NRXN1-DT (NRXN1 divergent transcript) - 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: NRXN1-DT (NRXN1 divergent transcript) Homo sapiens
Analyze
Symbol: NRXN1-DT (Ensembl: AC007402.1)
Name: NRXN1 divergent transcript (Ensembl:novel transcript)
RGD ID: 16555175
HGNC Page HGNC:52686
Description: ASSOCIATED WITH Autism; autistic disorder; Schizophrenia
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC007402.1; LOC730100; novel transcript; uncharacterized LOC730100
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38251,032,601 - 52,407,917 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl251,032,601 - 52,407,917 (+)EnsemblGRCh38hg38GRCh38
GRCh37251,259,739 - 52,635,055 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2p16.3NCBI
HuRef250,994,210 - 52,368,974 (+)NCBIHuRef
CHM1_1251,190,555 - 52,566,107 (+)NCBICHM1_1
T2T-CHM13v2.0251,028,763 - 52,404,220 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Autism  (IAGP)
Schizophrenia  (IAGP)
References
Additional References at PubMed
PMID:19734545   PMID:22491018   PMID:23518928   PMID:25201988   PMID:26563496   PMID:30914197   PMID:36758534  


Genomics

Variants

.
Variants in NRXN1-DT
55 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p16.3(chr2:50737710-51173556)x1 copy number loss See cases [RCV000054017] Chr2:50737710..51173556 [GRCh38]
Chr2:50964848..51400694 [GRCh37]
Chr2:50818352..51254198 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:49910932-52462336)x1 copy number loss See cases [RCV000139317] Chr2:49910932..52462336 [GRCh38]
Chr2:50138070..52689474 [GRCh37]
Chr2:49991574..52542978 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign
GRCh38/hg38 2p25.3-16.1(chr2:66097-55570637)x3 copy number gain See cases [RCV000052933] Chr2:66097..55570637 [GRCh38]
Chr2:66097..55797773 [GRCh37]
Chr2:56097..55651277 [NCBI36]
Chr2:2p25.3-16.1		 pathogenic
GRCh38/hg38 2p16.3(chr2:50619962-51329577)x1 copy number loss See cases [RCV000140869] Chr2:50619962..51329577 [GRCh38]
Chr2:50847100..51556715 [GRCh37]
Chr2:50700604..51410219 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:50734870-51033529)x1 copy number loss See cases [RCV000143148] Chr2:50734870..51033529 [GRCh38]
Chr2:50962008..51260667 [GRCh37]
Chr2:50815512..51114171 [NCBI36]
Chr2:2p16.3		 pathogenic
NC_000002.12:g.(?_50975328)_(51121693_?)del deletion Schizophrenia [RCV000754265] Chr2:50975328..51121693 [GRCh38]
Chr2:2p16.3		 pathogenic
NC_000002.12:g.(?_51001206)_(51200739_?)del deletion Autism [RCV000754266] Chr2:51001206..51200739 [GRCh38]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:50624294-51265729)x1 copy number loss See cases [RCV000140933] Chr2:50624294..51265729 [GRCh38]
Chr2:50851432..51492867 [GRCh37]
Chr2:50704936..51346371 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:50999032-51329577)x1 copy number loss See cases [RCV000133639] Chr2:50999032..51329577 [GRCh38]
Chr2:51226170..51556715 [GRCh37]
Chr2:51079674..51410219 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:50953423-51131743)x1 copy number loss See cases [RCV000138361] Chr2:50953423..51131743 [GRCh38]
Chr2:51180561..51358881 [GRCh37]
Chr2:51034065..51212385 [NCBI36]
Chr2:2p16.3		 pathogenic
NC_000002.12:g.(?_50496341)_(51317388_?)del deletion Autism [RCV000754262] Chr2:50496341..51317388 [GRCh38]
Chr2:2p16.3		 pathogenic
NC_000002.12:g.(?_50836961)_(51084060_?)del deletion Schizophrenia [RCV000754264] Chr2:50836961..51084060 [GRCh38]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p22.1-16.1(chr2:40738282-57863821)x3 copy number gain See cases [RCV000052943] Chr2:40738282..57863821 [GRCh38]
Chr2:40965422..58090956 [GRCh37]
Chr2:40818926..57944460 [NCBI36]
Chr2:2p22.1-16.1		 pathogenic
GRCh38/hg38 2p16.3(chr2:50809966-51219735)x1 copy number loss See cases [RCV000135555] Chr2:50809966..51219735 [GRCh38]
Chr2:51037104..51446873 [GRCh37]
Chr2:50890608..51300377 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:50999032-51087292)x1 copy number loss See cases [RCV000137251] Chr2:50999032..51087292 [GRCh38]
Chr2:51226170..51314430 [GRCh37]
Chr2:51079674..51167934 [NCBI36]
