CKAP4 (cytoskeleton associated protein 4) - Rat Genome Database

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Gene: CKAP4 (cytoskeleton associated protein 4) Homo sapiens
Analyze
Symbol: CKAP4
Name: cytoskeleton associated protein 4
RGD ID: 1323735
HGNC Page HGNC:16991
Description: Enables RNA binding activity. Located in lipid droplet and rough endoplasmic reticulum. Biomarker of hepatocellular carcinoma.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 63 kDa membrane protein; 63-kDa cytoskeleton-linking membrane protein; CLIMP-63; CLIMP63; cytoskeleton-associated protein 4; ERGIC-63; MGC99554; p63; transmembrane protein (63kD), endoplasmic reticulum/Golgi intermediate compartment; type-II transmembrane protein p63
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812106,237,881 - 106,248,020 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12106,237,881 - 106,304,279 (-)EnsemblGRCh38hg38GRCh38
GRCh3712106,631,659 - 106,641,798 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612105,155,910 - 105,165,843 (-)NCBINCBI36Build 36hg18NCBI36
Build 3412105,134,258 - 105,144,180NCBI
Celera12106,297,004 - 106,307,057 (-)NCBICelera
Cytogenetic Map12q23.3NCBI
HuRef12103,692,427 - 103,702,094 (-)NCBIHuRef
CHM1_112106,597,488 - 106,607,544 (-)NCBICHM1_1
T2T-CHM13v2.012106,200,876 - 106,211,009 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (ISO)
(-)-epigallocatechin 3-gallate  (EXP)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (ISO)
3-chloropropane-1,2-diol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-amino-2,6-dinitrotoluene  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (ISO)
acetamide  (ISO)
acrylamide  (ISO)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP)
amitrole  (ISO)
aristolochic acid A  (EXP)
arsane  (EXP)
arsenic atom  (EXP)
arsenous acid  (EXP)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (EXP)
benzoates  (EXP)
bisphenol A  (EXP,ISO)
Bisphenol B  (EXP)
bisphenol F  (EXP)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
CGP 52608  (EXP)
chloropicrin  (EXP)
clozapine  (EXP)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
coumarin  (EXP)
coumestrol  (EXP)
cyclosporin A  (EXP,ISO)
dexamethasone  (EXP)
diarsenic trioxide  (EXP)
disulfiram  (EXP)
dopamine  (ISO)
doxorubicin  (EXP)
endosulfan  (ISO)
fenoldopam  (ISO)
fenvalerate  (ISO)
formaldehyde  (EXP)
FR900359  (EXP)
furan  (ISO)
gentamycin  (ISO)
indole-3-methanol  (ISO)
indometacin  (EXP)
inulin  (ISO)
ivermectin  (EXP)
methapyrilene  (ISO)
methimazole  (ISO)
methotrexate  (EXP)
methoxychlor  (ISO)
methyl methanesulfonate  (EXP)
N-nitrosodiethylamine  (ISO)
oxaliplatin  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (EXP)
silicon dioxide  (ISO)
sulfadimethoxine  (ISO)
tacrolimus hydrate  (ISO)
temozolomide  (EXP)
tetrachloromethane  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
topotecan  (ISO)
trichloroethene  (ISO)
tris(2-butoxyethyl) phosphate  (EXP)
tungsten  (ISO)
urethane  (EXP)
valproic acid  (EXP)
vinclozolin  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Significant Down-Regulation of Urea Cycle Generates Clinically Relevant Proteomic Signature in Hepatocellular Carcinoma Patients with Macrovascular Invasion. Cao Y, etal., J Proteome Res. 2019 May 3;18(5):2032-2044. doi: 10.1021/acs.jproteome.8b00921. Epub 2019 Mar 29.
2. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1730740   PMID:7673362   PMID:8125298   PMID:8314870   PMID:8566419   PMID:11402071   PMID:12477932   PMID:12913003   PMID:14741744   PMID:15476176   PMID:15489334   PMID:15623521  
PMID:15703217   PMID:16169070   PMID:16398404   PMID:16546853   PMID:17030514   PMID:17620599   PMID:17975794   PMID:18296695   PMID:18333895   PMID:18468998   PMID:18708633   PMID:18816836  
PMID:19056867   PMID:19144824   PMID:19322201   PMID:19401338   PMID:19531213   PMID:19615732   PMID:19861536   PMID:20156774   PMID:20184665   PMID:20562859   PMID:20706999   PMID:20808887  
PMID:20870746   PMID:21111237   PMID:21143984   PMID:21145461   PMID:21150319   PMID:21655359   PMID:21820419   PMID:21873635   PMID:21907836   PMID:21988832   PMID:22056955   PMID:22190034  
PMID:22329826   PMID:22406481   PMID:22438586   PMID:22658674   PMID:22681889   PMID:22966120   PMID:22990118   PMID:23047949   PMID:23108156   PMID:23254330   PMID:23665508   PMID:23913486  
PMID:23921950   PMID:23979707   PMID:24244333   PMID:24454821   PMID:24711643   PMID:24755837   PMID:24838946   PMID:24981860   PMID:24999758   PMID:25008318   PMID:25144556   PMID:25192599  
PMID:25437307   PMID:25754235   PMID:25756610   PMID:25849921   PMID:25852190   PMID:25921289   PMID:25963833   PMID:26186194   PMID:26472760   PMID:26496610   PMID:26527279   PMID:26549023  
PMID:26638075   PMID:27025967   PMID:27322059   PMID:27342126   PMID:27562070   PMID:27705803   PMID:27880917   PMID:28514442   PMID:28514532   PMID:28515276   PMID:28611094   PMID:28675297  
PMID:28685749   PMID:28692057   PMID:28795417   PMID:28893174   PMID:28902428   PMID:29117568   PMID:29128334   PMID:29180619   PMID:29229926   PMID:29298432   PMID:29395067   PMID:29459360  
PMID:29467282   PMID:29507755   PMID:29509190   PMID:29563607   PMID:29568061   PMID:29751934   PMID:29845934   PMID:29911972   PMID:29961565   PMID:30021884   PMID:30089695   PMID:30181180  
PMID:30194290   PMID:30196744   PMID:30320910   PMID:30581152   PMID:30584103   PMID:30591555   PMID:30610103   PMID:30619736   PMID:30737378   PMID:30804502   PMID:30809309   PMID:30833792  
PMID:30940648   PMID:30948266   PMID:31048545   PMID:31056421   PMID:31059266   PMID:31067453   PMID:31073040   PMID:31091453   PMID:31160493   PMID:31177093   PMID:31180492   PMID:31280863  
PMID:31343991   PMID:31409639   PMID:31469817   PMID:31536960   PMID:31586073   PMID:31696529   PMID:31732153   PMID:31744930   PMID:31753913   PMID:31871319   PMID:32075961   PMID:32129710  
PMID:32149426   PMID:32203420   PMID:32239614   PMID:32382008   PMID:32552912   PMID:32587255   PMID:32788342   PMID:32807901   PMID:32850835   PMID:32877691   PMID:32913203   PMID:32941674  
PMID:32963011   PMID:32994395   PMID:33022573   PMID:33024031   PMID:33029523   PMID:33067255   PMID:33111431   PMID:33144569   PMID:33194618   PMID:33239621   PMID:33306668   PMID:33536335  
PMID:33545068   PMID:33567341   PMID:33658012   PMID:33731348   PMID:33742100   PMID:33766124   PMID:33845483   PMID:33863777   PMID:33957083   PMID:33961781   PMID:33999101   PMID:34079085  
PMID:34079125   PMID:34226595   PMID:34316702   PMID:34349018   PMID:34383978   PMID:34432599   PMID:34462429   PMID:34470047   PMID:34476666   PMID:34597346   PMID:34672954   PMID:34709727  
PMID:34718347   PMID:34732716   PMID:34901782   PMID:35013218   PMID:35031058   PMID:35122331   PMID:35271311   PMID:35338135   PMID:35384245   PMID:35509820   PMID:35563538   PMID:35652658  
PMID:35696571   PMID:35831895   PMID:35833506   PMID:35850772   PMID:35944360   PMID:35977942   PMID:36114006   PMID:36168627   PMID:36180527   PMID:36215168   PMID:36232890   PMID:36244648  
PMID:36373674   PMID:36376293   PMID:36517590   PMID:36526897   PMID:36574265   PMID:36590901   PMID:36610398   PMID:36634849   PMID:36779763   PMID:36847199   PMID:37208923   PMID:37232246  
PMID:37689310   PMID:37774976   PMID:37827155   PMID:37916373   PMID:37931956   PMID:38113892  


Genomics

Comparative Map Data
CKAP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812106,237,881 - 106,248,020 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12106,237,881 - 106,304,279 (-)EnsemblGRCh38hg38GRCh38
