CCDC8 (coiled-coil domain containing 8) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: CCDC8 (coiled-coil domain containing 8) Homo sapiens
Analyze
Symbol: CCDC8
Name: coiled-coil domain containing 8
RGD ID: 1351060
HGNC Page HGNC
Description: Involved in microtubule cytoskeleton organization; negative regulation of phosphatase activity; and regulation of mitotic nuclear division. Localizes to several cellular components, including 3M complex; centrosome; and nucleoplasm. Implicated in 3-M syndrome.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: 3M3; coiled-coil domain containing protein 8; coiled-coil domain-containing protein 8; DKFZp564K0322; p90; PPP1R20; protein phosphatase 1, regulatory subunit 20
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1946,410,329 - 46,413,564 (-)EnsemblGRCh38hg38GRCh38
GRCh381946,410,329 - 46,413,564 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371946,913,586 - 46,916,821 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361951,605,925 - 51,608,681 (-)NCBINCBI36hg18NCBI36
Build 341951,605,928 - 51,608,681NCBI
Celera1943,718,552 - 43,721,888 (-)NCBI
Cytogenetic Map19q13.32NCBI
HuRef1943,341,075 - 43,344,411 (-)NCBIHuRef
CHM1_11946,915,521 - 46,918,858 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
3M complex  (IBA,IDA)
centrosome  (IDA)
cytoplasm  (IDA)
cytosol  (IDA,TAS)
nucleoplasm  (IDA)
plasma membrane  (IDA)

Molecular Function

References

Additional References at PubMed
PMID:11230166   PMID:11256614   PMID:15489334   PMID:19389623   PMID:20301654   PMID:21572988   PMID:21737058   PMID:21873635   PMID:22084066   PMID:22156540   PMID:23018678   PMID:23443559  
PMID:23455922   PMID:23602568   PMID:24711643   PMID:24778252   PMID:24793695   PMID:25752541   PMID:26186194   PMID:26423533   PMID:26972000   PMID:27173435   PMID:27342910   PMID:27705803  
PMID:27880917   PMID:28514442   PMID:28700999   PMID:29229926   PMID:29507117   PMID:31343991   PMID:32651437  


Genomics

Comparative Map Data
CCDC8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1946,410,329 - 46,413,564 (-)EnsemblGRCh38hg38GRCh38
GRCh381946,410,329 - 46,413,564 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371946,913,586 - 46,916,821 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361951,605,925 - 51,608,681 (-)NCBINCBI36hg18NCBI36
Build 341951,605,928 - 51,608,681NCBI
Celera1943,718,552 - 43,721,888 (-)NCBI
Cytogenetic Map19q13.32NCBI
HuRef1943,341,075 - 43,344,411 (-)NCBIHuRef
CHM1_11946,915,521 - 46,918,858 (-)NCBICHM1_1
Ccdc8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39716,727,827 - 16,731,440 (+)NCBIGRCm39mm39
GRCm39 Ensembl716,726,633 - 16,731,441 (+)Ensembl
GRCm38716,993,902 - 16,997,515 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl716,992,708 - 16,997,516 (+)EnsemblGRCm38mm10GRCm38
MGSCv37717,579,937 - 17,581,994 (+)NCBIGRCm37mm9NCBIm37
MGSCv36717,579,937 - 17,581,994 (+)NCBImm8
Celera714,201,787 - 14,203,844 (+)NCBICelera
Cytogenetic Map7A2NCBI
Ccdc8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2177,679,521 - 77,682,849 (+)NCBI
Rnor_6.0 Ensembl178,933,372 - 78,936,700 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0178,933,372 - 78,936,700 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0180,180,875 - 80,184,203 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4177,334,504 - 77,337,832 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1177,412,614 - 77,415,946 (+)NCBI
Celera172,164,565 - 72,167,893 (+)NCBICelera
Cytogenetic Map1q21NCBI
Ccdc8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955574551,582 - 553,829 (-)NCBIChiLan1.0ChiLan1.0
CCDC8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11951,929,302 - 51,932,355 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1951,928,645 - 51,931,510 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01943,399,711 - 43,403,207 (-)NCBIMhudiblu_PPA_v0panPan3
CCDC8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11109,349,965 - 109,354,521 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1109,352,047 - 109,353,612 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1108,829,144 - 108,833,529 (-)NCBI
ROS_Cfam_1.01109,876,129 - 109,880,330 (-)NCBI
UMICH_Zoey_3.11109,552,986 - 109,557,370 (-)NCBI
UNSW_CanFamBas_1.01109,187,080 - 109,191,732 (-)NCBI
UU_Cfam_GSD_1.01110,055,960 - 110,060,345 (-)NCBI
Ccdc8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934918,811,581 - 18,814,544 (+)NCBI
SpeTri2.0NW_004936664429,733 - 432,673 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl652,476,117 - 52,477,532 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1652,474,508 - 52,478,257 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2647,679,728 - 47,682,688 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC8
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1639,793,931 - 39,796,665 (-)NCBI
ChlSab1.1 Ensembl639,794,179 - 39,795,819 (-)Ensembl
Ccdc8
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248327,089,777 - 7,092,557 (+)NCBI

