FAM53C (family with sequence similarity 53 member C) - Rat Genome Database

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Gene: FAM53C (family with sequence similarity 53 member C) Homo sapiens
Analyze
Symbol: FAM53C
Name: family with sequence similarity 53 member C
RGD ID: 1354003
Description:
Type: ncrna (Ensembl: protein-coding)
RefSeq Status: VALIDATED
Previously known as: C5orf6; family with sequence similarity 53, member C; hypothetical protein LOC51307; putative nuclear protein
RGD Orthologs
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
GRCh385138,332,105 - 138,337,146 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5138,331,935 - 138,349,729 (+)EnsemblGRCh38hg38GRCh38
GRCh375137,667,794 - 137,672,835 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365137,701,867 - 137,713,317 (+)NCBINCBI36Build 36hg18NCBI36
Build 345137,701,866 - 137,713,315NCBI
Celera5133,794,053 - 133,806,249 (+)NCBICelera
Cytogenetic Map5q31.2NCBI
HuRef5132,864,145 - 132,876,338 (+)NCBIHuRef
CHM1_15137,100,475 - 137,103,464 (+)NCBICHM1_1
T2T-CHM13v2.05138,858,324 - 138,863,363 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model



#
Reference Title
Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:18487259   PMID:19240791  



FAM53C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385138,332,105 - 138,337,146 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5138,331,935 - 138,349,729 (+)EnsemblGRCh38hg38GRCh38
GRCh375137,667,794 - 137,672,835 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365137,701,867 - 137,713,317 (+)NCBINCBI36Build 36hg18NCBI36
Build 345137,701,866 - 137,713,315NCBI
Celera5133,794,053 - 133,806,249 (+)NCBICelera
Cytogenetic Map5q31.2NCBI
HuRef5132,864,145 - 132,876,338 (+)NCBIHuRef
CHM1_15137,100,475 - 137,103,464 (+)NCBICHM1_1
T2T-CHM13v2.05138,858,324 - 138,863,363 (+)NCBIT2T-CHM13v2.0
Fam53c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554182,101,579 - 2,114,805 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554182,102,671 - 2,114,993 (-)NCBIChiLan1.0ChiLan1.0
FAM53C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24133,612,790 - 133,624,980 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15131,752,344 - 131,764,517 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05133,717,348 - 133,729,527 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15139,849,055 - 139,860,989 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5139,849,430 - 139,860,989 (+)Ensemblpanpan1.1panPan2
FAM53C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11125,940,360 - 25,951,314 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1125,943,864 - 26,023,866 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1124,709,503 - 24,720,615 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01126,796,321 - 26,807,433 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1126,796,627 - 26,807,420 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11125,503,348 - 25,514,425 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01125,326,179 - 25,337,300 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01125,990,371 - 26,001,483 (+)NCBIUU_Cfam_GSD_1.0
Fam53c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213154,092,321 - 154,106,431 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365317,505,396 - 7,519,384 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365317,505,506 - 7,519,171 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FAM53C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2140,330,836 - 140,343,187 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12140,330,601 - 140,343,212 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22146,029,698 - 146,042,573 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FAM53C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12341,012,466 - 41,024,622 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2341,016,255 - 41,021,859 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603436,863,108 - 36,875,658 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fam53c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474331,130,371 - 31,144,593 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474331,130,499 - 31,144,314 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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Variants in FAM53C
1 total Variants

1 to 7 of 7 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 5q23.3-33.2(chr5:130860928-155321811)x3 copy number gain See cases [RCV000051193] Chr5:130860928..155321811 [GRCh38]
Chr5:130196621..154701371 [GRCh37]
Chr5:130224520..154681564 [NCBI36]
Chr5:5q23.3-33.2		 pathogenic
GRCh38/hg38 5q31.1-31.2(chr5:133401565-138437038)x1 copy number loss See cases [RCV000052114] Chr5:133401565..138437038 [GRCh38]
Chr5:132737257..137772727 [GRCh37]
Chr5:132765156..137800626 [NCBI36]
Chr5:5q31.1-31.2		 pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2		 pathogenic
GRCh38/hg38 5q31.1-31.3(chr5:135297294-140106003)x3 copy number gain See cases [RCV000133750] Chr5:135297294..140106003 [GRCh38]
Chr5:134632984..139485588 [GRCh37]
Chr5:134660883..139465772 [NCBI36]
Chr5:5q31.1-31.3		 pathogenic
GRCh38/hg38 5q31.2-31.3(chr5:137836682-140696361)x3 copy number gain See cases [RCV000134725] Chr5:137836682..140696361 [GRCh38]
Chr5:137172371..140075946 [GRCh37]
Chr5:137200270..140056130 [NCBI36]
Chr5:5q31.2-31.3		 pathogenic
GRCh38/hg38 5q31.2(chr5:138179894-139039890)x3 copy number gain See cases [RCV000135679] Chr5:138179894..139039890 [GRCh38]
Chr5:137515583..138375579 [GRCh37]
Chr5:137543482..138403478 [NCBI36]
Chr5:5q31.2		 uncertain significance
GRCh38/hg38 5q23.3-33.2(chr5:129847794-153353546)x3 copy number gain See cases [RCV000138808] Chr5:129847794..153353546 [GRCh38]
Chr5:129183487..152733106 [GRCh37]
Chr5:129211386..152713299 [NCBI36]
Chr5:5q23.3-33.2		 pathogenic
1 to 7 of 7 rows