GRCh3712106,631,659 - 106,641,798 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612105,155,910 - 105,165,843 (-)NCBINCBI36Build 36hg18NCBI36
Build 3412105,134,258 - 105,144,180NCBI
Celera12106,297,004 - 106,307,057 (-)NCBICelera
Cytogenetic Map12q23.3NCBI
HuRef12103,692,427 - 103,702,094 (-)NCBIHuRef
CHM1_112106,597,488 - 106,607,544 (-)NCBICHM1_1
T2T-CHM13v2.012106,200,876 - 106,211,009 (-)NCBIT2T-CHM13v2.0
Ckap4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391084,362,169 - 84,369,752 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1084,362,169 - 84,369,926 (-)EnsemblGRCm39 Ensembl
GRCm381084,526,305 - 84,533,888 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1084,526,305 - 84,534,062 (-)EnsemblGRCm38mm10GRCm38
MGSCv371083,989,050 - 83,996,633 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361083,956,104 - 83,963,687 (-)NCBIMGSCv36mm8
Celera1086,505,218 - 86,512,538 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1041.52NCBI
Ckap4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8721,118,527 - 21,126,624 (+)NCBIGRCr8
mRatBN7.2719,230,814 - 19,238,914 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl719,230,203 - 19,238,914 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx721,191,759 - 21,199,836 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0723,354,431 - 23,362,511 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0723,131,395 - 23,139,469 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0724,935,243 - 24,947,595 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl724,939,498 - 24,947,595 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0725,080,829 - 25,093,002 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4721,360,351 - 21,368,448 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1721,380,378 - 21,388,718 (+)NCBI
Celera716,439,983 - 16,448,066 (+)NCBICelera
Cytogenetic Map7q13NCBI
Ckap4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540540,277,082 - 40,279,486 (-)NCBIChiLan1.0ChiLan1.0
CKAP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210114,305,691 - 114,316,052 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112114,302,088 - 114,312,039 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012103,817,736 - 103,827,575 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112107,212,467 - 107,221,835 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12107,212,467 - 107,221,842 (-)Ensemblpanpan1.1panPan2
CKAP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11032,389,226 - 32,398,464 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1032,389,086 - 32,398,475 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1032,309,072 - 32,318,318 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01033,230,145 - 33,239,393 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1033,229,742 - 33,239,291 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11032,966,175 - 32,975,415 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01033,254,845 - 33,264,099 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01033,442,555 - 33,451,808 (+)NCBIUU_Cfam_GSD_1.0
Ckap4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494515,625,519 - 15,628,150 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049364928,635,275 - 8,638,696 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CKAP4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl514,021,131 - 14,030,039 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1514,021,131 - 14,031,196 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2514,098,558 - 14,107,444 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CKAP4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111101,460,989 - 101,471,104 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11101,460,759 - 101,471,474 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037143,565,403 - 143,575,609 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ckap4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247503,067,167 - 3,079,095 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CKAP4
