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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	55036
Gene name	Coiled-coil domain 40 molecular ruler complex subunit
Gene symbol	CCDC40
Synonyms (NCBI Gene)	CFAP172CILD15FAP172
Chromosome	17
Chromosome location	17q25.3
Summary	This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in thi

Show/Hide all (30)

SNP ID	Visualize variation	Clinical significance	Consequence
rs138001923	A>G	Conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, intron variant
rs200958035	G>A,C	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, missense variant
rs369089505	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, genic upstream transcript variant, coding sequence variant
rs370706991	G>A,T	Likely-pathogenic, pathogenic	Genic downstream transcript variant, splice acceptor variant
rs371595543	A>T	Pathogenic, uncertain-significance	Non coding transcript variant, stop gained, coding sequence variant
rs387907091	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs387907092	C>A,T	Pathogenic	Genic downstream transcript variant, stop gained, coding sequence variant, missense variant, non coding transcript variant
rs387907093	C>A,G,T	Pathogenic, uncertain-significance	Synonymous variant, stop gained, coding sequence variant, missense variant, non coding transcript variant
rs397515393	C>-	Pathogenic	Non coding transcript variant, genic upstream transcript variant, coding sequence variant, frameshift variant
rs587778819	->CTGT,TGT	Pathogenic	Coding sequence variant, frameshift variant, inframe indel, non coding transcript variant, genic downstream transcript variant
rs745993158	G>A	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs747233125	C>G,T	Pathogenic	Coding sequence variant, stop gained, missense variant, non coding transcript variant, genic downstream transcript variant
rs750708201	A>G	Pathogenic	Splice acceptor variant, genic upstream transcript variant
rs751191119	GG>-	Pathogenic	Coding sequence variant, frameshift variant, downstream transcript variant, non coding transcript variant, genic downstream transcript variant
rs754867753	C>T	Pathogenic	Coding sequence variant, stop gained, genic upstream transcript variant, non coding transcript variant
rs755004291	C>G,T	Pathogenic	Coding sequence variant, stop gained, missense variant, genic downstream transcript variant, non coding transcript variant
rs762664261	A>C,G	Likely-pathogenic	Splice acceptor variant, genic downstream transcript variant
rs764011276	G>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs764551914	C>T	Pathogenic	Coding sequence variant, stop gained, genic upstream transcript variant, non coding transcript variant
rs773796940	G>A,T	Pathogenic	Stop gained, missense variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs774081599	G>A	Likely-pathogenic	Genic downstream transcript variant, splice acceptor variant
rs775299709	G>A,T	Pathogenic	Missense variant, stop gained, non coding transcript variant, coding sequence variant
rs878855041	C>-	Pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs878855042	->T	Pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs886042621	G>C	Pathogenic	Splice donor variant
rs1060501719	CA>ACCG	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs1278589861	->A	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant
rs1346603171	G>A	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1568667609	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained, genic upstream transcript variant
rs1568709952	G>T	Likely-pathogenic	Genic downstream transcript variant, downstream transcript variant, splice donor variant

Show/Hide all (8)

miRTarBase ID	miRNA	Experiments
MIRT868886	hsa-miR-3168	CLIP-seq
MIRT868887	hsa-miR-3649	CLIP-seq
MIRT868888	hsa-miR-4263	CLIP-seq
MIRT868889	hsa-miR-4324	CLIP-seq
MIRT868890	hsa-miR-4475	CLIP-seq
MIRT868891	hsa-miR-4521	CLIP-seq
MIRT868892	hsa-miR-4693-3p	CLIP-seq
MIRT868893	hsa-miR-492	CLIP-seq

Show/Hide all (37)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001947	Process	Heart looping	IBA
GO:0001947	Process	Heart looping	IMP	22693285
GO:0003341	Process	Cilium movement	IEA
GO:0003341	Process	Cilium movement	IMP	22499950
GO:0003351	Process	Epithelial cilium movement involved in extracellular fluid movement	IMP	21131974
GO:0003356	Process	Regulation of cilium beat frequency	IMP	23255504
GO:0003356	Process	Regulation of cilium beat frequency	IMP	21131974
GO:0003674	Function	Molecular_function	ND
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005576	Component	Extracellular region	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0005929	Component	Cilium	IBA
GO:0005929	Component	Cilium	IDA	27120127
GO:0005929	Component	Cilium	IEA
GO:0005929	Component	Cilium	ISS
GO:0005930	Component	Axoneme	IDA	23255504
GO:0007368	Process	Determination of left/right symmetry	IEA
GO:0030317	Process	Flagellated sperm motility	IMP	23255504
GO:0030324	Process	Lung development	IEA
GO:0030324	Process	Lung development	IMP	22693285
GO:0031514	Component	Motile cilium	IEA
GO:0035082	Process	Axoneme assembly	IBA
GO:0035082	Process	Axoneme assembly	IEA
GO:0035082	Process	Axoneme assembly	IEA
GO:0035469	Process	Determination of pancreatic left/right asymmetry	IMP	22693285
GO:0036159	Process	Inner dynein arm assembly	IMP	23255504
GO:0042995	Component	Cell projection	IEA
GO:0044458	Process	Motile cilium assembly	IMP	23255504
GO:0060287	Process	Epithelial cilium movement involved in determination of left/right asymmetry	IBA
GO:0060287	Process	Epithelial cilium movement involved in determination of left/right asymmetry	IEA
GO:0060287	Process	Epithelial cilium movement involved in determination of left/right asymmetry	IMP	21131974
GO:0061512	Process	Protein localization to cilium	IEA
GO:0070286	Process	Axonemal dynein complex assembly	IMP	21131974
GO:0071907	Process	Determination of digestive tract left/right asymmetry	IMP	22693285
GO:0071910	Process	Determination of liver left/right asymmetry	IMP	22693285

