SNORD3C (small nucleolar RNA, C/D box 3C) - Rat Genome Database

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Gene: SNORD3C (small nucleolar RNA, C/D box 3C) Homo sapiens
Analyze
Symbol: SNORD3C
Name: small nucleolar RNA, C/D box 3C
RGD ID: 2289762
HGNC Page HGNC:33191
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus; INTERACTS WITH 2-hydroxypropanoic acid; 5-aza-2'-deoxycytidine; cisplatin.
Type: snorna
RefSeq Status: VALIDATED
Previously known as: RNU3-3; U3-3
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381719,190,029 - 19,190,245 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1719,189,665 - 19,190,245 (-)EnsemblGRCh38hg38GRCh38
GRCh371719,093,342 - 19,093,558 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera1465,782,645 - 65,782,713 (+)NCBICelera
Cytogenetic Map17p11.2NCBI
HuRef1465,907,816 - 65,907,884 (+)NCBIHuRef
CHM1_11719,100,079 - 19,100,295 (+)NCBICHM1_1
T2T-CHM13v2.01719,138,015 - 19,138,225 (-)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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleolus  (IEA)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Autism  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
2. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Xiong Y, etal., Emerg Microbes Infect. 2020 Dec;9(1):761-770. doi: 10.1080/22221751.2020.1747363.
Additional References at PubMed
PMID:2531075   PMID:9365252   PMID:22751105   PMID:27174936   PMID:29117863  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17p11.2(chr17:18872617-20316151)x1 copy number loss See cases [RCV000133724] Chr17:18872617..20316151 [GRCh38]
Chr17:18775930..20219464 [GRCh37]
Chr17:18716655..20160056 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16879232-20316151)x3 copy number gain See cases [RCV000133695] Chr17:16879232..20316151 [GRCh38]
Chr17:16782546..20219464 [GRCh37]
Chr17:16723271..20160056 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16854250-20492169)x3 copy number gain See cases [RCV000134467] Chr17:16854250..20492169 [GRCh38]
Chr17:16757564..20395482 [GRCh37]
Chr17:16698289..20336074 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:17331511-20022528)x1 copy number loss See cases [RCV000135874] Chr17:17331511..20022528 [GRCh38]
Chr17:17234825..19925841 [GRCh37]
Chr17:17175550..19866433 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16879233-20390697)x1 copy number loss See cases [RCV000135996] Chr17:16879233..20390697 [GRCh38]
Chr17:16782547..20294010 [GRCh37]
Chr17:16723272..20234602 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16734558-20390697)x3 copy number gain See cases [RCV000135997] Chr17:16734558..20390697 [GRCh38]
Chr17:16637872..20294010 [GRCh37]
Chr17:16578597..20234602 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16734558-20390697)x1 copy number loss See cases [RCV000135998] Chr17:16734558..20390697 [GRCh38]
Chr17:16637872..20294010 [GRCh37]
Chr17:16578597..20234602 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16734588-20390725)x1 copy number loss See cases [RCV000136906] Chr17:16734588..20390725 [GRCh38]
Chr17:16637902..20294038 [GRCh37]
Chr17:16578627..20234630 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16734588-20316151)x1 copy number loss See cases [RCV000136951] Chr17:16734588..20316151 [GRCh38]
Chr17:16637902..20219464 [GRCh37]
Chr17:16578627..20160056 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:18859289-20316151)x1 copy number loss See cases [RCV000137991] Chr17:18859289..20316151 [GRCh38]
Chr17:18762602..20219464 [GRCh37]
Chr17:18703327..20160056 [NCBI36]
Chr17:17p11.2		 likely pathogenic