29 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q23.3-24.13(chr12:105234677-112194686)x1 copy number loss See cases [RCV000050807] Chr12:105234677..112194686 [GRCh38]
Chr12:105628455..112632490 [GRCh37]
Chr12:104152585..111116873 [NCBI36]
Chr12:12q23.3-24.13
pathogenic
GRCh38/hg38 12q23.1-23.3(chr12:100670616-108583607)x1 copy number loss See cases [RCV000051320] Chr12:100670616..108583607 [GRCh38]
Chr12:101064394..108977383 [GRCh37]
Chr12:99588525..107501512 [NCBI36]
Chr12:12q23.1-23.3
pathogenic
GRCh38/hg38 12q23.3(chr12:104550262-106565399)x1 copy number loss See cases [RCV000053281] Chr12:104550262..106565399 [GRCh38]
Chr12:104944040..106959177 [GRCh37]
Chr12:103468170..105483307 [NCBI36]
Chr12:12q23.3
uncertain significance
GRCh38/hg38 12q23.3-24.11(chr12:105644967-108994840)x1 copy number loss See cases [RCV000138537] Chr12:105644967..108994840 [GRCh38]
Chr12:106038745..109432645 [GRCh37]
Chr12:104562875..107917026 [NCBI36]
Chr12:12q23.3-24.11
uncertain significance
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33
pathogenic
GRCh38/hg38 12q21.33-24.11(chr12:91044318-109133210)x3 copy number gain See cases [RCV000142447] Chr12:91044318..109133210 [GRCh38]
Chr12:91438095..109571015 [GRCh37]
Chr12:89962226..108055398 [NCBI36]
Chr12:12q21.33-24.11
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic|likely pathogenic
NM_006825.4(CKAP4):c.1256G>C (p.Gly419Ala) single nucleotide variant not specified [RCV004317829] Chr12:106239577 [GRCh38]
Chr12:106633355 [GRCh37]
Chr12:12q23.3
uncertain significance
GRCh37/hg19 12q23.2-24.11(chr12:103044333-111639805)x1 copy number loss See cases [RCV000445832] Chr12:103044333..111639805 [GRCh37]
Chr12:12q23.2-24.11
likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
NM_006825.4(CKAP4):c.1433C>T (p.Thr478Ile) single nucleotide variant not specified [RCV004290454] Chr12:106239400 [GRCh38]
Chr12:106633178 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1699A>C (p.Ile567Leu) single nucleotide variant not specified [RCV004313223] Chr12:106239134 [GRCh38]
Chr12:106632912 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.919A>G (p.Met307Val) single nucleotide variant not specified [RCV004304858] Chr12:106239914 [GRCh38]
Chr12:106633692 [GRCh37]
Chr12:12q23.3
uncertain significance
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12q23.3(chr12:106632675-106642064)x1 copy number loss not provided [RCV000738024] Chr12:106632675..106642064 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106637876-106642064)x1 copy number loss not provided [RCV000738025] Chr12:106637876..106642064 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106637876-106649988)x1 copy number loss not provided [RCV000738026] Chr12:106637876..106649988 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106640871-106641886)x3 copy number gain not provided [RCV000738027] Chr12:106640871..106641886 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106640871-106650351)x1 copy number loss not provided [RCV000738028] Chr12:106640871..106650351 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106640981-106641886)x3 copy number gain not provided [RCV000738029] Chr12:106640981..106641886 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106640981-106642064)x1 copy number loss not provided [RCV000738030] Chr12:106640981..106642064 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106641137-106641767)x1 copy number loss not provided [RCV000738031] Chr12:106641137..106641767 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106641188-106642064)x1 copy number loss not provided [RCV000738032] Chr12:106641188..106642064 [GRCh37]
Chr12:12q23.3
benign
NM_006825.4(CKAP4):c.151C>T (p.Pro51Ser) single nucleotide variant not specified [RCV004304312] Chr12:106247701 [GRCh38]
Chr12:106641479 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.595C>T (p.Arg199Trp) single nucleotide variant not specified [RCV004306838] Chr12:106240238 [GRCh38]
Chr12:106634016 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1058C>T (p.Thr353Met) single nucleotide variant not specified [RCV004309455] Chr12:106239775 [GRCh38]
