AL353784.1 (novel transcript, antisense to PCDH15) - Rat Genome Database

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Gene: AL353784.1 (novel transcript, antisense to PCDH15) Homo sapiens
Analyze
Symbol: AL353784.1
Name: novel transcript, antisense to PCDH15
RGD ID: 16555845
Description: ASSOCIATED WITH Aganglionic megacolon; autosomal recessive nonsyndromic deafness 23; Hirschsprung's disease
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC105378311; uncharacterized LOC105378311
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381054,486,230 - 54,656,051 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1054,486,230 - 54,656,051 (+)EnsemblGRCh38hg38GRCh38
GRCh371056,245,990 - 56,415,811 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map10q21.1NCBI
CHM1_11056,527,766 - 56,697,525 (+)NCBICHM1_1
T2T-CHM13v2.01055,336,339 - 55,506,124 (+)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
References
Additional References at PubMed
PMID:12477932  


Genomics

Variants

.
Variants in AL353784.1
44 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001384140.1(PCDH15):c.92-816C>T single nucleotide variant not provided [RCV001547681] Chr10:54528693 [GRCh38]
Chr10:56288453 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-178G>C single nucleotide variant not provided [RCV001574482] Chr10:54528055 [GRCh38]
Chr10:56287815 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.139del (p.Asp47fs) deletion Usher syndrome type 1F [RCV000669464]|not provided [RCV001868231] Chr10:54527830 [GRCh38]
Chr10:56287590 [GRCh37]
Chr10:10q21.1
pathogenic|likely pathogenic
NM_001384140.1(PCDH15):c.139G>A (p.Asp47Asn) single nucleotide variant Aganglionic megacolon [RCV000984704] Chr10:54527830 [GRCh38]
Chr10:56287590 [GRCh37]
Chr10:10q21.1
uncertain significance
GRCh38/hg38 10q11.23-23.2(chr10:50729367-87147204)x3 copy number gain See cases [RCV000138007] Chr10:50729367..87147204 [GRCh38]
Chr10:52489127..88906961 [GRCh37]
Chr10:52159133..88896941 [NCBI36]
Chr10:10q11.23-23.2
pathogenic
Single allele deletion Usher syndrome [RCV000504833] Chr10:54069818..54963276 [GRCh38]
Chr10:55829578..56723036 [GRCh37]
Chr10:10q21.1
likely pathogenic
GRCh38/hg38 10q21.1(chr10:53308026-56420041)x3 copy number gain See cases [RCV000139643] Chr10:53308026..56420041 [GRCh38]
Chr10:55067786..58179802 [GRCh37]
Chr10:54737792..57849808 [NCBI36]
Chr10:10q21.1
likely benign
GRCh38/hg38 10q11.21-21.3(chr10:42112187-67400675)x3 copy number gain See cases [RCV000142967] Chr10:42112187..67400675 [GRCh38]
Chr10:42607635..69160433 [GRCh37]
Chr10:41927641..68830439 [NCBI36]
Chr10:10q11.21-21.3
pathogenic
NM_001384140.1(PCDH15):c.146A>G (p.Glu49Gly) single nucleotide variant Usher syndrome type 1 [RCV001108430]|Usher syndrome type 1F [RCV001279012]|not provided [RCV002555058] Chr10:54527823 [GRCh38]
Chr10:56287583 [GRCh37]
Chr10:10q21.1
uncertain significance
NM_001384140.1(PCDH15):c.92-528C>T single nucleotide variant Usher syndrome type 1D [RCV001199961]|Usher syndrome type 1F [RCV002560269] Chr10:54528405 [GRCh38]
Chr10:56288165 [GRCh37]
Chr10:10q21.1
pathogenic|uncertain significance
NM_001384140.1(PCDH15):c.157+3A>G single nucleotide variant Usher syndrome type 1 [RCV000316372]|Usher syndrome type 1F [RCV001276792]|not provided [RCV001523423]|not specified [RCV000039703] Chr10:54527809 [GRCh38]
Chr10:56287569 [GRCh37]
Chr10:10q21.1
benign|likely benign
NM_001384140.1(PCDH15):c.92-13796_92-13795insC insertion not specified [RCV000780577] Chr10:54541672..54541673 [GRCh38]
Chr10:56301432..56301433 [GRCh37]
Chr10:10q21.1
benign
GRCh38/hg38 10q21.1(chr10:54287239-57268543)x1 copy number loss See cases [RCV000052510] Chr10:54287239..57268543 [GRCh38]
Chr10:56046999..59028303 [GRCh37]
Chr10:55717005..58698309 [NCBI36]
Chr10:10q21.1
pathogenic
GRCh38/hg38 10q21.1(chr10:53366596-56420041)x4 copy number gain See cases [RCV000137162] Chr10:53366596..56420041 [GRCh38]
Chr10:55126356..58179802 [GRCh37]
Chr10:54796362..57849808 [NCBI36]
Chr10:10q21.1
uncertain significance
NM_033056.3(PCDH15):c.(?_-15)_(876_?)del deletion Rare genetic deafness [RCV000151618] Chr10:54317271..54664277 [GRCh38]
Chr10:56077031..56424037 [GRCh37]
Chr10:10q21.1
pathogenic
