HAR1B (highly accelerated region 1B) - Rat Genome Database

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Gene: HAR1B (highly accelerated region 1B) Homo sapiens
Analyze
Symbol: HAR1B
Name: highly accelerated region 1B
RGD ID: 1601891
HGNC Page HGNC:33118
Description: ASSOCIATED WITH autosomal dominant nocturnal frontal lobe epilepsy; benign familial infantile seizures 6; developmental and epileptic encephalopathy; INTERACTS WITH cisplatin; valproic acid
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: HAR1R; highly accelerated region 1B (non-protein coding); LINC00065; NCRNA00065
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382063,095,493 - 63,102,319 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2063,090,806 - 63,102,631 (-)EnsemblGRCh38hg38GRCh38
GRCh372061,726,845 - 61,733,671 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362061,197,290 - 61,204,116 (-)NCBINCBI36Build 36hg18NCBI36
Celera2058,404,374 - 58,411,201 (-)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2058,445,191 - 58,454,164 (-)NCBIHuRef
CHM1_12061,626,655 - 61,633,414 (-)NCBICHM1_1
T2T-CHM13v2.02064,897,543 - 64,904,921 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
cisplatin  (EXP)
valproic acid  (EXP)

References
Additional References at PubMed
PMID:16915236   PMID:21112873   PMID:35526243   PMID:36583781  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh37/hg19 20q13.33(chr20:61716119-62416074)x1 copy number loss not specified [RCV003986136] Chr20:61716119..62416074 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:61421505-62070966)x1 copy number loss not specified [RCV003986131] Chr20:61421505..62070966 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62455231-63839491)x1 copy number loss See cases [RCV000052768] Chr20:62455231..63839491 [GRCh38]
Chr20:61030287..62470844 [GRCh37]
Chr20:60463682..61941288 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62545370-64241486)x1 copy number loss See cases [RCV000052769] Chr20:62545370..64241486 [GRCh38]
Chr20:61142577..62872839 [GRCh37]
Chr20:60553022..62343283 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62561794-63331723)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052770]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052770]|See cases [RCV000052770] Chr20:62561794..63331723 [GRCh38]
Chr20:61211869..61963075 [GRCh37]
Chr20:60569446..61433519 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:63095686-63524980)x1 copy number loss See cases [RCV000052771] Chr20:63095686..63524980 [GRCh38]
Chr20:61727038..62156333 [GRCh37]
Chr20:61197483..61626777 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.32-13.33(chr20:59041966-64277321)x3 copy number gain See cases [RCV000135805] Chr20:59041966..64277321 [GRCh38]
Chr20:57617021..62908674 [GRCh37]
Chr20:57050416..62379118 [NCBI36]
Chr20:20q13.32-13.33		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62561794-64277321)x1 copy number loss See cases [RCV000133842] Chr20:62561794..64277321 [GRCh38]
Chr20:61211869..62908674 [GRCh37]
Chr20:60569446..62379118 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.31-13.33(chr20:57229415-64273089)x3 copy number gain See cases [RCV000141347] Chr20:57229415..64273089 [GRCh38]
Chr20:55804471..62904442 [GRCh37]
Chr20:55237878..62374886 [NCBI36]
Chr20:20q13.31-13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:61326549-64277326)x3 copy number gain See cases [RCV000139100] Chr20:61326549..64277326 [GRCh38]
Chr20:59901605..62908679 [GRCh37]
Chr20:59335000..62379123 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:56198032-64277321)x3 copy number gain See cases [RCV000138035] Chr20:56198032..64277321 [GRCh38]
Chr20:54773088..62908674 [GRCh37]
Chr20:54206495..62379118 [NCBI36]
Chr20:20q13.2-13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62663307-64284202)x1 copy number loss See cases [RCV000141676] Chr20:62663307..64284202 [GRCh38]
Chr20:61294659..62915555 [GRCh37]
Chr20:60765104..62385999 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62582073-64284202)x1 copy number loss See cases [RCV000141744] Chr20:62582073..64284202 [GRCh38]
Chr20:61179280..62915555 [GRCh37]
Chr20:60589725..62385999 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62939140-63198970)x3 copy number gain See cases [RCV000139758] Chr20:62939140..63198970 [GRCh38]
Chr20:61570492..61830322 [GRCh37]
Chr20:61040937..61300767 [NCBI36]
Chr20:20q13.33		 likely benign
GRCh38/hg38 20q13.33(chr20:63095686-63170849)x3 copy number gain See cases [RCV000141043] Chr20:63095686..63170849 [GRCh38]
Chr20:61727038..61802201 [GRCh37]
Chr20:61197483..61272646 [NCBI36]
Chr20:20q13.33		 likely benign
GRCh38/hg38 20q13.2-13.33(chr20:53236165-64284202)x3 copy number gain See cases [RCV000143584] Chr20:53236165..64284202 [GRCh38]
Chr20:51852704..62915555 [GRCh37]
Chr20:51286111..62385999 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh37/hg19 20q13.33(chr20:60882468-62045494)x1 copy number loss Breast ductal adenocarcinoma [RCV000207130] Chr20:60882468..62045494 [GRCh37]
