SNX10-AS1 (SNX10 antisense RNA 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: SNX10-AS1 (SNX10 antisense RNA 1) Homo sapiens
Analyze
Symbol: SNX10-AS1
Name: SNX10 antisense RNA 1
RGD ID: 16553290
HGNC Page HGNC:55845
Description: ASSOCIATED WITH genetic disease
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC004540.2; LOC105375304; uncharacterized LOC105375304
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38726,372,019 - 26,399,418 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl726,369,310 - 26,376,701 (-)EnsemblGRCh38hg38GRCh38
GRCh37726,411,639 - 26,439,038 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map7p15.2NCBI
CHM1_1726,411,243 - 26,438,663 (-)NCBICHM1_1
T2T-CHM13v2.0726,507,709 - 26,535,104 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:11329013  


Genomics

Variants

.
Variants in SNX10-AS1
17 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7p21.1-14.3(chr7:20561456-32005143)x1 copy number loss See cases [RCV000136775] Chr7:20561456..32005143 [GRCh38]
Chr7:20601079..32044755 [GRCh37]
Chr7:20567604..32011280 [NCBI36]
Chr7:7p21.1-14.3		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:54185-26827634)x3 copy number gain See cases [RCV000136557] Chr7:54185..26827634 [GRCh38]
Chr7:54185..26867253 [GRCh37]
Chr7:149268..26833778 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p22.3-14.1(chr7:54185-41875885)x3 copy number gain See cases [RCV000051159] Chr7:54185..41875885 [GRCh38]
Chr7:54185..41915483 [GRCh37]
Chr7:149268..41882008 [NCBI36]
Chr7:7p22.3-14.1		 pathogenic
GRCh38/hg38 7p22.3-14.2(chr7:54185-37089712)x3 copy number gain See cases [RCV000053530] Chr7:54185..37089712 [GRCh38]
Chr7:54185..37129317 [GRCh37]
Chr7:149268..37095842 [NCBI36]
Chr7:7p22.3-14.2		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:1698124-27207295)x3 copy number gain See cases [RCV000143060] Chr7:1698124..27207295 [GRCh38]
Chr7:1737760..27246914 [GRCh37]
Chr7:1704286..27213439 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
NM_013322.3(SNX10):c.531C>T (p.Ser177=) single nucleotide variant not provided [RCV000910836] Chr7:26372497 [GRCh38]
Chr7:26412117 [GRCh37]
Chr7:7p15.2		 likely benign
GRCh38/hg38 7p22.1-15.2(chr7:5682209-27230311)x3 copy number gain See cases [RCV000136649] Chr7:5682209..27230311 [GRCh38]
Chr7:5721840..27269930 [GRCh37]
Chr7:5688366..27236455 [NCBI36]
Chr7:7p22.1-15.2		 pathogenic
GRCh38/hg38 7p21.1-15.2(chr7:20210912-27849400)x1 copy number loss See cases [RCV000134333] Chr7:20210912..27849400 [GRCh38]
Chr7:20250535..27889019 [GRCh37]
Chr7:20217060..27855544 [NCBI36]
Chr7:7p21.1-15.2		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:43360-27196404)x3 copy number gain See cases [RCV000143586] Chr7:43360..27196404 [GRCh38]
Chr7:43360..27236023 [GRCh37]
Chr7:138443..27202548 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p15.2-14.3(chr7:25511691-30421133)x1 copy number loss See cases [RCV000052310] Chr7:25511691..30421133 [GRCh38]
Chr7:25551310..30460749 [GRCh37]
Chr7:25517835..30427274 [NCBI36]
Chr7:7p15.2-14.3		 pathogenic
GRCh38/hg38 7p15.2(chr7:25903388-27022498)x1 copy number loss See cases [RCV000140657] Chr7:25903388..27022498 [GRCh38]
Chr7:25943008..27062117 [GRCh37]
Chr7:25909533..27028642 [NCBI36]
Chr7:7p15.2		 likely pathogenic
NM_013322.3(SNX10):c.535G>T (p.Gly179Trp) single nucleotide variant not provided [RCV001876484] Chr7:26372501 [GRCh38]
Chr7:26412121 [GRCh37]
Chr7:7p15.2		 uncertain significance
NM_013322.3(SNX10):c.593C>T (p.Pro198Leu) single nucleotide variant Inborn genetic diseases [RCV002545461]|not provided [RCV002035839] Chr7:26372559 [GRCh38]
Chr7:26412179 [GRCh37]
Chr7:7p15.2		 likely benign|uncertain significance
NM_013322.3(SNX10):c.524+1G>T single nucleotide variant not provided [RCV001877477] Chr7:26372034 [GRCh38]
Chr7:26411654 [GRCh37]
Chr7:7p15.2		 uncertain significance
NM_013322.3(SNX10):c.529T>C (p.Ser177Pro) single nucleotide variant not provided [RCV001956864] Chr7:26372495 [GRCh38]
Chr7:26412115 [GRCh37]
Chr7:7p15.2		 uncertain significance
NM_013322.3(SNX10):c.525-16del deletion not provided [RCV002193045] Chr7:26372471 [GRCh38]
Chr7:26412091 [GRCh37]
Chr7:7p15.2		 benign
NM_013322.3(SNX10):c.537G>A (p.Gly179=) single nucleotide variant SNX10-related condition [RCV003923547]|not provided [RCV002216075] Chr7:26372503 [GRCh38]