MIM	HGNC	e!Ensembl
613799	26090	ENSG00000141519

Q4G0X9

Protein name

Coiled-coil domain-containing protein 40

Protein function

Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella (PubMed:21131974). Probably acts t

PDB

8J07

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08647	BRE1	780 → 878		Family

Sequence

MAEPGGAAGRSHPEDGSASEGEKEGNNESHMVSPPEKDDGQKGEEAVGSTEHPEEVTTQA
EAAIEEGEVETEGEAAVEGEEEAVSYGDAESEEEYYYTETSSPEGQISAADTTYPYFSPP
QELPGEEAYDSVSGEAGLQGFQQEATGPPESRERRVTSPEPSHGVLGPSEQMGQVTSGPA
VGRLTGSTEEPQGQVLPMGVQHRFRLSHGSDIESSDLEEFVSQEPVIPPGVPDAHPREGD
LPVFQDQIQQPSTEEGAMAERVESEGSDEEAEDEGSQLVVLDPDHPLMVRFQAALKNYLN
RQIEKLKLDLQELVVATKQSRAQRQELGVNLYEVQQHLVHLQKLLEKSHDRHAMASSERR
QKEEELQAARALYTKTCAAANEERKKLAALQTEMENLALHLFYMQNIDQDMRDDIRVMTQ
VVKKAETERIRAEIEKKKQDLYVDQLTTRAQQLEEDIALFEAQYLAQAEDTRILRKAVSE
ACTEIDAISVEKRRIMQQWASSLVGMKHRDEAHRAVLEALRGCQHQAKSTDGEIEAYKKS
IMKEEEKNEKLASILNRTETEATLLQKLTTQCLTKQVALQSQFNTYRLTLQDTEDALSQD
QLEQMILTEELQAIRQAIQGELELRRKTDAAIREKLQEHMTSNKTTKYFNQLILRLQKEK
TNMMTHLSKINGDIAQTTLDITHTSSRLDAHQKTLVELDQDVKKVNELITNSQSEISRRT
ILIERKQGLINFLNKQLERMVSELGGEEVGPLELEIKRLSKLIDEHDGKAVQAQVTWLRL
QQEMVKVTQEQEEQLASLDASKKELHIMEQKKLRVESKIEQEKKEQKEIEHHMKDLDNDL
KKLNMLMNKNRCSSEELEQNNRVTENEFVRSLKASERETIKMQDKLNQLSEEKATLLNQL
VEAEHQIMLWEKKIQLAKEMRSSVDSEIGQTEIRAMKGEIHRMKVRLGQLLKQQEKMIRA
MELAVARRETVTTQAEGQRKMDRKALTRTDFHHKQLELRRKIRDVRKATDECTKTVLELE
ETQRNVSSSLLEKQEKLSVIQADFDTLEADLTRLGALKRQNLSEIVALQTRLKHLQAVKE
GRYVFLFRSKQSLVLERQRLDKRLALIATILDRVRDEYPQFQEALHKVSQMIANKLESPG
PS

