miR-4459	CLIP-seq
MIRT869908	hsa-miR-4722-5p	CLIP-seq
MIRT2498409	hsa-miR-4728-5p	CLIP-seq
MIRT869909	hsa-miR-504	CLIP-seq
MIRT2498410	hsa-miR-548c-3p	CLIP-seq
MIRT2498411	hsa-miR-548o	CLIP-seq
MIRT869910	hsa-miR-593	CLIP-seq
MIRT869912	hsa-miR-766	CLIP-seq
MIRT869913	hsa-miR-940	CLIP-seq
MIRT869892	hsa-miR-10a	CLIP-seq
MIRT869893	hsa-miR-10b	CLIP-seq
MIRT869894	hsa-miR-1285	CLIP-seq
MIRT869895	hsa-miR-1304	CLIP-seq
MIRT869897	hsa-miR-1827	CLIP-seq
MIRT2498401	hsa-miR-3122	CLIP-seq
MIRT869899	hsa-miR-338-3p	CLIP-seq
MIRT869900	hsa-miR-339-5p	CLIP-seq
MIRT869901	hsa-miR-3607-3p	CLIP-seq
MIRT869902	hsa-miR-3614-5p	CLIP-seq
MIRT869903	hsa-miR-3686	CLIP-seq
MIRT2498403	hsa-miR-3689a-3p	CLIP-seq
MIRT2498404	hsa-miR-3689c	CLIP-seq
MIRT2498405	hsa-miR-3913-5p	CLIP-seq
MIRT2498406	hsa-miR-4282	CLIP-seq
MIRT2498407	hsa-miR-4310	CLIP-seq
MIRT869906	hsa-miR-4421	CLIP-seq
MIRT869907	hsa-miR-4459	CLIP-seq
MIRT869908	hsa-miR-4722-5p	CLIP-seq
MIRT2498409	hsa-miR-4728-5p	CLIP-seq
MIRT869909	hsa-miR-504	CLIP-seq
MIRT869910	hsa-miR-593	CLIP-seq
MIRT869912	hsa-miR-766	CLIP-seq
MIRT869913	hsa-miR-940	CLIP-seq

Show/Hide all (16)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000226	Process	Microtubule cytoskeleton organization	IBA
GO:0000226	Process	Microtubule cytoskeleton organization	IMP	24793695
GO:0005515	Function	Protein binding	IPI	25752541
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IDA	24793695
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	24793695
GO:0005813	Component	Centrosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IDA
GO:0007088	Process	Regulation of mitotic nuclear division	IBA
GO:0007088	Process	Regulation of mitotic nuclear division	IMP	24793695
GO:1990393	Component	3M complex	IBA
GO:1990393	Component	3M complex	IDA	24793695

MIM	HGNC	e!Ensembl
614145	25367	ENSG00000169515

Q9H0W5

Protein name

Coiled-coil domain-containing protein 8

Protein function

Core component of the 3M complex, a complex required to regulate microtubule dynamics and genome integrity. It is unclear how the 3M complex regulates microtubules, it could act by controlling the level of a microtubule stabilizer (PubMed:247936

PDB

4LG6

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF14893	PNMA	1 → 116	PNMA	Family

Tissue specificity

TISSUE SPECIFICITY: Widely expressed with low levels in spleen, skeletal muscle, small intestine, kidney and liver. {ECO:0000269|PubMed:21737058}.

Sequence

MLQIGEDVDYLLIPREVRLAGGVWRVISKPATKEAEFRERLTQFLEEEGRTLEDVARIME
KSTPHPPQPPKKPKEPRVRRRVQQMVTPPPRLVVGTYDSSNASDSEFSDFETSRDKSRQG
PRRGKKVRKMPVSYLGSKFLGSDLESEDDEELVEAFLRRQEKQPSAPPARRRVNLPVPMF
EDNLGPQLSKADRWREYVSQVSWGKLKRRVKGWAPRAGPGVGEARLASTAVESAGVSSAP
EGTSPGDRLGNAGDVCVPQASPRRWRPKINWASFRRRRKEQTAPTGQGADIEADQGGEAA
DSQREEAIADQREGAAGNQRAGAPADQGAEAADNQREEAADNQRAGAPAEEGAEAADNQR
EEAADNQRAEAPADQRSQGTDNHREEAADNQRAEAPADQGSEVTDNQREEAVHDQRERAP
AVQGADNQRAQARAGQRAEAAHNQRAGAPGIQEAEVSAAQGTTGTAPGARARKQVKTVRF
QTPGRFSWFCKRRRAFWHTPRLPTLPKRVPRAGEARNLRVLRAEARAEAEQGEQEDQL