GRCh38/hg38 17p11.2(chr17:16699816-20390725)x1 copy number loss See cases [RCV000137974] Chr17:16699816..20390725 [GRCh38]
Chr17:16603130..20294038 [GRCh37]
Chr17:16543855..20234630 [NCBI36]
Chr17:17p11.2		 pathogenic|likely benign
GRCh38/hg38 17p11.2(chr17:16854250-20492214)x3 copy number gain See cases [RCV000138255] Chr17:16854250..20492214 [GRCh38]
Chr17:16757564..20395527 [GRCh37]
Chr17:16698289..20336119 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16989087-20370816)x1 copy number loss See cases [RCV000139239] Chr17:16989087..20370816 [GRCh38]
Chr17:16892401..20274129 [GRCh37]
Chr17:16833126..20214721 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16854250-20560048)x3 copy number gain See cases [RCV000139188] Chr17:16854250..20560048 [GRCh38]
Chr17:16757564..20463361 [GRCh37]
Chr17:16698289..20403953 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16699694-20530646)x3 copy number gain See cases [RCV000140217] Chr17:16699694..20530646 [GRCh38]
Chr17:16603008..20433959 [GRCh37]
Chr17:16543733..20374551 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:15883037-20620700)x1 copy number loss See cases [RCV000139510] Chr17:15883037..20620700 [GRCh38]
Chr17:15786351..20524013 [GRCh37]
Chr17:15727076..20464605 [NCBI36]
Chr17:17p12-11.2		 pathogenic|likely pathogenic
GRCh38/hg38 17p11.2(chr17:16656162-20390697)x1 copy number loss See cases [RCV000139558] Chr17:16656162..20390697 [GRCh38]
Chr17:16559476..20294010 [GRCh37]
Chr17:16500201..20234602 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:17018951-20148630)x1 copy number loss See cases [RCV000141105] Chr17:17018951..20148630 [GRCh38]
Chr17:16922265..20051943 [GRCh37]
Chr17:16862990..19992535 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16699816-20492214)x3 copy number gain See cases [RCV000140852] Chr17:16699816..20492214 [GRCh38]
Chr17:16603130..20395527 [GRCh37]
Chr17:16543855..20336119 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16838097-20436415)x1 copy number loss See cases [RCV000141975] Chr17:16838097..20436415 [GRCh38]
Chr17:16741411..20339728 [GRCh37]
Chr17:16682136..20280320 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16858500-20570955)x3 copy number gain See cases [RCV000142075] Chr17:16858500..20570955 [GRCh38]
Chr17:16761814..20474268 [GRCh37]
Chr17:16702539..20414860 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16696708-20492860)x3 copy number gain See cases [RCV000143381] Chr17:16696708..20492860 [GRCh38]
Chr17:16600022..20396173 [GRCh37]
Chr17:16540747..20336765 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16718415-20546210)x3 copy number gain See cases [RCV000143417] Chr17:16718415..20546210 [GRCh38]
Chr17:16621729..20449523 [GRCh37]
Chr17:16562454..20390115 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16699816-20428292)x1 copy number loss See cases [RCV000143181] Chr17:16699816..20428292 [GRCh38]
Chr17:16603130..20331605 [GRCh37]
Chr17:16543855..20272197 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16858500-20559337)x1 copy number loss See cases [RCV000143210] Chr17:16858500..20559337 [GRCh38]
Chr17:16761814..20462650 [GRCh37]
Chr17:16702539..20403242 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:15883037-20658018)x1 copy number loss See cases [RCV000143177] Chr17:15883037..20658018 [GRCh38]
Chr17:15786351..20561331 [GRCh37]
Chr17:15727076..20501923 [NCBI36]
Chr17:17p12-11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16426633-20998588)x3 copy number gain See cases [RCV000143715] Chr17:16426633..20998588 [GRCh38]
Chr17:16329947..20901901 [GRCh37]