Predicted Target Of
Summary Value
Count of predictions:4409
Count of miRNA genes:1188
Interacting mature miRNAs:1524
Transcripts:ENST00000239906, ENST00000434981, ENST00000505136, ENST00000505768, ENST00000506710, ENST00000507506, ENST00000511024, ENST00000511276, ENST00000511595, ENST00000512180, ENST00000513056
Prediction methods:Microtar, 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.


The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1357314AASTH54_HAllergic/atopic asthma related QTL 54 (human)3.560.0003Reversible airflow obstructiontotal serum IgE5135892246150155845Human
597498723GWAS1594797_Hpain measurement, response to opioid QTL GWAS1594797 (human)0.000002nociception system physiology trait (VT:0015100)5138339617138339618Human

RH12724  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375137,685,214 - 137,685,378UniSTSGRCh37
Build 365137,713,113 - 137,713,277RGDNCBI36
Celera5133,806,045 - 133,806,209RGD
Cytogenetic Map5q31UniSTS
HuRef5132,876,134 - 132,876,298UniSTS
GeneMap99-GB4 RH Map5524.56UniSTS
bac51558S  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375137,672,558 - 137,672,733UniSTSGRCh37
Build 365137,700,457 - 137,700,632RGDNCBI36
Celera5133,793,387 - 133,793,562RGD
Cytogenetic Map5q31.2UniSTS
Cytogenetic Map5q31UniSTS
HuRef5132,863,479 - 132,863,654UniSTS
RH69348  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375137,672,901 - 137,673,066UniSTSGRCh37
Build 365137,700,800 - 137,700,965RGDNCBI36
Celera5133,793,730 - 133,793,895RGD
Cytogenetic Map5q31.2UniSTS
Cytogenetic Map5q31UniSTS
HuRef5132,863,822 - 132,863,987UniSTS
GeneMap99-GB4 RH Map5524.46UniSTS
RH48553  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375137,682,414 - 137,682,534UniSTSGRCh37
Build 365137,710,313 - 137,710,433RGDNCBI36
Celera5133,803,243 - 133,803,363RGD
Cytogenetic Map5q31UniSTS
HuRef5132,873,334 - 132,873,454UniSTS
GeneMap99-GB4 RH Map5524.46UniSTS




adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2439 2788 2253 4974 1726 2351 6 624 1951 465 2270 7306 6472 53 3734 1 852 1744 1617 174 1



RefSeq Acc Id: NR_146628
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385138,332,105 - 138,337,146 (+)NCBI
T2T-CHM13v2.05138,858,324 - 138,863,363 (+)NCBI
Sequence:
GenBank Protein EAW62151 (Get FASTA)   NCBI Sequence Viewer  

RGD ID:6803603
Promoter ID:HG_KWN:51203
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:UC003LCV.1,   UC003LCW.1,   UC003LCX.1,   UC010JEV.1
Position:
Human AssemblyChrPosition (strand)Source
Build 365137,700,949 - 137,701,449 (+)MPROMDB


Database
Acc Id
Source(s)
COSMIC FAM53C COSMIC
Ensembl Genes ENSG00000120709 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000511595 ENTREZGENE
GTEx ENSG00000120709 GTEx
Human Proteome Map FAM53C Human Proteome Map
NCBI Gene LOC100128966 ENTREZGENE
RNAcentral URS00008B4804 RNACentral


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-24 FAM53C  family with sequence similarity 53 member C    family with sequence similarity 53, member C  Symbol and/or name change 5135510 APPROVED