LMCD1-AS1 (LMCD1 antisense RNA 1) - Rat Genome Database

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Gene: LMCD1-AS1 (LMCD1 antisense RNA 1) Homo sapiens
Analyze
Symbol: LMCD1-AS1
Name: LMCD1 antisense RNA 1
RGD ID: 7056190
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC087859.1; LMCD1 antisense RNA 1 (head to head)
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3837,952,805 - 8,016,307 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl37,951,263 - 8,611,924 (-)EnsemblGRCh38hg38GRCh38
GRCh3737,994,492 - 8,057,994 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera38,200,749 - 8,479,945 (-)NCBICelera
Cytogenetic Map3p26.1NCBI
HuRef37,929,560 - 7,993,333 (-)NCBIHuRef
CHM1_137,945,124 - 8,008,606 (-)NCBICHM1_1
T2T-CHM13v2.037,943,713 - 8,007,235 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14702039  


Genomics

Variants

.
Variants in LMCD1-AS1
8 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p26.1-25.3(chr3:7401136-8995777)x3 copy number gain See cases [RCV000133877] Chr3:7401136..8995777 [GRCh38]
Chr3:7442823..9037461 [GRCh37]
Chr3:7417823..9012461 [NCBI36]
Chr3:3p26.1-25.3		 uncertain significance
NR_033378.1(LMCD1-AS1):n.575-43959G>A single nucleotide variant Lung cancer [RCV000093749] Chr3:8266678 [GRCh38]
Chr3:8308365 [GRCh37]
Chr3:3p25.3		 uncertain significance
NR_033378.1(LMCD1-AS1):n.575-45844A>G single nucleotide variant Lung cancer [RCV000093750] Chr3:8268563 [GRCh38]
Chr3:8310250 [GRCh37]
Chr3:3p25.3		 uncertain significance
NR_033378.1(LMCD1-AS1):n.575-114007A>G single nucleotide variant Lung cancer [RCV000093758] Chr3:8336726 [GRCh38]
Chr3:8378414 [GRCh37]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p26.3-25.3(chr3:52266-9450310)x1 copy number loss See cases [RCV000137109] Chr3:52266..9450310 [GRCh38]
Chr3:93949..9491994 [GRCh37]
Chr3:68949..9466994 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.1-25.3(chr3:7401136-8485500)x3 copy number gain See cases [RCV000136629] Chr3:7401136..8485500 [GRCh38]
Chr3:7442823..8527186 [GRCh37]
Chr3:7417823..8502186 [NCBI36]
Chr3:3p26.1-25.3		 uncertain significance
GRCh38/hg38 3p26.1-25.2(chr3:7975734-12636917)x3 copy number gain See cases [RCV000137309] Chr3:7975734..12636917 [GRCh38]
Chr3:8017421..12678416 [GRCh37]
Chr3:7992421..12653416 [NCBI36]
Chr3:3p26.1-25.2		 likely pathogenic
GRCh38/hg38 3p26.3-25.2(chr3:32241-12681483)x1 copy number loss See cases [RCV000138143] Chr3:32241..12681483 [GRCh38]
Chr3:73914..12722982 [GRCh37]
Chr3:48914..12697982 [NCBI36]
Chr3:3p26.3-25.2		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-11379835)x1 copy number loss See cases [RCV000138376] Chr3:32241..11379835 [GRCh38]
Chr3:73914..11421309 [GRCh37]
Chr3:48914..11396309 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic|likely benign
GRCh38/hg38 3p26.3-25.3(chr3:32241-9469506)x1 copy number loss See cases [RCV000139253] Chr3:32241..9469506 [GRCh38]
Chr3:73914..9511190 [GRCh37]
Chr3:48914..9486190 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52747-8370373)x1 copy number loss See cases [RCV000139164] Chr3:52747..8370373 [GRCh38]
Chr3:94430..8412059 [GRCh37]
Chr3:69430..8387059 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.1(chr3:32241-13613818)x3 copy number gain See cases [RCV000138946] Chr3:32241..13613818 [GRCh38]
Chr3:73914..13655318 [GRCh37]
Chr3:48914..13630319 [NCBI36]
Chr3:3p26.3-25.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-9574994)x1 copy number loss See cases [RCV000140239] Chr3:32241..9574994 [GRCh38]
Chr3:73914..9616678 [GRCh37]
Chr3:48914..9591678 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-9066287)x1 copy number loss See cases [RCV000140848] Chr3:32241..9066287 [GRCh38]
Chr3:73914..9107971 [GRCh37]
