AP002490.1 (novel transcript) - Rat Genome Database

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Gene: AP002490.1 (novel transcript) Homo sapiens
Analyze
Symbol: AP002490.1
Name: novel transcript
RGD ID: 16559139
Description: ASSOCIATED WITH Acute promyelocytic leukemia; acute promyelocytic leukemia; genetic disease
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC100128494; uncharacterized LOC100128494
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381172,014,291 - 72,020,910 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1172,014,291 - 72,020,910 (+)EnsemblGRCh38hg38GRCh38
GRCh371171,725,337 - 71,731,956 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11q13.4NCBI
CHM1_11171,609,215 - 71,615,817 (+)NCBICHM1_1
T2T-CHM13v2.01171,941,206 - 71,947,807 (+)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

Genomics

Variants

.
Variants in AP002490.1
54 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_006185.4(NUMA1):c.1781C>T (p.Ala594Val) single nucleotide variant Inborn genetic diseases [RCV003280471] Chr11:72015722 [GRCh38]
Chr11:71726768 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1891C>T (p.Arg631Trp) single nucleotide variant Inborn genetic diseases [RCV003244310] Chr11:72015612 [GRCh38]
Chr11:71726658 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1328G>A (p.Arg443Gln) single nucleotide variant NUMA1-related condition [RCV003940472]|not provided [RCV000883336] Chr11:72016175 [GRCh38]
Chr11:71727221 [GRCh37]
Chr11:11q13.4		 benign
GRCh38/hg38 11q13.4-13.5(chr11:71928796-77064521)x1 copy number loss See cases [RCV000052708] Chr11:71928796..77064521 [GRCh38]
Chr11:71639842..76751808 [GRCh37]
Chr11:71317490..76453216 [NCBI36]
Chr11:11q13.4-13.5		 pathogenic
NM_006185.4(NUMA1):c.3152C>T (p.Ala1051Val) single nucleotide variant not provided [RCV000887998] Chr11:72014351 [GRCh38]
Chr11:71725397 [GRCh37]
Chr11:11q13.4		 benign
GRCh38/hg38 11q13.4(chr11:71164008-72309374)x3 copy number gain See cases [RCV000051910] Chr11:71164008..72309374 [GRCh38]
Chr11:71088949..72020418 [GRCh37]
Chr11:70552702..71698066 [NCBI36]
Chr11:11q13.4		 uncertain significance
GRCh38/hg38 11q13.4-14.1(chr11:71969881-78232895)x1 copy number loss See cases [RCV000052709] Chr11:71969881..78232895 [GRCh38]
Chr11:71680927..77943941 [GRCh37]
Chr11:71358575..77621589 [NCBI36]
Chr11:11q13.4-14.1		 pathogenic
NM_006185.4(NUMA1):c.1430A>G (p.Asn477Ser) single nucleotide variant NUMA1-related condition [RCV003930591]|not provided [RCV000883226] Chr11:72016073 [GRCh38]
Chr11:71727119 [GRCh37]
Chr11:11q13.4		 benign|likely benign
NM_006185.4(NUMA1):c.725A>G (p.Lys242Arg) single nucleotide variant not provided [RCV000883337] Chr11:72018840 [GRCh38]
Chr11:71729886 [GRCh37]
Chr11:11q13.4		 benign
NM_006185.4(NUMA1):c.2306C>T (p.Ala769Val) single nucleotide variant Inborn genetic diseases [RCV003272792] Chr11:72015197 [GRCh38]
Chr11:71726243 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2178A>G (p.Ala726=) single nucleotide variant not provided [RCV000894936] Chr11:72015325 [GRCh38]
Chr11:71726371 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.981G>A (p.Leu327=) single nucleotide variant not provided [RCV000889350] Chr11:72017825 [GRCh38]
Chr11:71728871 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.2915G>A (p.Arg972Gln) single nucleotide variant not provided [RCV000958624] Chr11:72014588 [GRCh38]
Chr11:71725634 [GRCh37]
Chr11:11q13.4		 benign
NM_006185.4(NUMA1):c.2937T>C (p.Asn979=) single nucleotide variant Acute promyelocytic leukemia [RCV002503096]|not provided [RCV000973476] Chr11:72014566 [GRCh38]
Chr11:71725612 [GRCh37]
Chr11:11q13.4		 benign|likely benign
NM_006185.4(NUMA1):c.584A>G (p.Asn195Ser) single nucleotide variant not provided [RCV001354643] Chr11:72019494 [GRCh38]
Chr11:71730540 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1025A>G (p.Asn342Ser) single nucleotide variant Inborn genetic diseases [RCV002905732] Chr11:72017781 [GRCh38]
Chr11:71728827 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.3170C>T (p.Thr1057Met) single nucleotide variant Inborn genetic diseases [RCV002686824] Chr11:72014333 [GRCh38]
Chr11:71725379 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.2402G>A (p.Ser801Asn) single nucleotide variant Inborn genetic diseases [RCV002992794] Chr11:72015101 [GRCh38]
Chr11:71726147 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2435C>G (p.Ala812Gly) single nucleotide variant Inborn genetic diseases [RCV002902329] Chr11:72015068 [GRCh38]