Chr2:2p16.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 2p16.3(chr2:50751328-51301336)x1 copy number loss See cases [RCV000138563] Chr2:50751328..51301336 [GRCh38]
Chr2:50978466..51528474 [GRCh37]
Chr2:50831970..51381978 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:51087233-51240324)x1 copy number loss See cases [RCV000135016] Chr2:51087233..51240324 [GRCh38]
Chr2:51314371..51467462 [GRCh37]
Chr2:51167875..51320966 [NCBI36]
Chr2:2p16.3		 benign
GRCh38/hg38 2p16.3(chr2:50682627-51107991)x1 copy number loss See cases [RCV000141354] Chr2:50682627..51107991 [GRCh38]
Chr2:50909765..51335129 [GRCh37]
Chr2:50763269..51188633 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:50856272-51155734)x1 copy number loss See cases [RCV000054019] Chr2:50856272..51155734 [GRCh38]
Chr2:51083410..51382872 [GRCh37]
Chr2:50936914..51236376 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:50915711-51283823)x1 copy number loss See cases [RCV000142614] Chr2:50915711..51283823 [GRCh38]
Chr2:51142849..51510961 [GRCh37]
Chr2:50996353..51364465 [NCBI36]
Chr2:2p16.3		 pathogenic
Single allele deletion Normal pregnancy [RCV000161212] Chr2:51118336..51183988 [GRCh38]
Chr2:51345474..51411126 [GRCh37]
Chr2:2p16.3		 not provided
GRCh38/hg38 2p16.3(chr2:51131684-51155675)x1 copy number loss See cases [RCV000135250] Chr2:51131684..51155675 [GRCh38]
Chr2:51358822..51382813 [GRCh37]
Chr2:51212326..51236317 [NCBI36]
Chr2:2p16.3		 likely benign
GRCh38/hg38 2p16.3(chr2:51009862-51155675)x1 copy number loss See cases [RCV000135318] Chr2:51009862..51155675 [GRCh38]
Chr2:51237000..51382813 [GRCh37]
Chr2:51090504..51236317 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:50839440-51033529)x1 copy number loss See cases [RCV000143151] Chr2:50839440..51033529 [GRCh38]
Chr2:51066578..51260667 [GRCh37]
Chr2:50920082..51114171 [NCBI36]
Chr2:2p16.3		 pathogenic
GRCh38/hg38 2p16.3(chr2:51065432-51244648)x1 copy number loss See cases [RCV000052122] Chr2:51065432..51244648 [GRCh38]
Chr2:51292570..51471786 [GRCh37]
Chr2:51146074..51325290 [NCBI36]
Chr2:2p16.3		 uncertain significance
GRCh38/hg38 2p16.3(chr2:50999032-51155734)x1 copy number loss See cases [RCV000135658] Chr2:50999032..51155734 [GRCh38]
Chr2:51226170..51382872 [GRCh37]
Chr2:51079674..51236376 [NCBI36]
Chr2:2p16.3		 pathogenic
NR_135237.1(LOC730100):n.754-62628_754-62323del deletion Gestational diabetes mellitus uncontrolled [RCV000161216]|Large for gestational age [RCV000161215]|Normal pregnancy [RCV000161214]|Preeclampsia [RCV000161213] Chr2:51699460..51699765 [GRCh38]
Chr2:51926598..51926903 [GRCh37]
Chr2:2p16.3		 not provided
GRCh38/hg38 2p16.3(chr2:50710306-51087292)x1 copy number loss See cases [RCV000054016] Chr2:50710306..51087292 [GRCh38]
Chr2:50937444..51314430 [GRCh37]
Chr2:50790948..51167934 [NCBI36]
Chr2:2p16.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:54
Interacting mature miRNAs:54
Transcripts:ENST00000410760
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
Low 5 6 2 17 2 78 18 3 7 13
Below cutoff 249 170 296 51 230 42 620 171 2041 99 529 235 16 43 393 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000440698
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl251,032,601 - 52,407,917 (+)Ensembl
RefSeq Acc Id: NR_135237
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38251,032,601 - 52,407,917 (+)NCBI
T2T-CHM13v2.0251,028,763 - 52,404,220 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC NRXN1-DT COSMIC
Ensembl Genes ENSG00000231918 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000440698 ENTREZGENE
GTEx ENSG00000231918 GTEx
HGNC ID HGNC:52686 ENTREZGENE
Human Proteome Map NRXN1-DT Human Proteome Map
NCBI Gene LOC730100 ENTREZGENE
RNAcentral URS00001142E8 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-06-26 NRXN1-DT  NRXN1 divergent transcript  AC007402.1  novel transcript  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AC007402.1  novel transcript  LOC730100  uncharacterized LOC730100  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC730100  uncharacterized LOC730100  AC007402.1  novel transcript  Symbol and/or name change 5135510 APPROVED