NM_001384140.1(PCDH15):c.145G>T (p.Glu49Ter) single nucleotide variant Autosomal recessive nonsyndromic hearing loss 23 [RCV003472126]|Usher syndrome type 1F [RCV000670660] Chr10:54527824 [GRCh38]
Chr10:56287584 [GRCh37]
Chr10:10q21.1
pathogenic|likely pathogenic
GRCh38/hg38 10q11.21-22.2(chr10:42685306-73715908)x3 copy number gain See cases [RCV000134848] Chr10:42685306..73715908 [GRCh38]
Chr10:43180754..75475666 [GRCh37]
Chr10:42500760..75145672 [NCBI36]
Chr10:10q11.21-22.2
pathogenic
NM_001384140.1(PCDH15):c.92-131T>A single nucleotide variant not provided [RCV001556059] Chr10:54528008 [GRCh38]
Chr10:56287768 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.157+75G>A single nucleotide variant not provided [RCV001674502] Chr10:54527737 [GRCh38]
Chr10:56287497 [GRCh37]
Chr10:10q21.1
benign
NM_001384140.1(PCDH15):c.157+1G>C single nucleotide variant Usher syndrome type 1F [RCV000411565] Chr10:54527811 [GRCh38]
Chr10:56287571 [GRCh37]
Chr10:10q21.1
likely pathogenic
GRCh38/hg38 10q21.1(chr10:53051023-54726415)x1 copy number loss See cases [RCV000137246] Chr10:53051023..54726415 [GRCh38]
Chr10:54810783..56486175 [GRCh37]
Chr10:54480789..56156181 [NCBI36]
Chr10:10q21.1
uncertain significance
NM_001384140.1(PCDH15):c.157+41373T>C single nucleotide variant not specified [RCV003230831] Chr10:54486439 [GRCh38]
Chr10:56246199 [GRCh37]
Chr10:10q21.1
uncertain significance
NM_001384140.1(PCDH15):c.157+301G>A single nucleotide variant not provided [RCV001594165] Chr10:54527511 [GRCh38]
Chr10:56287271 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-483A>G single nucleotide variant not provided [RCV001561463] Chr10:54528360 [GRCh38]
Chr10:56288120 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.157+198A>C single nucleotide variant not provided [RCV001663204] Chr10:54527614 [GRCh38]
Chr10:56287374 [GRCh37]
Chr10:10q21.1
benign
NM_001384140.1(PCDH15):c.92-444C>T single nucleotide variant not provided [RCV001676931] Chr10:54528321 [GRCh38]
Chr10:56288081 [GRCh37]
Chr10:10q21.1
benign
NM_001384140.1(PCDH15):c.131T>C (p.Val44Ala) single nucleotide variant Autosomal recessive nonsyndromic hearing loss 23 [RCV001004802]|Usher syndrome type 1F [RCV001275408]|not provided [RCV000522599] Chr10:54527838 [GRCh38]
Chr10:56287598 [GRCh37]
Chr10:10q21.1
pathogenic|uncertain significance
NM_001384140.1(PCDH15):c.92-10C>T single nucleotide variant not provided [RCV000919727]|not specified [RCV000611349] Chr10:54527887 [GRCh38]
Chr10:56287647 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.128T>C (p.Ile43Thr) single nucleotide variant Usher syndrome type 1F [RCV001828082]|not provided [RCV002518184]|not specified [RCV000222910] Chr10:54527841 [GRCh38]
Chr10:56287601 [GRCh37]
Chr10:10q21.1
uncertain significance
NM_001384140.1(PCDH15):c.93T>C (p.Asp31=) single nucleotide variant not provided [RCV000981276] Chr10:54527876 [GRCh38]
Chr10:56287636 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-515T>G single nucleotide variant Usher syndrome type 1F [RCV000668059] Chr10:54528392 [GRCh38]
Chr10:56288152 [GRCh37]
Chr10:10q21.1
uncertain significance
NM_001384140.1(PCDH15):c.92-165G>A single nucleotide variant not provided [RCV001725693] Chr10:54528042 [GRCh38]
Chr10:56287802 [GRCh37]
Chr10:10q21.1
benign
NM_001384140.1(PCDH15):c.92-52T>G single nucleotide variant Usher syndrome type 1F [RCV001533583]|not provided [RCV001673138] Chr10:54527929 [GRCh38]
Chr10:56287689 [GRCh37]
Chr10:10q21.1
benign
NM_001384140.1(PCDH15):c.92-501C>T single nucleotide variant not provided [RCV000977221] Chr10:54528378 [GRCh38]
Chr10:56288138 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-493A>T single nucleotide variant not provided [RCV000513721] Chr10:54528370 [GRCh38]
Chr10:56288130 [GRCh37]
Chr10:10q21.1
benign|likely benign
NM_001384140.1(PCDH15):c.149G>T (p.Ser50Ile) single nucleotide variant not provided [RCV000658085] Chr10:54527820 [GRCh38]
Chr10:56287580 [GRCh37]
Chr10:10q21.1
uncertain significance
GRCh38/hg38 10q21.1(chr10:53477144-54916701)x3 copy number gain See cases [RCV000051627] Chr10:53477144..54916701 [GRCh38]
Chr10:55236904..56676461 [GRCh37]
Chr10:54906910..56346467 [NCBI36]
Chr10:10q21.1
uncertain significance
GRCh38/hg38 10q21.1(chr10:53051046-54726547)x1 copy number loss See cases [RCV000138417] Chr10:53051046..54726547 [GRCh38]
Chr10:54810806..56486307 [GRCh37]
Chr10:54480812..56156313 [NCBI36]