Chr11:71726114 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2168G>A (p.Arg723His) single nucleotide variant Inborn genetic diseases [RCV002945906] Chr11:72015335 [GRCh38]
Chr11:71726381 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1927C>T (p.Arg643Trp) single nucleotide variant Inborn genetic diseases [RCV002990204] Chr11:72015576 [GRCh38]
Chr11:71726622 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1868A>G (p.Gln623Arg) single nucleotide variant Inborn genetic diseases [RCV002836962] Chr11:72015635 [GRCh38]
Chr11:71726681 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1652A>G (p.His551Arg) single nucleotide variant Inborn genetic diseases [RCV002686692] Chr11:72015851 [GRCh38]
Chr11:71726897 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.3097C>T (p.Arg1033Trp) single nucleotide variant Inborn genetic diseases [RCV002749732] Chr11:72014406 [GRCh38]
Chr11:71725452 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2449T>C (p.Tyr817His) single nucleotide variant Inborn genetic diseases [RCV002949977] Chr11:72015054 [GRCh38]
Chr11:71726100 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1364G>T (p.Gly455Val) single nucleotide variant Inborn genetic diseases [RCV002981602] Chr11:72016139 [GRCh38]
Chr11:71727185 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1856T>C (p.Ile619Thr) single nucleotide variant Inborn genetic diseases [RCV002783614] Chr11:72015647 [GRCh38]
Chr11:71726693 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2029G>C (p.Glu677Gln) single nucleotide variant Inborn genetic diseases [RCV002692689] Chr11:72015474 [GRCh38]
Chr11:71726520 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1712C>T (p.Ala571Val) single nucleotide variant Inborn genetic diseases [RCV002951255] Chr11:72015791 [GRCh38]
Chr11:71726837 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1426T>C (p.Ser476Pro) single nucleotide variant Inborn genetic diseases [RCV002977318] Chr11:72016077 [GRCh38]
Chr11:71727123 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1462G>A (p.Ala488Thr) single nucleotide variant Inborn genetic diseases [RCV002693623] Chr11:72016041 [GRCh38]
Chr11:71727087 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2354T>G (p.Leu785Arg) single nucleotide variant Inborn genetic diseases [RCV002799559] Chr11:72015149 [GRCh38]
Chr11:71726195 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.480T>G (p.Cys160Trp) single nucleotide variant Inborn genetic diseases [RCV002868988] Chr11:72019598 [GRCh38]
Chr11:71730644 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.868A>G (p.Met290Val) single nucleotide variant Inborn genetic diseases [RCV002709121] Chr11:72018293 [GRCh38]
Chr11:71729339 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.1937C>G (p.Ala646Gly) single nucleotide variant Inborn genetic diseases [RCV002789591] Chr11:72015566 [GRCh38]
Chr11:71726612 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.897C>G (p.Cys299Trp) single nucleotide variant Inborn genetic diseases [RCV002744581] Chr11:72018264 [GRCh38]
Chr11:71729310 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1894G>A (p.Asp632Asn) single nucleotide variant Inborn genetic diseases [RCV002986355] Chr11:72015609 [GRCh38]
Chr11:71726655 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.790C>G (p.Leu264Val) single nucleotide variant Inborn genetic diseases [RCV002961034] Chr11:72018466 [GRCh38]
Chr11:71729512 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.806C>T (p.Ala269Val) single nucleotide variant Inborn genetic diseases [RCV002713897] Chr11:72018450 [GRCh38]
Chr11:71729496 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1389G>C (p.Gln463His) single nucleotide variant Inborn genetic diseases [RCV002965492] Chr11:72016114 [GRCh38]
Chr11:71727160 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2948G>A (p.Arg983Gln) single nucleotide variant Inborn genetic diseases [RCV002832422] Chr11:72014555 [GRCh38]
Chr11:71725601 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1744G>A (p.Ala582Thr) single nucleotide variant Inborn genetic diseases [RCV002792956] Chr11:72015759 [GRCh38]
Chr11:71726805 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.3117C>A (p.Asn1039Lys) single nucleotide variant Inborn genetic diseases [RCV002680461] Chr11:72014386 [GRCh38]
Chr11:71725432 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2343G>T (p.Glu781Asp) single nucleotide variant Inborn genetic diseases [RCV003207709] Chr11:72015160 [GRCh38]