Chr17:16270672..20842493 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:15729893-20510251)x1 copy number loss See cases [RCV000143485] Chr17:15729893..20510251 [GRCh38]
Chr17:15633207..20413564 [GRCh37]
Chr17:15573932..20354156 [NCBI36]
Chr17:17p12-11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:15850859-20649235)x1 copy number loss See cases [RCV000143650] Chr17:15850859..20649235 [GRCh38]
Chr17:15754173..20552548 [GRCh37]
Chr17:15694898..20493140 [NCBI36]
Chr17:17p12-11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16853120-20436482)x1 copy number loss See cases [RCV000143596] Chr17:16853120..20436482 [GRCh38]
Chr17:16756434..20339795 [GRCh37]
Chr17:16697159..20280387 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:15898032-20620700)x1 copy number loss See cases [RCV000050602] Chr17:15898032..20620700 [GRCh38]
Chr17:15801346..20524013 [GRCh37]
Chr17:15742071..20464605 [NCBI36]
Chr17:17p12-11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16879232-20390725)x3 copy number gain See cases [RCV000050622] Chr17:16879232..20390725 [GRCh38]
Chr17:16782546..20294038 [GRCh37]
Chr17:16723271..20234630 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16692462-20390725)x3 copy number gain See cases [RCV000051858] Chr17:16692462..20390725 [GRCh38]
Chr17:16595776..20294038 [GRCh37]
Chr17:16536501..20234630 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16713514-20582527)x3 copy number gain See cases [RCV000051860] Chr17:16713514..20582527 [GRCh38]
Chr17:16616828..20485840 [GRCh37]
Chr17:16557553..20426432 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16713515-20340442)x3 copy number gain See cases [RCV000051871] Chr17:16713515..20340442 [GRCh38]
Chr17:16616829..20243755 [GRCh37]
Chr17:16557554..20184347 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16760817-20429770)x3 copy number gain See cases [RCV000051872] Chr17:16760817..20429770 [GRCh38]
Chr17:16664131..20333083 [GRCh37]
Chr17:16604856..20273675 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16760818-20504849)x3 copy number gain See cases [RCV000051873] Chr17:16760818..20504849 [GRCh38]
Chr17:16664132..20408162 [GRCh37]
Chr17:16604857..20348754 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16836827-20340442)x3 copy number gain See cases [RCV000051876] Chr17:16836827..20340442 [GRCh38]
Chr17:16740141..20243755 [GRCh37]
Chr17:16680866..20184347 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16836827-20504849)x3 copy number gain See cases [RCV000051877] Chr17:16836827..20504849 [GRCh38]
Chr17:16740141..20408162 [GRCh37]
Chr17:16680866..20348754 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16919369-20289856)x3 copy number gain See cases [RCV000051879] Chr17:16919369..20289856 [GRCh38]
Chr17:16822683..20193169 [GRCh37]
Chr17:16763408..20133761 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:15234685-20620700)x3 copy number gain See cases [RCV000051849] Chr17:15234685..20620700 [GRCh38]
Chr17:15138002..20524013 [GRCh37]
Chr17:15078727..20464605 [NCBI36]
Chr17:17p12-11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:15259164-20925299)x3 copy number gain See cases [RCV000051852] Chr17:15259164..20925299 [GRCh38]
Chr17:15162481..20828612 [GRCh37]
Chr17:15103206..20769204 [NCBI36]
Chr17:17p12-11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:15897832-20620841)x3 copy number gain See cases [RCV000051853] Chr17:15897832..20620841 [GRCh38]
Chr17:15801146..20524154 [GRCh37]
Chr17:15741871..20464746 [NCBI36]
Chr17:17p12-11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16656168-20390725)x3 copy number gain See cases [RCV000051855] Chr17:16656168..20390725 [GRCh38]