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:480
Count of miRNA genes:372
Interacting mature miRNAs:406
Transcripts:ENST00000307522
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 293 1885 1196 67 26 22 1218 481 479 189 1132 985 49 1 263 822 2
Low 2020 354 284 321 686 203 2932 1550 3125 188 289 487 121 941 1816 3 2
Below cutoff 36 587 225 221 792 223 177 159 102 32 13 61 2 150 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000307522   ⟹   ENSP00000303158
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1946,410,329 - 46,413,564 (-)Ensembl
RefSeq Acc Id: NM_032040   ⟹   NP_114429
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381946,410,329 - 46,413,564 (-)NCBI
GRCh371946,913,586 - 46,916,919 (-)RGD
Build 361951,605,925 - 51,608,681 (-)NCBI Archive
Celera1943,718,552 - 43,721,888 (-)RGD
HuRef1943,341,075 - 43,344,411 (-)RGD
CHM1_11946,915,521 - 46,918,858 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_114429   ⟸   NM_032040
- UniProtKB: Q9H0W5 (UniProtKB/Swiss-Prot),   G8IFA7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000303158   ⟸   ENST00000307522

Promoters
RGD ID:6795253
Promoter ID:HG_KWN:30336
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562,   Lymphoblastoid,   NB4
Transcripts:NM_032040
Position:
Human AssemblyChrPosition (strand)Source
Build 361951,608,421 - 51,608,921 (-)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_032040.5(CCDC8):c.612dup (p.Lys205fs) duplication Three M syndrome 3 [RCV000024100] Chr19:46412198..46412199 [GRCh38]
Chr19:46915455..46915456 [GRCh37]
Chr19:19q13.32
pathogenic
NM_032040.5(CCDC8):c.84dup (p.Lys29Ter) duplication Three M syndrome 3 [RCV000024101] Chr19:46412726..46412727 [GRCh38]
Chr19:46915983..46915984 [GRCh37]
Chr19:19q13.32
pathogenic|uncertain significance
GRCh38/hg38 19q13.32(chr19:45595873-46600026)x1 copy number loss See cases [RCV000050710] Chr19:45595873..46600026 [GRCh38]
Chr19:46099131..47103283 [GRCh37]
Chr19:50790971..51795123 [NCBI36]
Chr19:19q13.32
pathogenic
GRCh38/hg38 19q13.32-13.33(chr19:44971420-48257402)x3 copy number gain See cases [RCV000136578] Chr19:44971420..48257402 [GRCh38]
Chr19:45474677..48760659 [GRCh37]
Chr19:50166517..53452471 [NCBI36]
Chr19:19q13.32-13.33
pathogenic
GRCh38/hg38 19q13.32(chr19:45387389-46831000)x1 copy number loss See cases [RCV000137832] Chr19:45387389..46831000 [GRCh38]
Chr19:45890647..47334257 [GRCh37]
Chr19:50582487..52026097 [NCBI36]
Chr19:19q13.32
likely pathogenic
GRCh37/hg19 19q13.2-13.32(chr19:43013365-47241534)x1 copy number loss See cases [RCV000240182] Chr19:43013365..47241534 [GRCh37]
Chr19:19q13.2-13.32
pathogenic
NM_032040.5(CCDC8):c.1521G>C (p.Lys507Asn) single nucleotide variant not specified [RCV000247205] Chr19:46411290 [GRCh38]
Chr19:46914547 [GRCh37]
Chr19:19q13.32
benign
NM_032040.5(CCDC8):c.1141G>A (p.Asp381Asn) single nucleotide variant not specified [RCV000242410] Chr19:46411670 [GRCh38]
Chr19:46914927 [GRCh37]
Chr19:19q13.32
benign
NM_032040.5(CCDC8):c.954T>G (p.Asn318Lys) single nucleotide variant not provided [RCV000431700] Chr19:46411857 [GRCh38]
Chr19:46915114 [GRCh37]
Chr19:19q13.32
benign|likely benign
NM_032040.5(CCDC8):c.1555del (p.Arg519fs) deletion Three M syndrome 3 [RCV001333305]|not provided [RCV000523098] Chr19:46411256 [GRCh38]
