LOXL2-AS1 (LOXL2 antisense RNA 1) - Rat Genome Database

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Gene: LOXL2-AS1 (LOXL2 antisense RNA 1) Homo sapiens
Analyze
Symbol: LOXL2-AS1
Name: LOXL2 antisense RNA 1
RGD ID: 16559957
HGNC Page HGNC:56648
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC090197.1; LOC100507156; novel transcript; uncharacterized LOC100507156
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38823,336,208 - 23,366,125 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl823,336,171 - 23,366,125 (+)EnsemblGRCh38hg38GRCh38
GRCh37823,193,721 - 23,223,638 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8p21.3NCBI
HuRef821,739,143 - 21,769,052 (+)NCBIHuRef
CHM1_1823,395,847 - 23,425,747 (+)NCBICHM1_1
T2T-CHM13v2.0823,611,088 - 23,641,005 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics

Variants

.
Variants in LOXL2-AS1
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_002318.3(LOXL2):c.381C>T (p.His127=) single nucleotide variant not provided [RCV000975182] Chr8:23360240 [GRCh38]
Chr8:23217753 [GRCh37]
Chr8:8p21.3		 benign
GRCh38/hg38 8p23.1-11.22(chr8:7141697-38695546)x3 copy number gain See cases [RCV000139891] Chr8:7141697..38695546 [GRCh38]
Chr8:6999219..38553064 [GRCh37]
Chr8:6986629..38672221 [NCBI36]
Chr8:8p23.1-11.22		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12182421-43673207)x3 copy number gain See cases [RCV000137249] Chr8:12182421..43673207 [GRCh38]
Chr8:12039930..43528350 [GRCh37]
Chr8:12077339..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.3-12(chr8:226452-34491890)x3 copy number gain See cases [RCV000141410] Chr8:226452..34491890 [GRCh38]
Chr8:176452..34349408 [GRCh37]
Chr8:166452..34468950 [NCBI36]
Chr8:8p23.3-12		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12633490-40685533)x3 copy number gain See cases [RCV000143508] Chr8:12633490..40685533 [GRCh38]
Chr8:12490999..40543052 [GRCh37]
Chr8:12535370..40662209 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-12(chr8:96310-30614703)x3 copy number gain See cases [RCV000053599] Chr8:96310..30614703 [GRCh38]
Chr8:46310..30472220 [GRCh37]
Chr8:36310..30591762 [NCBI36]
Chr8:8p23.3-12		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12750796-43532444)x3 copy number gain See cases [RCV000053632] Chr8:12750796..43532444 [GRCh38]
Chr8:12608305..43387587 [GRCh37]
Chr8:12652676..43506744 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.3-21.2(chr8:241605-24656971)x3 copy number gain See cases [RCV000136026] Chr8:241605..24656971 [GRCh38]
Chr8:191605..24514484 [GRCh37]
Chr8:181605..24570374 [NCBI36]
Chr8:8p23.3-21.2		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
NM_002318.3(LOXL2):c.411A>C (p.Ala137=) single nucleotide variant not provided [RCV000889196] Chr8:23360210 [GRCh38]
Chr8:23217723 [GRCh37]
Chr8:8p21.3		 benign
GRCh38/hg38 8p23.1-11.1(chr8:12728904-43673207)x3 copy number gain See cases [RCV000050912] Chr8:12728904..43673207 [GRCh38]
Chr8:12586413..43528350 [GRCh37]
Chr8:12630784..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12725750-30180521)x3 copy number gain See cases [RCV000136825] Chr8:12725750..30180521 [GRCh38]
Chr8:12583259..30038037 [GRCh37]
Chr8:12627630..30157579 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12609975-43336172)x3 copy number gain See cases [RCV000053630] Chr8:12609975..43336172 [GRCh38]
Chr8:12467484..43191315 [GRCh37]
Chr8:12511855..43310472 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.1-21.1(chr8:12382844-28625564)x3 copy number gain See cases [RCV000138244] Chr8:12382844..28625564 [GRCh38]
Chr8:12240353..28483081 [GRCh37]
Chr8:12284724..28539000 [NCBI36]
Chr8:8p23.1-21.1		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p22-q11.21(chr8:14940110-47929925)x3 copy number gain See cases [RCV000053635] Chr8:14940110..47929925 [GRCh38]
Chr8:14797619..48842485 [GRCh37]
Chr8:14841990..49005038 [NCBI36]
Chr8:8p22-q11.21		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12728904-41928741)x3 copy number gain See cases [RCV000051110] Chr8:12728904..41928741 [GRCh38]
Chr8:12586413..41786259 [GRCh37]