Chr11:71726206 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1483C>T (p.Arg495Trp) single nucleotide variant Inborn genetic diseases [RCV003192859] Chr11:72016020 [GRCh38]
Chr11:71727066 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1930G>A (p.Glu644Lys) single nucleotide variant Inborn genetic diseases [RCV003211617] Chr11:72015573 [GRCh38]
Chr11:71726619 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2791G>C (p.Glu931Gln) single nucleotide variant Inborn genetic diseases [RCV003211979] Chr11:72014712 [GRCh38]
Chr11:71725758 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2966T>C (p.Met989Thr) single nucleotide variant Inborn genetic diseases [RCV003191211] Chr11:72014537 [GRCh38]
Chr11:71725583 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2606G>A (p.Arg869Gln) single nucleotide variant Inborn genetic diseases [RCV003266183] Chr11:72014897 [GRCh38]
Chr11:71725943 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2903A>G (p.Gln968Arg) single nucleotide variant Inborn genetic diseases [RCV003287984] Chr11:72014600 [GRCh38]
Chr11:71725646 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.539G>A (p.Arg180His) single nucleotide variant Inborn genetic diseases [RCV003358982] Chr11:72019539 [GRCh38]
Chr11:71730585 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.752T>C (p.Ile251Thr) single nucleotide variant NUMA1-related condition [RCV003404437] Chr11:72018504 [GRCh38]
Chr11:71729550 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.2752C>T (p.Arg918Cys) single nucleotide variant NUMA1-related condition [RCV003919101]|not provided [RCV003398107] Chr11:72014751 [GRCh38]
Chr11:71725797 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.3104A>G (p.Gln1035Arg) single nucleotide variant not provided [RCV003398106] Chr11:72014399 [GRCh38]
Chr11:71725445 [GRCh37]
Chr11:11q13.4		 uncertain significance
NM_006185.4(NUMA1):c.1033A>T (p.Thr345Ser) single nucleotide variant not provided [RCV003398109] Chr11:72017773 [GRCh38]
Chr11:71728819 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.2427A>T (p.Glu809Asp) single nucleotide variant not provided [RCV003398108] Chr11:72015076 [GRCh38]
Chr11:71726122 [GRCh37]
Chr11:11q13.4		 benign
NM_006185.4(NUMA1):c.2932G>A (p.Gly978Ser) single nucleotide variant NUMA1-related condition [RCV003963867] Chr11:72014571 [GRCh38]
Chr11:71725617 [GRCh37]
Chr11:11q13.4		 benign
NM_006185.4(NUMA1):c.1505C>G (p.Ser502Cys) single nucleotide variant not provided [RCV003884221] Chr11:72015998 [GRCh38]
Chr11:71727044 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.1396A>C (p.Ser466Arg) single nucleotide variant NUMA1-related condition [RCV003969249] Chr11:72016107 [GRCh38]
Chr11:71727153 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.1743T>C (p.His581=) single nucleotide variant NUMA1-related condition [RCV003974186] Chr11:72015760 [GRCh38]
Chr11:71726806 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.1030C>G (p.Leu344Val) single nucleotide variant NUMA1-related condition [RCV003927346] Chr11:72017776 [GRCh38]
Chr11:71728822 [GRCh37]
Chr11:11q13.4		 likely benign
NM_006185.4(NUMA1):c.2484C>T (p.Gly828=) single nucleotide variant NUMA1-related condition [RCV003903858] Chr11:72015019 [GRCh38]
Chr11:71726065 [GRCh37]
Chr11:11q13.4		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:209
Count of miRNA genes:200
Interacting mature miRNAs:205
Transcripts:ENST00000390800, ENST00000502284
Prediction methods:Miranda, Rnahybrid, Targetscan
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 3 11 22 2 10 1 10 39 21 10
Low 2310 2435 1458 408 1333 250 4050 1954 3086 263 1310 1449 167 1197 2725 4
Below cutoff 110 530 226 197 581 197 281 238 606 148 96 131 3 7 53

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000502284
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1172,014,291 - 72,020,910 (+)Ensembl
RefSeq Acc Id: NR_104178
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381172,014,291 - 72,020,910 (+)NCBI
T2T-CHM13v2.01171,941,206 - 71,947,807 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC AP002490.1 COSMIC
Ensembl Genes ENSG00000251143 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000502284 ENTREZGENE
GTEx ENSG00000251143 GTEx
Human Proteome Map AP002490.1 Human Proteome Map
NCBI Gene LOC100128494 ENTREZGENE
RNAcentral URS000025588D RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AP002490.1  novel transcript  LOC100128494  uncharacterized LOC100128494  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC100128494  uncharacterized LOC100128494  AP002490.1  novel transcript  Symbol and/or name change 5135510 APPROVED