Chr19:46914513 [GRCh37]
Chr19:19q13.32
pathogenic|uncertain significance
GRCh37/hg19 19q13.32-13.33(chr19:46404248-48488721)x1 copy number loss See cases [RCV000511362] Chr19:46404248..48488721 [GRCh37]
Chr19:19q13.32-13.33
likely pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888) copy number gain See cases [RCV000512296] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888)x3 copy number gain See cases [RCV000511289] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic|uncertain significance
GRCh37/hg19 19p13.3-q13.43(chr19:68029-59110290)x3 copy number gain not provided [RCV000752439] Chr19:68029..59110290 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-59097160)x3 copy number gain not provided [RCV000752444] Chr19:260912..59097160 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
NM_032040.5(CCDC8):c.1045G>C (p.Ala349Pro) single nucleotide variant not provided [RCV000962730] Chr19:46411766 [GRCh38]
Chr19:46915023 [GRCh37]
Chr19:19q13.32
benign
NM_032040.5(CCDC8):c.1113C>G (p.Ala371=) single nucleotide variant not provided [RCV000970907] Chr19:46411698 [GRCh38]
Chr19:46914955 [GRCh37]
Chr19:19q13.32
benign
NM_032040.5(CCDC8):c.402C>T (p.Tyr134=) single nucleotide variant not provided [RCV000923970] Chr19:46412409 [GRCh38]
Chr19:46915666 [GRCh37]
Chr19:19q13.32
likely benign
NM_032040.5(CCDC8):c.876G>T (p.Glu292Asp) single nucleotide variant not provided [RCV000970362] Chr19:46411935 [GRCh38]
Chr19:46915192 [GRCh37]
Chr19:19q13.32
likely benign
NM_032040.5(CCDC8):c.67G>A (p.Val23Ile) single nucleotide variant not provided [RCV000925176] Chr19:46412744 [GRCh38]
Chr19:46916001 [GRCh37]
Chr19:19q13.32
likely benign
NM_032040.5(CCDC8):c.818C>T (p.Ser273Phe) single nucleotide variant Immunodeficiency [RCV001007938] Chr19:46411993 [GRCh38]
Chr19:46915250 [GRCh37]
Chr19:19q13.32
uncertain significance
NM_032040.5(CCDC8):c.43C>T (p.Arg15Trp) single nucleotide variant Three M syndrome 3 [RCV001333306]|not provided [RCV000886267] Chr19:46412768 [GRCh38]
Chr19:46916025 [GRCh37]
Chr19:19q13.32
likely benign|uncertain significance
NM_032040.5(CCDC8):c.599A>T (p.Gln200Leu) single nucleotide variant not provided [RCV000893838] Chr19:46412212 [GRCh38]
Chr19:46915469 [GRCh37]
Chr19:19q13.32
benign
NM_032040.5(CCDC8):c.167C>T (p.Ala56Val) single nucleotide variant not provided [RCV000897225] Chr19:46412644 [GRCh38]
Chr19:46915901 [GRCh37]
Chr19:19q13.32
likely benign
NM_032040.5(CCDC8):c.1235T>A (p.Val412Glu) single nucleotide variant not provided [RCV000964389] Chr19:46411576 [GRCh38]
Chr19:46914833 [GRCh37]
Chr19:19q13.32
benign
NM_032040.5(CCDC8):c.824G>A (p.Arg275Gln) single nucleotide variant not provided [RCV000906045] Chr19:46411987 [GRCh38]
Chr19:46915244 [GRCh37]
Chr19:19q13.32
likely benign
NM_032040.5(CCDC8):c.543G>A (p.Glu181=) single nucleotide variant not provided [RCV000921076] Chr19:46412268 [GRCh38]
Chr19:46915525 [GRCh37]
Chr19:19q13.32
likely benign
NM_032040.5(CCDC8):c.60T>C (p.Ala20=) single nucleotide variant not provided [RCV000963186] Chr19:46412751 [GRCh38]
Chr19:46916008 [GRCh37]
Chr19:19q13.32
benign
