SNORD3B-2 (small nucleolar RNA, C/D box 3B-2) - Rat Genome Database

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Gene: SNORD3B-2 (small nucleolar RNA, C/D box 3B-2) Homo sapiens
Analyze
Symbol: SNORD3B-2
Name: small nucleolar RNA, C/D box 3B-2
RGD ID: 1642510
HGNC Page HGNC:33190
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus; INTERACTS WITH bisphenol A; doxorubicin; lipopolysaccharide.
Type: snorna
RefSeq Status: VALIDATED
Previously known as: U3-2B; U3b2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381719,063,920 - 19,064,136 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1719,063,346 - 19,064,136 (-)EnsemblGRCh38hg38GRCh38
GRCh371718,967,233 - 18,967,449 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361718,907,958 - 18,908,174 (-)NCBINCBI36Build 36hg18NCBI36
Celera1937,418,900 - 37,418,971 (-)NCBICelera
Cytogenetic Map17p11.2NCBI
HuRef1937,056,189 - 37,056,260 (-)NCBIHuRef
CHM1_11719,102,121 - 19,102,337 (-)NCBICHM1_1
T2T-CHM13v2.01719,011,810 - 19,012,026 (-)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
Additional References at PubMed
PMID:2531075   PMID:9365252   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(chr17:19031266-19148137)x1 copy number loss See cases [RCV000137085] Chr17:19031266..19148137 [GRCh38]
Chr17:18934579..19051450 [GRCh37]
Chr17:18875304..18992175 [NCBI36]
Chr17:17p11.2		 benign
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(chr17:19031805-19185457)x1 copy number loss See cases [RCV000138386] Chr17:19031805..19185457 [GRCh38]
Chr17:18935118..19088770 [GRCh37]
Chr17:18875843..19029363 [NCBI36]
Chr17:17p11.2		 likely benign
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(chr17:16879232-20390725)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:476
Count of miRNA genes:391
Interacting mature miRNAs:421
Transcripts:ENST00000364880, ENST00000571722
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 entire extraembryonic component
High
Medium 5 10 6 2 37 1 13 5 5 1 19 3 1 2 8
Low 387 322 161 60 352 47 1245 126 310 22 490 246 16 368 603 2
Below cutoff 1192 1119 849 315 680 206 1848 915 1466 166 498 768 115 603 1224 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000364880
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1719,063,919 - 19,064,136 (-)Ensembl
RefSeq Acc Id: ENST00000571722
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1719,063,346 - 19,064,136 (-)Ensembl
RefSeq Acc Id: ENST00000628329
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1719,063,920 - 19,064,136 (-)Ensembl
RefSeq Acc Id: NR_003924
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381719,063,920 - 19,064,136 (-)NCBI
GRCh371718,967,233 - 18,967,449 (-)RGD
Build 361718,907,958 - 18,908,174 (-)NCBI Archive
CHM1_11719,024,496 - 19,024,712 (-)NCBI
T2T-CHM13v2.01719,011,810 - 19,012,026 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SNORD3B-2 COSMIC
Ensembl Genes ENSG00000262074 Ensembl
GTEx ENSG00000262074 GTEx
HGNC ID HGNC:33190 ENTREZGENE
Human Proteome Map SNORD3B-2 Human Proteome Map
NCBI Gene 780852 ENTREZGENE
PharmGKB PA162404299 PharmGKB
RNAcentral URS0000650B1E RNACentral