Chr12:106633553 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.708G>A (p.Thr236=) single nucleotide variant not provided [RCV000911032] Chr12:106240125 [GRCh38]
Chr12:106633903 [GRCh37]
Chr12:12q23.3
benign
NM_006825.4(CKAP4):c.1332C>T (p.His444=) single nucleotide variant not provided [RCV000888160] Chr12:106239501 [GRCh38]
Chr12:106633279 [GRCh37]
Chr12:12q23.3
benign
NM_006825.4(CKAP4):c.1449C>T (p.Tyr483=) single nucleotide variant not provided [RCV000888337] Chr12:106239384 [GRCh38]
Chr12:106633162 [GRCh37]
Chr12:12q23.3
likely benign
NM_006825.4(CKAP4):c.1738T>G (p.Leu580Val) single nucleotide variant not provided [RCV000954968] Chr12:106239095 [GRCh38]
Chr12:106632873 [GRCh37]
Chr12:12q23.3
benign
GRCh37/hg19 12q23.3(chr12:106510497-107070575)x3 copy number gain not provided [RCV001006529] Chr12:106510497..107070575 [GRCh37]
Chr12:12q23.3
uncertain significance
GRCh37/hg19 12q23.3-24.12(chr12:106498814-112252906)x1 copy number loss not provided [RCV001259630] Chr12:106498814..112252906 [GRCh37]
Chr12:12q23.3-24.12
pathogenic
GRCh37/hg19 12q23.3-24.12(chr12:104230462-111984801)x1 copy number loss not provided [RCV001834231] Chr12:104230462..111984801 [GRCh37]
Chr12:12q23.3-24.12
pathogenic
GRCh37/hg19 12q23.2-24.11(chr12:103044333-111639805) copy number loss not specified [RCV002053016] Chr12:103044333..111639805 [GRCh37]
Chr12:12q23.2-24.11
likely pathogenic
NM_006825.4(CKAP4):c.1700T>G (p.Ile567Arg) single nucleotide variant not specified [RCV004148965] Chr12:106239133 [GRCh38]
Chr12:106632911 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1340G>A (p.Arg447His) single nucleotide variant not specified [RCV004125190] Chr12:106239493 [GRCh38]
Chr12:106633271 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1088T>C (p.Val363Ala) single nucleotide variant not specified [RCV004128448] Chr12:106239745 [GRCh38]
Chr12:106633523 [GRCh37]
Chr12:12q23.3
likely benign
NM_006825.4(CKAP4):c.1246G>A (p.Val416Met) single nucleotide variant not specified [RCV004223860] Chr12:106239587 [GRCh38]
Chr12:106633365 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.128C>A (p.Pro43Gln) single nucleotide variant not specified [RCV004200898] Chr12:106247724 [GRCh38]
Chr12:106641502 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1031C>T (p.Thr344Met) single nucleotide variant not specified [RCV004090715] Chr12:106239802 [GRCh38]
Chr12:106633580 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1181G>A (p.Arg394Lys) single nucleotide variant not specified [RCV004084540] Chr12:106239652 [GRCh38]
Chr12:106633430 [GRCh37]
Chr12:12q23.3
likely benign
NM_006825.4(CKAP4):c.410T>A (p.Val137Asp) single nucleotide variant not specified [RCV004104533] Chr12:106247442 [GRCh38]
Chr12:106641220 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1019A>G (p.Glu340Gly) single nucleotide variant not specified [RCV004127531] Chr12:106239814 [GRCh38]
Chr12:106633592 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1132C>T (p.Arg378Cys) single nucleotide variant not specified [RCV004190171] Chr12:106239701 [GRCh38]
Chr12:106633479 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.692C>T (p.Thr231Met) single nucleotide variant not specified [RCV004189148] Chr12:106240141 [GRCh38]
Chr12:106633919 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.883G>C (p.Glu295Gln) single nucleotide variant not specified [RCV004160364] Chr12:106239950 [GRCh38]
Chr12:106633728 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1076C>G (p.Ser359Cys) single nucleotide variant not specified [RCV004253332] Chr12:106239757 [GRCh38]
Chr12:106633535 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1109T>G (p.Ile370Ser) single nucleotide variant not specified [RCV004315755] Chr12:106239724 [GRCh38]
Chr12:106633502 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.737A>G (p.Lys246Arg) single nucleotide variant not specified [RCV004263121] Chr12:106240096 [GRCh38]
Chr12:106633874 [GRCh37]
Chr12:12q23.3
uncertain significance