GRCh37/hg19 19q13.32-13.33(chr19:45531056-48174177)x3 copy number gain not provided [RCV001007051] Chr19:45531056..48174177 [GRCh37]
Chr19:19q13.32-13.33
uncertain significance
GRCh37/hg19 19q11-13.33(chr19:28271106-49213832)x3 copy number gain not provided [RCV000845733] Chr19:28271106..49213832 [GRCh37]
Chr19:19q11-13.33
pathogenic
GRCh37/hg19 19q13.31-13.42(chr19:44738088-53621561)x3 copy number gain not provided [RCV001007050] Chr19:44738088..53621561 [GRCh37]
Chr19:19q13.31-13.42
pathogenic
NM_032040.5(CCDC8):c.817_829del (p.Ser273fs) deletion Three M syndrome 3 [RCV001199107] Chr19:46411982..46411994 [GRCh38]
Chr19:46915239..46915251 [GRCh37]
Chr19:19q13.32
likely pathogenic
NM_032040.5(CCDC8):c.203_204del (p.Gln68fs) deletion Three M syndrome 3 [RCV001198938] Chr19:46412607..46412608 [GRCh38]
Chr19:46915864..46915865 [GRCh37]
Chr19:19q13.32
likely pathogenic
NM_032040.5(CCDC8):c.126C>T (p.Thr42=) single nucleotide variant not provided [RCV000962704] Chr19:46412685 [GRCh38]
Chr19:46915942 [GRCh37]
Chr19:19q13.32
benign
NM_032040.5(CCDC8):c.1446C>T (p.Thr482=) single nucleotide variant not provided [RCV000888143] Chr19:46411365 [GRCh38]
Chr19:46914622 [GRCh37]
Chr19:19q13.32
likely benign
NM_032040.5(CCDC8):c.1371A>C (p.Ser457=) single nucleotide variant not provided [RCV000914732] Chr19:46411440 [GRCh38]
Chr19:46914697 [GRCh37]
Chr19:19q13.32
likely benign
NM_032040.5(CCDC8):c.963del (p.Ala323fs) deletion Three M syndrome 3 [RCV001283853] Chr19:46411848 [GRCh38]
Chr19:46915105 [GRCh37]
Chr19:19q13.32
likely pathogenic
NM_032040.5(CCDC8):c.1609C>T (p.Gln537Ter) single nucleotide variant Three M syndrome 3 [RCV001329459] Chr19:46411202 [GRCh38]
Chr19:46914459 [GRCh37]
Chr19:19q13.32
pathogenic
NM_032040.5(CCDC8):c.287C>G (p.Thr96Arg) single nucleotide variant Three M syndrome 3 [RCV001329460] Chr19:46412524 [GRCh38]
Chr19:46915781 [GRCh37]
Chr19:19q13.32
uncertain significance
NM_032040.5(CCDC8):c.346_347del (p.Lys116fs) deletion Three M syndrome 3 [RCV001329461] Chr19:46412464..46412465 [GRCh38]
Chr19:46915721..46915722 [GRCh37]
Chr19:19q13.32
pathogenic
NM_032040.5(CCDC8):c.803_807delinsT (p.Lys268fs) indel Three M syndrome 3 [RCV001329462] Chr19:46412004..46412008 [GRCh38]
Chr19:46915261..46915265 [GRCh37]
Chr19:19q13.32
likely pathogenic
NM_032040.5(CCDC8):c.1027C>T (p.Gln343Ter) single nucleotide variant Three M syndrome 3 [RCV001333304] Chr19:46411784 [GRCh38]
Chr19:46915041 [GRCh37]
Chr19:19q13.32
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:25367 AgrOrtholog
COSMIC CCDC8 COSMIC
Ensembl Genes ENSG00000169515 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000303158 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000307522 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000169515 GTEx
HGNC ID HGNC:25367 ENTREZGENE
Human Proteome Map CCDC8 Human Proteome Map
InterPro PNMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:83987 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 83987 ENTREZGENE
OMIM 614145 OMIM
  614205 OMIM
Pfam PNMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134931534 PharmGKB
UniProt A0A142DDU4_HUMAN UniProtKB/TrEMBL
  CCDC8_HUMAN UniProtKB/Swiss-Prot
  G8IFA7 ENTREZGENE, UniProtKB/TrEMBL
  Q9H0W5 ENTREZGENE
UniProt Secondary Q8TB26 UniProtKB/Swiss-Prot