Sequence length

538

Interactions

View interactions

	Reactome
			Neddylation

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
3M syndrome 3	Likely pathogenic; Pathogenic	rs1973237748, rs2513602574, rs752254407, rs1568590155, rs1973248576, rs746873023	RCV001329462 RCV003990920 RCV000024100 RCV000024101 RCV001198938 RCV001283853 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
3-M SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CCDC8-related disorder	Uncertain significance; Benign; Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Immunodeficiency	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MILLER-MCKUSICK-MALVAUX-SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA TYPE 40	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THREE M SYNDROME 3	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (56)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
3M syndrome	3M Syndrome	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	27236820		★★★★★ ★☆☆☆☆ Found in Text Mining only
Arteriosclerosis	Arteriosclerosis	BEFREE	23243209		★★★★★ ★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	BEFREE	23243209		★★★★★ ★☆☆☆☆ Found in Text Mining only
Benign Prostatic Hyperplasia	Benign Prostatic Hyperplasia	BEFREE	15538718		★★★★★ ★☆☆☆☆ Found in Text Mining only
Biliary Atresia	Biliary atresia	Pubtator	36350824	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	27028868		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	38235137	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	28700999	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	27342910		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	34569727	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Childhood Medulloblastoma	Medulloblastoma	BEFREE	23940083		★★★★★ ★☆☆☆☆ Found in Text Mining only
Clinodactyly of the 5th finger	Camptodactyly of fingers	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Dysplasia Of The Hip	Developmental dysplasia of the hip	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	21132003		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	30581781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	23243209, 30581781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetic Angiopathies	Diabetic cardiomyopathy	BEFREE	10997688		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	25752541		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism tall vertebrae	Dwarfism	ORPHANET_DG	21737058		★★★★★ ★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	27436023		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	27436023		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	19544381	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	24711643, 24793695, 25752541, 28675896	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	BEFREE	30292428		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypospadias	Hypospadias	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	12118381, 28700999		★★★★★ ★☆☆☆☆ Found in Text Mining only
Long narrow head	Dolichocephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	27028868		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	27342910		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	15538718, 15833840, 27342910		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	12118381, 31677131		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	12118381, 27342910		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	24627490, 30356079		★★★★★ ★☆☆☆☆ Found in Text Mining only
Micromelia	Micromelia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Miller-McKusick-Malvaux-Syndrome (3M Syndrome)	3M Syndrome	BEFREE	21737058, 23018678, 25752541, 26488604, 28675896		★★★★★ ★☆☆☆☆ Found in Text Mining only
Miller-McKusick-Malvaux-Syndrome (3M Syndrome)	3M Syndrome	ORPHANET_DG	21737058		★★★★★ ★☆☆☆☆ Found in Text Mining only
Miller-McKusick-Malvaux-Syndrome (3M Syndrome)	3M Syndrome	GENOMICS_ENGLAND_DG	28675896		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	12118381, 15342917, 21132003, 22614021, 27342910		★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	27342910		★★★★★ ★☆☆☆☆ Found in Text Mining only
Primary central nervous system lymphoma	Central Nervous System Lymphoma	BEFREE	27436023		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	15538718, 15833840		★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	21132003		★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Somatotropin deficiency	Somatotropin Deficiency	BEFREE	23517720		★★★★★ ★☆☆☆☆ Found in Text Mining only
Spinal Muscular Atrophy	Spinal Muscular Atrophy	BEFREE	27907033		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	20234090		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	12118381, 31677131		★★★★★ ★☆☆☆☆ Found in Text Mining only
Three M Syndrome 1	3M Syndrome	ORPHANET_DG	21737058		★★★★★ ★☆☆☆☆ Found in Text Mining only
THREE M SYNDROME 3	3M Syndrome	GENOMICS_ENGLAND_DG	21737058, 28675896		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THREE M SYNDROME 3	3M Syndrome	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	23593654		★★★★★ ★☆☆☆☆ Found in Text Mining only
Tuberous Sclerosis	Tuberous Sclerosis	BEFREE	15342917		★★★★★ ★☆☆☆☆ Found in Text Mining only
Vertical Talus	Vertical Talus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

CCDC8 (coiled-coil domain containing 8 subunit of 3M complex)