Chr3:48914..9082971 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:20213-11221602)x1 copy number loss See cases [RCV000141731] Chr3:20213..11221602 [GRCh38]
Chr3:61891..11263288 [GRCh37]
Chr3:36891..11238288 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:20213-9362037)x1 copy number loss See cases [RCV000142284] Chr3:20213..9362037 [GRCh38]
Chr3:61891..9403721 [GRCh37]
Chr3:36891..9378721 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10323124)x1 copy number loss See cases [RCV000143325] Chr3:32241..10323124 [GRCh38]
Chr3:73914..10364808 [GRCh37]
Chr3:48914..10339808 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10631310)x1 copy number loss See cases [RCV000143173] Chr3:32241..10631310 [GRCh38]
Chr3:73914..10672995 [GRCh37]
Chr3:48914..10647995 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.1-25.1(chr3:7356110-14360442)x3 copy number gain See cases [RCV000143766] Chr3:7356110..14360442 [GRCh38]
Chr3:7397797..14401942 [GRCh37]
Chr3:7372797..14376946 [NCBI36]
Chr3:3p26.1-25.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:688897-11051142)x1 copy number loss See cases [RCV000143706] Chr3:688897..11051142 [GRCh38]
Chr3:730581..11092828 [GRCh37]
Chr3:705581..11067828 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.1-25.3(chr3:7975734-9038133)x3 copy number gain See cases [RCV000051434] Chr3:7975734..9038133 [GRCh38]
Chr3:8017421..9079817 [GRCh37]
Chr3:7992421..9054817 [NCBI36]
Chr3:3p26.1-25.3		 uncertain significance
GRCh38/hg38 3p26.3-25.3(chr3:52266-11089569)x1 copy number loss See cases [RCV000051447] Chr3:52266..11089569 [GRCh38]
Chr3:93949..11131255 [GRCh37]
Chr3:68949..11106255 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52266-8582037)x1 copy number loss See cases [RCV000051474] Chr3:52266..8582037 [GRCh38]
Chr3:93949..8623723 [GRCh37]
Chr3:68949..8598723 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:63843-9507969)x1 copy number loss See cases [RCV000051476] Chr3:63843..9507969 [GRCh38]
Chr3:105526..9549653 [GRCh37]
Chr3:80526..9524653 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:63843-8258109)x1 copy number loss See cases [RCV000051478] Chr3:63843..8258109 [GRCh38]
Chr3:105526..8299796 [GRCh37]
Chr3:80526..8274796 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.1-25.3(chr3:7400936-9450451)x1 copy number loss See cases [RCV000051479] Chr3:7400936..9450451 [GRCh38]
Chr3:7442623..9492135 [GRCh37]
Chr3:7417623..9467135 [NCBI36]
Chr3:3p26.1-25.3		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3 copy number gain See cases [RCV000051690] Chr3:52066..20280127 [GRCh38]
Chr3:93749..20321619 [GRCh37]
Chr3:68749..20296623 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:52266-29248782)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|See cases [RCV000051718] Chr3:52266..29248782 [GRCh38]
Chr3:93949..29290273 [GRCh37]
Chr3:68949..29265277 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-8165256)x3 copy number gain See cases [RCV000141319] Chr3:32241..8165256 [GRCh38]
Chr3:73914..8206943 [GRCh37]
Chr3:48914..8181943 [NCBI36]
Chr3:3p26.3-25.3		 likely pathogenic
GRCh38/hg38 3p26.1(chr3:7947823-8038727)x1 copy number loss See cases [RCV000141002] Chr3:7947823..8038727 [GRCh38]
Chr3:7989510..8080414 [GRCh37]
Chr3:7964510..8055414 [NCBI36]
Chr3:3p26.1		 benign
GRCh38/hg38 3p26.1(chr3:7834569-7975734)x1 copy number loss See cases [RCV000141013] Chr3:7834569..7975734 [GRCh38]
Chr3:7876256..8017421 [GRCh37]
Chr3:7851256..7992421 [NCBI36]
Chr3:3p26.1		 benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:927
Count of miRNA genes:640
Interacting mature miRNAs:727
Transcripts:ENST00000420095, ENST00000439407, ENST00000441861, ENST00000446281, ENST00000452802, ENST00000455811, ENST00000458666
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.