Chr8:12630784..41905416 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.2-21.1(chr8:2475295-27504279)x1 copy number loss See cases [RCV000148252] Chr8:2475295..27504279 [GRCh38]
Chr8:2292235..27361796 [GRCh37]
Chr8:2121457..27417713 [NCBI36]
Chr8:8p23.2-21.1		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12609975-43673207)x3 copy number gain See cases [RCV000135786] Chr8:12609975..43673207 [GRCh38]
Chr8:12467484..43528350 [GRCh37]
Chr8:12511855..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12646123-43686843)x3 copy number gain See cases [RCV000139796] Chr8:12646123..43686843 [GRCh38]
Chr8:12503632..43541986 [GRCh37]
Chr8:12548003..43661143 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12609975-42085703)x3 copy number gain See cases [RCV000050294] Chr8:12609975..42085703 [GRCh38]
Chr8:12467484..41943221 [GRCh37]
Chr8:12511855..42062378 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.1-11.23(chr8:11851113-37216333)x3 copy number gain See cases [RCV000139549] Chr8:11851113..37216333 [GRCh38]
Chr8:11708622..37073851 [GRCh37]
Chr8:11746031..37193009 [NCBI36]
Chr8:8p23.1-11.23		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12383584-29033946)x1 copy number loss See cases [RCV000142516] Chr8:12383584..29033946 [GRCh38]
Chr8:12241093..28891463 [GRCh37]
Chr8:12285464..28947382 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12609975-42085703)x3 copy number gain See cases [RCV000148249] Chr8:12609975..42085703 [GRCh38]
Chr8:12467484..41943221 [GRCh37]
Chr8:12511855..42062378 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.3-11.23(chr8:226452-38021728)x3 copy number gain See cases [RCV000137807] Chr8:226452..38021728 [GRCh38]
Chr8:176452..37879246 [GRCh37]
Chr8:166452..37998403 [NCBI36]
Chr8:8p23.3-11.23		 pathogenic|likely pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12383584-43673207)x3 copy number gain See cases [RCV000135566] Chr8:12383584..43673207 [GRCh38]
Chr8:12241093..43528350 [GRCh37]
Chr8:12285464..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-11.23(chr8:12609975-37892000)x3 copy number gain See cases [RCV000053629] Chr8:12609975..37892000 [GRCh38]
Chr8:12467484..37749518 [GRCh37]
Chr8:12511855..37868676 [NCBI36]
Chr8:8p23.1-11.23		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12750796-29445409)x3 copy number gain See cases [RCV000053633] Chr8:12750796..29445409 [GRCh38]
Chr8:12608305..29302926 [GRCh37]
Chr8:12652676..29358845 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12728904-40169194)x3 copy number gain See cases [RCV000136516] Chr8:12728904..40169194 [GRCh38]
Chr8:12586413..40026713 [GRCh37]
Chr8:12630784..40145870 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12698495-35476082)x3 copy number gain See cases [RCV000138058] Chr8:12698495..35476082 [GRCh38]
Chr8:12556004..35333600 [GRCh37]
Chr8:12600375..35453142 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.3-12(chr8:241605-31091074)x3 copy number gain See cases [RCV000138831] Chr8:241605..31091074 [GRCh38]
Chr8:191605..30948590 [GRCh37]
Chr8:181605..31068132 [NCBI36]
Chr8:8p23.3-12		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12728904-43673207)x3 copy number gain See cases [RCV000148237] Chr8:12728904..43673207 [GRCh38]
Chr8:12586413..43528350 [GRCh37]
Chr8:12630784..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12383584-36370018)x3 copy number gain See cases [RCV000051145] Chr8:12383584..36370018 [GRCh38]
Chr8:12241093..36227536 [GRCh37]
Chr8:12285464..36347088 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.1-11.22(chr8:12729023-39235934)x3 copy number gain See cases [RCV000139770] Chr8:12729023..39235934 [GRCh38]
Chr8:12586532..39093453 [GRCh37]
Chr8:12630903..39212610 [NCBI36]
Chr8:8p23.1-11.22		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-21.1(chr8:2475295-27504279)x1 copy number loss See cases [RCV000050297] Chr8:2475295..27504279 [GRCh38]
Chr8:2292235..27361796 [GRCh37]
Chr8:2121457..27417713 [NCBI36]
Chr8:8p23.3-21.1		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p22-12(chr8:18972996-33619264)x1 copy number loss See cases [RCV000142747] Chr8:18972996..33619264 [GRCh38]
Chr8:18830506..33476782 [GRCh37]
Chr8:18874786..33596324 [NCBI36]
Chr8:8p22-12		 pathogenic