Sequence length

1142

Interactions

View interactions

1057

Show/Hide Causal Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
CCDC40-related disorder	Likely pathogenic; Pathogenic	rs2510320263, rs397515393, rs370706991, rs371595543	RCV003391422 RCV004754277 RCV003902644 RCV004754462 RCV003965446
Combined immunodeficiency due to DOCK8 deficiency	Pathogenic	rs747233125	RCV003448338
Heterotaxy	Pathogenic	rs1363364769	RCV001732150
Kartagener syndrome	Pathogenic	rs587778819, rs745993158	RCV000578183 RCV000578202
Primary ciliary dyskinesia	Pathogenic; Likely pathogenic	rs2143733843, rs780516910, rs145595957, rs1277942930, rs1434356376, rs2143789412, rs2037179047, rs201223986, rs1185054167, rs2143577665, rs757076408, rs1312712049, rs1472033145, rs746285699, rs2510295858 View all (54 more)	RCV001383942 RCV003829883 RCV001389986 RCV002541177 RCV001849605 RCV001849606 RCV001849607 RCV001867529 RCV002028558 RCV001994571 RCV002000013 RCV001864564 RCV001910836 RCV003774923 RCV002362387 RCV002459704 RCV002439957 RCV000538390 RCV000544631 RCV002634121 RCV002711773 RCV002904835 RCV002932922 RCV000198649 RCV000196101 RCV003050195 RCV000204611 RCV000221299 RCV000230208 RCV000233917 RCV003537878 RCV003536614 RCV003537009 RCV003650944 RCV003652439 RCV003649977 RCV003650122 RCV003651619 RCV003651554 RCV003843031 RCV003874888 RCV003870381 RCV000199691 RCV000629328 RCV001065148 RCV000472562 RCV000465864 RCV000471764 RCV000539034 RCV000549409 RCV000528091 RCV002530363 RCV000701340 RCV000696160 RCV000694885 RCV000697808 RCV000705308 RCV000698577 RCV000693536 RCV000691179 RCV000689717 RCV005056539 RCV000822169 RCV000819424 RCV001068100 RCV001056046 RCV001071112 RCV001215091 RCV001236952 RCV001255298
Primary ciliary dyskinesia 15	Likely pathogenic; Pathogenic	rs1312712049, rs2143748349, rs2143781646, rs746285699, rs2510289393, rs587778819, rs374909386, rs754867753, rs2510295924, rs2510289441, rs1225389709, rs761619279, rs1188440303, rs397515393, rs387907092 View all (11 more)	RCV002503443 RCV002272652 RCV002272743 RCV002282755 RCV002282767 RCV001781534 RCV005868015 RCV000763421 RCV003140564 RCV003141233 RCV003233347 RCV005419685 RCV004547381 RCV000024063 RCV000024065 RCV000024066 RCV001782939 RCV000779234 RCV004556816 RCV001784323 RCV004788138 RCV002507205 RCV001333981 RCV000056177 RCV001197909 RCV001198567 RCV001198762
Primary ciliary dyskinesia 3	Pathogenic	rs2510290432	RCV003234812
Respiratory ciliopathies including non-CF bronchiectasis	Likely pathogenic; Pathogenic	rs374909386	RCV004782285
Thyroid cancer, nonmedullary, 1	Likely pathogenic	rs774081599	RCV005899464

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
axonemas with defects on microtubules	Uncertain significance	rs569842522	RCV000128823
Cervical cancer	Likely benign	rs117430046	RCV005918906
Familial cancer of breast	Benign	rs7219552	RCV005919461
Hepatocellular carcinoma	Uncertain significance	rs141588728	RCV005924139
Lung cancer	Benign	rs79483216	RCV005918052
Male infertility	Conflicting classifications of pathogenicity; Uncertain significance	rs201042940, rs2038463011	RCV001283738 RCV001283737
Malignant lymphoma, large B-cell, diffuse	Benign	rs79483216	RCV005918047
Malignant tumor of esophagus	Likely benign	rs117430046	RCV005918905
Ovarian serous cystadenocarcinoma	Benign; Uncertain significance	rs79483216, rs141588728, rs2037242845	RCV005918049 RCV005924140 RCV005910959
Sarcoma	Likely benign; Benign	rs117430046, rs79483216	RCV005918907 RCV005918048
See cases	Uncertain significance	rs371890970, rs751821953	RCV003128425 RCV002287804
sperm axonema without dynein arms and nexin bridges	Uncertain significance	rs569842522	RCV000128823
Thymoma	Benign	rs79483216	RCV005918051
Usher syndrome	Conflicting classifications of pathogenicity	rs759468416	RCV003389486
Uterine carcinosarcoma	Benign	rs79483216	RCV005918050
Uterine corpus endometrial carcinoma	Likely benign; Benign	rs117430046, rs79483216	RCV005918908 RCV005918053

Show/Hide Text Mining Associations (11)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Arm Injuries	Associate	39383539
Ciliary Motility Disorders	Associate	22499950, 23255504, 25186273, 30067075, 30209139, 30296669, 31443223, 33577779, 34941110, 37998386, 38072392, 39383539, 39879322
Congenital Abnormalities	Associate	23255504, 30067075
Hypogonadism	Associate	33574797
Immotile cilia syndrome due to defective radial spokes	Associate	23255504
Infertility	Associate	34941110
Infertility Male	Associate	33574797
Kartagener Syndrome	Associate	31443223
Lung Diseases	Associate	25493340, 30209139
Lung Injury	Associate	30067075
Metatropic dwarfism	Associate	30067075, 39383539

CCDC40 (coiled-coil domain 40 molecular ruler complex subunit)