Chr20:20q13.33		 uncertain significance
chr20:60885242-61929348 complex variant complex Breast ductal adenocarcinoma [RCV000207152] Chr20:60885242..61929348 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61429900-62293991)x1 copy number loss See cases [RCV000240573] Chr20:61429900..62293991 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:60473339-62915555)x3 copy number gain See cases [RCV000446009] Chr20:60473339..62915555 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61612628-61820201)x3 copy number gain not provided [RCV000741363] Chr20:61612628..61820201 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20p13-q13.33(chr20:63244-62912463)x3 copy number gain not provided [RCV000741057] Chr20:63244..62912463 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62948788)x3 copy number gain not provided [RCV000741058] Chr20:63244..62948788 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62961294)x3 copy number gain not provided [RCV000741059] Chr20:63244..62961294 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:60053234-62961294)x3 copy number gain not provided [RCV000741328] Chr20:60053234..62961294 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:60063645-62961294)x3 copy number gain not provided [RCV000741329] Chr20:60063645..62961294 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:61337529-62904501)x1 copy number loss not provided [RCV000488148] Chr20:61337529..62904501 [GRCh37]
Chr20:20q13.33		 likely pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)x3 copy number gain See cases [RCV000510832] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555) copy number gain See cases [RCV000512450] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20q13.2-13.33(chr20:51542616-62915555)x3 copy number gain See cases [RCV000511980] Chr20:51542616..62915555 [GRCh37]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh37/hg19 20q13.33(chr20:61602977-62450998)x3 copy number gain See cases [RCV000511879] Chr20:61602977..62450998 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61530581-61911114)x1 copy number loss See cases [RCV000512342] Chr20:61530581..61911114 [GRCh37]
Chr20:20q13.33		 likely benign
GRCh37/hg19 20q13.33(chr20:61022397-61738592)x1 copy number loss not provided [RCV000684122] Chr20:61022397..61738592 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61658787-62070966)x3 copy number gain not provided [RCV000684115] Chr20:61658787..62070966 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.2-13.33(chr20:54143747-62194881) copy number gain not provided [RCV000767669] Chr20:54143747..62194881 [GRCh37]
Chr20:20q13.2-13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:60946209-61975606)x3 copy number gain not provided [RCV000847979] Chr20:60946209..61975606 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61678415-62247462)x3 copy number gain not provided [RCV000848406] Chr20:61678415..62247462 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61152321-62915555)x1 copy number loss not provided [RCV001007103] Chr20:61152321..62915555 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.31-13.33(chr20:55743522-62032989)x3 copy number gain not provided [RCV001007097] Chr20:55743522..62032989 [GRCh37]
Chr20:20q13.31-13.33		 pathogenic
GRCh37/hg19 20q13.32-13.33(chr20:56788101-62762405)x3 copy number gain not provided [RCV001007098] Chr20:56788101..62762405 [GRCh37]
Chr20:20q13.32-13.33		 pathogenic
NC_000020.10:g.(?_60831241)_(62664346_?)dup duplication Developmental and epileptic encephalopathy, 33 [RCV001295457]|Early infantile epileptic encephalopathy with suppression bursts [RCV001316934] Chr20:60831241..62664346 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61507440-62318983)x3 copy number gain not provided [RCV001258919] Chr20:61507440..62318983 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61510452-62315381) copy number loss Epileptic spasm [RCV001352668] Chr20:61510452..62315381 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.2-13.33(chr20:51799648-62916626)x3 copy number gain not provided [RCV001537917] Chr20:51799648..62916626 [GRCh37]
Chr20:20q13.2-13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:61673691-62230974)x3 copy number gain not provided [RCV001834200] Chr20:61673691..62230974 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61634256-61975378)x1 copy number loss not provided [RCV001829210] Chr20:61634256..61975378 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61041481-62680992) copy number loss Seizures, benign familial neonatal, 1 [RCV001786555] Chr20:61041481..62680992 [GRCh37]
Chr20:20q13.33		 likely pathogenic
GRCh37/hg19 20q13.33(chr20:61038552-62907579) copy number loss Seizures, benign familial neonatal, 1 [RCV001786557] Chr20:61038552..62907579 [GRCh37]
Chr20:20q13.33		 likely pathogenic
GRCh37/hg19 20q13.33(chr20:61273854-62907579) copy number loss Seizures, benign familial neonatal, 1 [RCV001786556] Chr20:61273854..62907579 [GRCh37]
Chr20:20q13.33		 likely pathogenic
GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555) copy number gain not specified [RCV002052713] Chr20:56835739..62915555 [GRCh37]
Chr20:20q13.32-13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:61003263-62915555) copy number loss not specified [RCV002052717] Chr20:61003263..62915555 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:61619222-62915555) copy number loss not specified [RCV002052718] Chr20:61619222..62915555 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:60473339-62915555) copy number gain not specified [RCV002052714] Chr20:60473339..62915555 [GRCh37]
Chr20:20q13.33		 uncertain significance
NC_000020.10:g.(?_61448417)_(62124660_?)del deletion Autosomal dominant nocturnal frontal lobe epilepsy [RCV001916149]|Developmental and epileptic encephalopathy, 33 [RCV003107883] Chr20:61448417..62124660 [GRCh37]
Chr20:20q13.33		 uncertain significance
Single allele duplication not provided [RCV002266602] Chr20:62941782..63658260 [GRCh38]
Chr20:20q13.33		 uncertain significance
Single allele duplication not specified [RCV002286379] Chr20:61800345..63644611 [GRCh38]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:60621074-62915555)x3 copy number gain not provided [RCV002473575] Chr20:60621074..62915555 [GRCh37]
Chr20:20q13.33		 uncertain significance
NC_000020.10:g.(?_61471874)_(62078210_?)del deletion Early infantile epileptic encephalopathy with suppression bursts [RCV003113817] Chr20:61471874..62078210 [GRCh37]
Chr20:20q13.33		 pathogenic
NC_000020.10:g.(?_60831241)_(62680869_?)dup duplication Developmental and epileptic encephalopathy, 33 [RCV003107566]|Early infantile epileptic encephalopathy with suppression bursts [RCV003122564] Chr20:60831241..62680869 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh38/hg38 20q13.33(chr20:62632017-63794804)x1 copy number loss Neurodevelopmental disorder [RCV003327727] Chr20:62632017..63794804 [GRCh38]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.2-13.33(chr20:52773668-62965020)x3 copy number gain See cases [RCV003329549] Chr20:52773668..62965020 [GRCh37]
Chr20:20q13.2-13.33		 uncertain significance
GRCh37/hg19 20q13.33(chr20:61704244-62169893)x3 copy number gain See cases [RCV003458262] Chr20:61704244..62169893 [GRCh37]
Chr20:20q13.33		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:714
Count of miRNA genes:330
Interacting mature miRNAs:355
Transcripts:ENST00000447910, ENST00000608031
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 10 7 4 1 1 36 208 11
Low 580 434 504 39 409 27 496 248 2870 44 508 406 14 224 333
Below cutoff 1595 1801 908 405 933 285 2388 1065 648 206 482 899 125 786 1474

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000447910
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,095,493 - 63,102,319 (-)Ensembl
RefSeq Acc Id: ENST00000608031
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,095,493 - 63,102,319 (-)Ensembl
RefSeq Acc Id: ENST00000651266
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,093,173 - 63,102,309 (-)Ensembl
RefSeq Acc Id: ENST00000651299
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,095,530 - 63,102,264 (-)Ensembl
RefSeq Acc Id: ENST00000651861
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,092,256 - 63,102,371 (-)Ensembl
RefSeq Acc Id: ENST00000657642
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,093,378 - 63,102,631 (-)Ensembl
RefSeq Acc Id: ENST00000658410
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,090,806 - 63,092,735 (-)Ensembl
RefSeq Acc Id: ENST00000665105
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,095,487 - 63,102,371 (-)Ensembl
RefSeq Acc Id: NR_003245
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382063,095,493 - 63,102,319 (-)NCBI
GRCh372061,726,845 - 61,733,671 (-)RGD
Build 362061,197,290 - 61,204,116 (-)NCBI Archive
Celera2058,404,374 - 58,411,201 (-)RGD
HuRef2058,445,191 - 58,454,164 (-)RGD
CHM1_12061,626,655 - 61,633,414 (-)NCBI
T2T-CHM13v2.02064,897,543 - 64,904,921 (-)NCBI
Sequence:
RefSeq Acc Id: NR_152601
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382063,095,493 - 63,102,319 (-)NCBI
T2T-CHM13v2.02064,897,543 - 64,904,921 (-)NCBI
Sequence:
Promoters
RGD ID:15097311
Promoter ID:EPDNEWNC_H2152
Type:initiation region
Name:HAR1B_1
Description:highly accelerated region 1B [Source:HGNCSymbol;Acc:HGNC:33118]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382063,102,311 - 63,102,371EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC HAR1B COSMIC
Ensembl Genes ENSG00000231133 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000447910 ENTREZGENE
  ENST00000608031 ENTREZGENE
GTEx ENSG00000231133 GTEx
HGNC ID HGNC:33118 ENTREZGENE
Human Proteome Map HAR1B Human Proteome Map
NCBI Gene 768097 ENTREZGENE
OMIM 610557 OMIM
PharmGKB PA162390576 PharmGKB
RNAcentral URS000015EEC8 RNACentral
  URS00002D35F2 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 HAR1B  highly accelerated region 1B    highly accelerated region 1B (non-protein coding)  Symbol and/or name change 5135510 APPROVED