Chr17:16559482..20294038 [GRCh37]
Chr17:16500207..20234630 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p12-11.2(chr17:16060129-20620841)x1 copy number loss See cases [RCV000054330] Chr17:16060129..20620841 [GRCh38]
Chr17:15963443..20524154 [GRCh37]
Chr17:15904168..20464746 [NCBI36]
Chr17:17p12-11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16760818-20390725)x1 copy number loss See cases [RCV000054337] Chr17:16760818..20390725 [GRCh38]
Chr17:16664132..20294038 [GRCh37]
Chr17:16604857..20234630 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16836827-20465067)x1 copy number loss See cases [RCV000054355] Chr17:16836827..20465067 [GRCh38]
Chr17:16740141..20368380 [GRCh37]
Chr17:16680866..20308972 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16858444-20340442)x1 copy number loss See cases [RCV000054356] Chr17:16858444..20340442 [GRCh38]
Chr17:16761758..20243755 [GRCh37]
Chr17:16702483..20184347 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:16858444-20465067)x1 copy number loss See cases [RCV000054357] Chr17:16858444..20465067 [GRCh38]
Chr17:16761758..20368380 [GRCh37]
Chr17:16702483..20308972 [NCBI36]
Chr17:17p11.2		 pathogenic
GRCh38/hg38 17p11.2(chr17:18828089-20467764)x3 copy number gain See cases [RCV000054008] Chr17:18828089..20467764 [GRCh38]
Chr17:18731402..20371077 [GRCh37]
Chr17:18672127..20311669 [NCBI36]
Chr17:17p11.2		 uncertain significance
GRCh38/hg38 17p11.2(chr17:19070690-21619442)x3 copy number gain See cases [RCV000054009] Chr17:19070690..21619442 [GRCh38]
Chr17:18974003..21522709 [GRCh37]
Chr17:18914728..21463302 [NCBI36]
Chr17:17p11.2		 uncertain significance
GRCh38/hg38 17p11.2(chr17:16879232-20390725)x1 copy number loss See cases [RCV000050624] Chr17:16879232..20390725 [GRCh38]
Chr17:16782546..20294038 [GRCh37]
Chr17:16723271..20234630 [NCBI36]
Chr17:17p11.2		 pathogenic
Single allele duplication Autism [RCV000754201] Chr17:16770855..20422847 [GRCh38]
Chr17:17p11.2		 pathogenic
NC_000017.11:g.(?_16770855)_(20585863_?)del deletion Autism [RCV000754202] Chr17:16770855..20585863 [GRCh38]
Chr17:17p11.2		 pathogenic
NC_000017.11:g.(?_18856298)_(20402192_?)del deletion Meckel syndrome, type 9 [RCV000024099] Chr17:18856298..20402192 [GRCh38]
Chr17:17p11.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:455
Count of miRNA genes:337
Interacting mature miRNAs:363
Transcripts:ENST00000362428, ENST00000580533
Prediction methods:Miranda, Rnahybrid
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 adipose tissue appendage
High
Medium 179 100 115 45 48 6 290 87 173 4 236 180 39 85 221
Low 481 394 278 86 230 55 1041 267 386 15 285 240 31 404 575
Below cutoff 390 455 327 111 204 61 733 325 493 38 231 296 50 258 514

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000580533
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1719,189,665 - 19,190,245 (-)Ensembl
RefSeq Acc Id: ENST00000620446
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1719,190,028 - 19,190,245 (-)Ensembl
RefSeq Acc Id: ENST00000625845
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1719,190,029 - 19,190,245 (-)Ensembl
RefSeq Acc Id: NR_006881
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381719,190,029 - 19,190,245 (-)NCBI
GRCh371719,093,342 - 19,093,558 (-)RGD
CHM1_11719,102,121 - 19,102,337 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SNORD3C COSMIC
Ensembl Genes ENSG00000264940 Ensembl
GTEx ENSG00000264940 GTEx
HGNC ID HGNC:33191 ENTREZGENE
Human Proteome Map SNORD3C Human Proteome Map
NCBI Gene 780853 ENTREZGENE
PharmGKB PA162404300 PharmGKB
RNAcentral URS00006B41C9 RNACentral