Chr7:26412123 [GRCh37]
Chr7:7p15.2		 benign|likely benign
NM_013322.3(SNX10):c.602C>T (p.Ser201Phe) single nucleotide variant Inborn genetic diseases [RCV002817004] Chr7:26372568 [GRCh38]
Chr7:26412188 [GRCh37]
Chr7:7p15.2		 uncertain significance
NM_013322.3(SNX10):c.531C>G (p.Ser177=) single nucleotide variant not provided [RCV003057068] Chr7:26372497 [GRCh38]
Chr7:26412117 [GRCh37]
Chr7:7p15.2		 likely benign
NM_013322.3(SNX10):c.525-4C>G single nucleotide variant not provided [RCV002814298] Chr7:26372487 [GRCh38]
Chr7:26412107 [GRCh37]
Chr7:7p15.2		 likely benign
NM_013322.3(SNX10):c.525-20C>T single nucleotide variant not provided [RCV002942208] Chr7:26372471 [GRCh38]
Chr7:26412091 [GRCh37]
Chr7:7p15.2		 likely benign
NM_013322.3(SNX10):c.524+11G>A single nucleotide variant not provided [RCV002609939] Chr7:26372044 [GRCh38]
Chr7:26411664 [GRCh37]
Chr7:7p15.2		 likely benign
NM_013322.3(SNX10):c.566C>T (p.Ser189Leu) single nucleotide variant Inborn genetic diseases [RCV003193660] Chr7:26372532 [GRCh38]
Chr7:26412152 [GRCh37]
Chr7:7p15.2		 uncertain significance
NM_013322.3(SNX10):c.525-14C>T single nucleotide variant not provided [RCV003544551] Chr7:26372477 [GRCh38]
Chr7:26412097 [GRCh37]
Chr7:7p15.2		 likely benign
NM_013322.3(SNX10):c.525-16CT[2] microsatellite not provided [RCV003825667] Chr7:26372475..26372476 [GRCh38]
Chr7:26412095..26412096 [GRCh37]
Chr7:7p15.2		 likely benign
GRCh38/hg38 7p15.2(chr7:25988742-26495573) copy number gain Autism spectrum disorder [RCV003883395] Chr7:25988742..26495573 [GRCh38]
Chr7:7p15.2		 uncertain significance
NM_013322.3(SNX10):c.525-20C>A single nucleotide variant not provided [RCV003568780] Chr7:26372471 [GRCh38]
Chr7:26412091 [GRCh37]
Chr7:7p15.2		 likely benign
NM_013322.3(SNX10):c.525-4C>T single nucleotide variant not provided [RCV003870146] Chr7:26372487 [GRCh38]
Chr7:26412107 [GRCh37]
Chr7:7p15.2		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:72
Interacting mature miRNAs:74
Transcripts:ENST00000451264, ENST00000451368
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 visual system adipose tissue appendage entire extraembryonic component
High
Medium 16 137 20 7 20 1 3 624 90 91 135
Low 1321 798 876 395 966 358 2227 519 2841 272 989 810 43 1 1071 1191 2
Below cutoff 986 1825 608 184 737 69 1739 1288 224 43 311 532 123 130 1263 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000451264
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,372,332 - 26,376,701 (-)Ensembl
RefSeq Acc Id: ENST00000451368
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,372,144 - 26,376,272 (-)Ensembl
RefSeq Acc Id: ENST00000656289
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,371,146 - 26,376,237 (-)Ensembl
RefSeq Acc Id: ENST00000663469
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,369,310 - 26,371,764 (-)Ensembl
RefSeq Acc Id: ENST00000702153
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,372,037 - 26,376,073 (-)Ensembl
RefSeq Acc Id: NR_136270
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38726,372,019 - 26,376,701 (-)NCBI
T2T-CHM13v2.0726,507,709 - 26,512,387 (-)NCBI
Sequence:
RefSeq Acc Id: NR_136271
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38726,372,019 - 26,376,269 (-)NCBI
T2T-CHM13v2.0726,507,709 - 26,511,955 (-)NCBI
Sequence:
RefSeq Acc Id: NR_136272
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38726,372,019 - 26,399,418 (-)NCBI
T2T-CHM13v2.0726,507,709 - 26,535,104 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SNX10-AS1 COSMIC
Ensembl Genes ENSG00000225792 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000451368 ENTREZGENE
GTEx ENSG00000225792 GTEx
HGNC ID HGNC:55845 ENTREZGENE
Human Proteome Map SNX10-AS1 Human Proteome Map
NCBI Gene LOC105375304 ENTREZGENE
RNAcentral URS0000A76624 RNACentral
  URS0000A76872 RNACentral
  URS0000A775DB RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-08-23 SNX10-AS1  SNX10 antisense RNA 1  AC004540.2  novel transcript  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AC004540.2  novel transcript  LOC105375304  uncharacterized LOC105375304  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC105375304  uncharacterized LOC105375304  AC004540.2  novel transcript  Symbol and/or name change 5135510 APPROVED