GRCh37/hg19 12q23.3(chr12:106460580-107090224)x1 copy number loss not provided [RCV003326873] Chr12:106460580..107090224 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.248C>T (p.Ser83Phe) single nucleotide variant not specified [RCV004335760] Chr12:106247604 [GRCh38]
Chr12:106641382 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1094G>A (p.Arg365His) single nucleotide variant not specified [RCV004341118] Chr12:106239739 [GRCh38]
Chr12:106633517 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.131C>T (p.Pro44Leu) single nucleotide variant not specified [RCV004444055] Chr12:106247721 [GRCh38]
Chr12:106641499 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1535C>T (p.Thr512Met) single nucleotide variant not specified [RCV004444059] Chr12:106239298 [GRCh38]
Chr12:106633076 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.250T>G (p.Ser84Ala) single nucleotide variant not specified [RCV004444061] Chr12:106247602 [GRCh38]
Chr12:106641380 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.784A>G (p.Ser262Gly) single nucleotide variant not specified [RCV004444066] Chr12:106240049 [GRCh38]
Chr12:106633827 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.500C>G (p.Ala167Gly) single nucleotide variant not specified [RCV004444062] Chr12:106240333 [GRCh38]
Chr12:106634111 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.581A>G (p.Glu194Gly) single nucleotide variant not specified [RCV004444064] Chr12:106240252 [GRCh38]
Chr12:106634030 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.585T>A (p.Ser195Arg) single nucleotide variant not specified [RCV004444065] Chr12:106240248 [GRCh38]
Chr12:106634026 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.503C>T (p.Thr168Ile) single nucleotide variant not specified [RCV004444063] Chr12:106240330 [GRCh38]
Chr12:106634108 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1360C>T (p.Arg454Cys) single nucleotide variant not specified [RCV004444057] Chr12:106239473 [GRCh38]
Chr12:106633251 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1156G>A (p.Gly386Arg) single nucleotide variant not specified [RCV004444054] Chr12:106239677 [GRCh38]
Chr12:106633455 [GRCh37]
Chr12:12q23.3
likely benign
NM_006825.4(CKAP4):c.146C>A (p.Pro49Gln) single nucleotide variant not specified [RCV004444058] Chr12:106247706 [GRCh38]
Chr12:106641484 [GRCh37]
Chr12:12q23.3
uncertain significance
NM_006825.4(CKAP4):c.1579C>A (p.Gln527Lys) single nucleotide variant not specified [RCV004444060] Chr12:106239254 [GRCh38]
Chr12:106633032 [GRCh37]
Chr12:12q23.3
uncertain significance
miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR7-2hsa-miR-7-5pMirtarbaseexternal_infoMicroarray//Microarray;OtherFunctional MTI (Weak)19073608
MIR7-2hsa-miR-7-5pMirtarbaseexternal_infoSequencingFunctional MTI (Weak)20371350
MIR7-1hsa-miR-7-5pMirtarbaseexternal_infoMicroarray//Microarray;OtherFunctional MTI (Weak)19073608
MIR7-1hsa-miR-7-5pMirtarbaseexternal_infoSequencingFunctional MTI (Weak)20371350

Predicted Target Of
Summary Value
Count of predictions:987
Count of miRNA genes:692
Interacting mature miRNAs:784
Transcripts:ENST00000378026, ENST00000552828, ENST00000553039
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.

Markers in Region
RH17418  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3712106,632,538 - 106,632,696UniSTSGRCh37
Build 3612105,156,668 - 105,156,826RGDNCBI36
Celera12106,297,882 - 106,298,040RGD
Cytogenetic Map12q23.3UniSTS
HuRef12103,693,305 - 103,693,463UniSTS
GeneMap99-GB4 RH Map12421.8UniSTS
NCBI RH Map12708.3UniSTS
STS-X69910  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3712106,632,015 - 106,632,151UniSTSGRCh37
Build 3612105,156,145 - 105,156,281RGDNCBI36
Celera12106,297,359 - 106,297,495RGD
Cytogenetic Map12q23.3UniSTS
HuRef12103,692,782 - 103,692,918UniSTS
GeneMap99-GB4 RH Map12421.8UniSTS
NCBI RH Map12708.3UniSTS
WI-20313  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3712106,631,912 - 106,632,176UniSTSGRCh37
Build 3612105,156,042 - 105,156,306RGDNCBI36
Celera12106,297,256 - 106,297,520RGD
Cytogenetic Map12q23.3UniSTS
GeneMap99-GB4 RH Map12423.63UniSTS
Whitehead-RH Map12512.6UniSTS
D12S1903  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3712106,632,475 - 106,632,620UniSTSGRCh37