Chr10:10q21.1
pathogenic
NM_001384140.1(PCDH15):c.92-18del deletion not provided [RCV001812319] Chr10:54527895 [GRCh38]
Chr10:56287655 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-8C>G single nucleotide variant not provided [RCV001434279] Chr10:54527885 [GRCh38]
Chr10:56287645 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-8C>T single nucleotide variant not provided [RCV001407678] Chr10:54527885 [GRCh38]
Chr10:56287645 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-13T>C single nucleotide variant not provided [RCV001590646] Chr10:54527890 [GRCh38]
Chr10:56287650 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.157+41381G>C single nucleotide variant not specified [RCV001779501] Chr10:54486431 [GRCh38]
Chr10:56246191 [GRCh37]
Chr10:10q21.1
benign
NM_001384140.1(PCDH15):c.144A>G (p.Glu48=) single nucleotide variant not provided [RCV002167733] Chr10:54527825 [GRCh38]
Chr10:56287585 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.126C>A (p.Thr42=) single nucleotide variant not provided [RCV002215889] Chr10:54527843 [GRCh38]
Chr10:56287603 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.157+3_157+6del deletion Autosomal recessive nonsyndromic hearing loss 23 [RCV002223342] Chr10:54527806..54527809 [GRCh38]
Chr10:56287566..56287569 [GRCh37]
Chr10:10q21.1
uncertain significance
NM_001384140.1(PCDH15):c.157+9G>T single nucleotide variant not provided [RCV002198350] Chr10:54527803 [GRCh38]
Chr10:56287563 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.108G>A (p.Arg36=) single nucleotide variant not provided [RCV002203462] Chr10:54527861 [GRCh38]
Chr10:56287621 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.153G>T (p.Arg51=) single nucleotide variant not provided [RCV002102679] Chr10:54527816 [GRCh38]
Chr10:56287576 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-7T>C single nucleotide variant not provided [RCV002201072] Chr10:54527884 [GRCh38]
Chr10:56287644 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.152G>A (p.Arg51Gln) single nucleotide variant not provided [RCV002275452] Chr10:54527817 [GRCh38]
Chr10:56287577 [GRCh37]
Chr10:10q21.1
uncertain significance
NM_001384140.1(PCDH15):c.111A>C (p.Gly37=) single nucleotide variant not provided [RCV003034756] Chr10:54527858 [GRCh38]
Chr10:56287618 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.96C>T (p.Cys32=) single nucleotide variant not provided [RCV002816339] Chr10:54527873 [GRCh38]
Chr10:56287633 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.157+12T>G single nucleotide variant not provided [RCV003018330] Chr10:54527800 [GRCh38]
Chr10:56287560 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.157+7G>A single nucleotide variant not provided [RCV002961957] Chr10:54527805 [GRCh38]
Chr10:56287565 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.157+9G>A single nucleotide variant not provided [RCV003029709] Chr10:54527803 [GRCh38]
Chr10:56287563 [GRCh37]
Chr10:10q21.1
likely benign
NM_001384140.1(PCDH15):c.92-19G>A single nucleotide variant not provided [RCV003573011] Chr10:54527896 [GRCh38]
Chr10:56287656 [GRCh37]
Chr10:10q21.1
likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:38
Interacting mature miRNAs:38
Transcripts:ENST00000422842
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
Low 2 176 1
Below cutoff 28 51 128 4 36 3 73 22 549 22 204 96 1 9 39

Sequence


RefSeq Acc Id: ENST00000422842
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1054,486,230 - 54,656,051 (+)Ensembl
RefSeq Acc Id: NR_134503
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381054,486,230 - 54,656,051 (+)NCBI
T2T-CHM13v2.01055,336,339 - 55,506,124 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC AL353784.1 COSMIC
Ensembl Genes ENSG00000234173 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000422842 ENTREZGENE
GTEx ENSG00000234173 GTEx
Human Proteome Map AL353784.1 Human Proteome Map
NCBI Gene LOC105378311 ENTREZGENE
RNAcentral URS0000A768E8 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AL353784.1  novel transcript, antisense to PCDH15  LOC105378311  uncharacterized LOC105378311  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC105378311  uncharacterized LOC105378311  AL353784.1  novel transcript, antisense to PCDH15  Symbol and/or name change 5135510 APPROVED