GRCh38/hg38 8p21.3-21.2(chr8:22946697-25125997)x3 copy number gain See cases [RCV000137878] Chr8:22946697..25125997 [GRCh38]
Chr8:22804210..24983512 [GRCh37]
Chr8:22860155..25039429 [NCBI36]
Chr8:8p21.3-21.2		 uncertain significance
NM_002318.3(LOXL2):c.586C>T (p.Arg196Cys) single nucleotide variant not specified [RCV004239395] Chr8:23341149 [GRCh38]
Chr8:23198662 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.731C>G (p.Thr244Ser) single nucleotide variant not specified [RCV004095087] Chr8:23341004 [GRCh38]
Chr8:23198517 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.715G>C (p.Glu239Gln) single nucleotide variant not specified [RCV004231194] Chr8:23341020 [GRCh38]
Chr8:23198533 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.460G>A (p.Val154Ile) single nucleotide variant not specified [RCV004213704] Chr8:23360161 [GRCh38]
Chr8:23217674 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.512C>T (p.Ser171Leu) single nucleotide variant not specified [RCV004247141] Chr8:23360109 [GRCh38]
Chr8:23217622 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.598C>A (p.Pro200Thr) single nucleotide variant not specified [RCV004151210] Chr8:23341137 [GRCh38]
Chr8:23198650 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.683G>A (p.Arg228His) single nucleotide variant not specified [RCV004091678] Chr8:23341052 [GRCh38]
Chr8:23198565 [GRCh37]
Chr8:8p21.3		 likely benign
NM_002318.3(LOXL2):c.592C>T (p.Arg198Cys) single nucleotide variant not specified [RCV004323252] Chr8:23341143 [GRCh38]
Chr8:23198656 [GRCh37]
Chr8:8p21.3		 uncertain significance
GRCh38/hg38 8p23.1-12(chr8:12721809-30183737)x1 copy number loss Microcephaly [RCV003327707] Chr8:12721809..30183737 [GRCh38]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.3-21.2(chr8:449893-23854904)x1 copy number loss Neurodevelopmental disorder [RCV003327729] Chr8:449893..23854904 [GRCh38]
Chr8:8p23.3-21.2		 pathogenic
NM_002318.3(LOXL2):c.478G>A (p.Asp160Asn) single nucleotide variant not specified [RCV004410454] Chr8:23360143 [GRCh38]
Chr8:23217656 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.627G>C (p.Lys209Asn) single nucleotide variant not specified [RCV004410455] Chr8:23341108 [GRCh38]
Chr8:23198621 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.668C>T (p.Thr223Met) single nucleotide variant not specified [RCV004410457] Chr8:23341067 [GRCh38]
Chr8:23198580 [GRCh37]
Chr8:8p21.3		 uncertain significance
NM_002318.3(LOXL2):c.699G>A (p.Met233Ile) single nucleotide variant not specified [RCV004410458] Chr8:23341036 [GRCh38]
Chr8:23198549 [GRCh37]
Chr8:8p21.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:273
Count of miRNA genes:235
Interacting mature miRNAs:240
Transcripts:ENST00000517420, ENST00000519692
Prediction methods:Microtar, 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 1 1 1
Low 324 965 568 13 140 13 719 187 578 167 450 639 4 218 553 2
Below cutoff 1989 1747 1036 488 1398 333 3527 1950 3110 239 954 925 165 985 2169 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000517420
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl823,336,171 - 23,341,536 (+)Ensembl
RefSeq Acc Id: ENST00000519692
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl823,336,208 - 23,366,125 (+)Ensembl
RefSeq Acc Id: NR_038323
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38823,336,208 - 23,366,125 (+)NCBI
T2T-CHM13v2.0823,611,088 - 23,641,005 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LOXL2-AS1 COSMIC
Ensembl Genes ENSG00000253837 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000519692 ENTREZGENE
GTEx ENSG00000253837 GTEx
HGNC ID HGNC:56648 ENTREZGENE
Human Proteome Map LOXL2-AS1 Human Proteome Map
NCBI Gene LOC100507156 ENTREZGENE
RNAcentral URS000075CE0C RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-12-05 LOXL2-AS1  LOXL2 antisense RNA 1  AC090197.1  novel transcript  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AC090197.1  novel transcript  LOC100507156  uncharacterized LOC100507156  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC100507156  uncharacterized LOC100507156  AC090197.1  novel transcript  Symbol and/or name change 5135510 APPROVED