Build 3612105,156,605 - 105,156,750RGDNCBI36
Celera12106,297,819 - 106,297,964RGD
Cytogenetic Map12q23.3UniSTS
HuRef12103,693,242 - 103,693,387UniSTS
TNG Radiation Hybrid Map1252226.0UniSTS
Stanford-G3 RH Map124539.0UniSTS
GeneMap99-G3 RH Map124485.0UniSTS
G20771  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3712106,631,696 - 106,631,841UniSTSGRCh37
Build 3612105,155,826 - 105,155,971RGDNCBI36
Celera12106,297,041 - 106,297,185RGD
Cytogenetic Map12q23.3UniSTS
HuRef12103,692,464 - 103,692,608UniSTS
A006F36  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3712106,631,696 - 106,631,841UniSTSGRCh37
Build 3612105,155,826 - 105,155,971RGDNCBI36
Celera12106,297,041 - 106,297,185RGD
Cytogenetic Map12q23.3UniSTS
HuRef12103,692,464 - 103,692,608UniSTS
GeneMap99-GB4 RH Map12427.06UniSTS
NCBI RH Map12708.3UniSTS
CKAP4_3780  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3712106,631,595 - 106,632,511UniSTSGRCh37
Build 3612105,155,725 - 105,156,641RGDNCBI36
Celera12106,296,940 - 106,297,855RGD
HuRef12103,692,363 - 103,693,278UniSTS


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 1 1 1
Medium 2426 2866 1657 562 1805 404 3904 1655 2353 395 1396 1605 171 1204 2338 3
Low 11 122 69 62 110 61 451 540 1364 23 56 7 3 1 450 2
Below cutoff 2 2 24 13 1 5 1 1

Sequence


RefSeq Acc Id: ENST00000378026   ⟹   ENSP00000367265
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12106,237,881 - 106,248,020 (-)Ensembl
RefSeq Acc Id: ENST00000552828
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12106,239,894 - 106,304,251 (-)Ensembl
RefSeq Acc Id: ENST00000553039   ⟹   ENSP00000449240
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12106,240,322 - 106,304,279 (-)Ensembl
RefSeq Acc Id: NM_006825   ⟹   NP_006816
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3812106,237,881 - 106,248,020 (-)NCBI
GRCh3712106,631,659 - 106,641,713 (-)ENTREZGENE
Build 3612105,155,910 - 105,165,843 (-)NCBI Archive
HuRef12103,692,427 - 103,702,094 (-)ENTREZGENE
CHM1_112106,597,488 - 106,607,544 (-)NCBI
T2T-CHM13v2.012106,200,876 - 106,211,009 (-)NCBI
Sequence:
RefSeq Acc Id: NP_006816   ⟸   NM_006825
- UniProtKB: Q504S5 (UniProtKB/Swiss-Prot),   Q53ES6 (UniProtKB/Swiss-Prot),   Q07065 (UniProtKB/Swiss-Prot),   B3KVX6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000367265   ⟸   ENST00000378026
RefSeq Acc Id: ENSP00000449240   ⟸   ENST00000553039

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q07065-F1-model_v2 AlphaFold Q07065 1-602 view protein structure

Promoters
RGD ID:6789806
Promoter ID:HG_KWN:16533
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   HeLa_S3,   K562,   Lymphoblastoid
Transcripts:ENST00000258512,   NM_006825
Position:
Human AssemblyChrPosition (strand)Source
Build 3612105,165,366 - 105,166,612 (-)MPROMDB
RGD ID:7225267
Promoter ID:EPDNEW_H18379
Type:initiation region
Name:CKAP4_1
Description:cytoskeleton associated protein 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh3812106,247,992 - 106,248,052EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:16991 AgrOrtholog
COSMIC CKAP4 COSMIC
Ensembl Genes ENSG00000136026 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000378026 ENTREZGENE
  ENST00000378026.5 UniProtKB/Swiss-Prot
  ENST00000553039.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.1490 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000136026 GTEx
HGNC ID HGNC:16991 ENTREZGENE
Human Proteome Map CKAP4 Human Proteome Map
KEGG Report hsa:10970 UniProtKB/Swiss-Prot
NCBI Gene 10970 ENTREZGENE
OMIM 618595 OMIM
PANTHER CYTOSKELETON-ASSOCIATED PROTEIN 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR45161 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA26527 PharmGKB
UniProt B3KVX6 ENTREZGENE, UniProtKB/TrEMBL
  CKAP4_HUMAN UniProtKB/Swiss-Prot
  F8VVU0_HUMAN UniProtKB/TrEMBL
  Q07065 ENTREZGENE
  Q504S5 ENTREZGENE
  Q53ES6 ENTREZGENE
  Q6NWZ1_HUMAN UniProtKB/TrEMBL
UniProt Secondary Q504S5 UniProtKB/Swiss-Prot
  Q53ES6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-12 CKAP4  cytoskeleton associated protein 4    cytoskeleton-associated protein 4  Symbol and/or name change 5135510 APPROVED