Markers in Region
D3S1537  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,307,698 - 8,307,921UniSTSGRCh37
Build 3638,282,698 - 8,282,921RGDNCBI36
Celera38,245,629 - 8,245,840RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,243,439 - 8,243,650UniSTS
Marshfield Genetic Map327.72UniSTS
Marshfield Genetic Map327.72RGD
deCODE Assembly Map323.18UniSTS
D16S3131  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,472,081 - 8,472,690UniSTSGRCh37
GRCh371626,005,238 - 26,005,476UniSTSGRCh37
Build 361625,912,739 - 25,912,977RGDNCBI36
Celera38,408,174 - 8,408,783UniSTS
Celera1624,781,645 - 24,781,883RGD
Cytogenetic Map16p11.2UniSTS
Cytogenetic Map16p12-p11.2UniSTS
Cytogenetic Map3p26.1UniSTS
HuRef1624,097,035 - 24,097,275UniSTS
Marshfield Genetic Map1650.6UniSTS
Marshfield Genetic Map1650.6RGD
Genethon Genetic Map1649.6UniSTS
TNG Radiation Hybrid Map1614554.0UniSTS
deCODE Assembly Map1650.49UniSTS
Whitehead-YAC Contig Map16 UniSTS
RH80992  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,467,362 - 8,467,471UniSTSGRCh37
Build 3638,442,362 - 8,442,471RGDNCBI36
Celera38,403,455 - 8,403,564RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,401,424 - 8,401,533UniSTS
SHGC-80102  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,468,525 - 8,468,837UniSTSGRCh37
Build 3638,443,525 - 8,443,837RGDNCBI36
Celera38,404,618 - 8,404,930RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,402,581 - 8,402,893UniSTS
TNG Radiation Hybrid Map35304.0UniSTS
SHGC-83688  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,401,060 - 8,401,261UniSTSGRCh37
Build 3638,376,060 - 8,376,261RGDNCBI36
Celera38,337,820 - 8,338,021RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,335,666 - 8,335,867UniSTS
TNG Radiation Hybrid Map35284.0UniSTS
G60126  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,265,015 - 8,265,214UniSTSGRCh37
Build 3638,240,015 - 8,240,214RGDNCBI36
Celera38,202,930 - 8,203,129RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,200,727 - 8,200,926UniSTS
TNG Radiation Hybrid Map35231.0UniSTS
SHGC-132793  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,307,877 - 8,308,149UniSTSGRCh37
Build 3638,282,877 - 8,283,149RGDNCBI36
Celera38,245,796 - 8,246,068RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,243,606 - 8,243,878UniSTS
TNG Radiation Hybrid Map35248.0UniSTS
SHGC-144674  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,434,788 - 8,435,130UniSTSGRCh37
Build 3638,409,788 - 8,410,130RGDNCBI36
Celera38,371,547 - 8,371,889RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,369,393 - 8,369,735UniSTS
TNG Radiation Hybrid Map35296.0UniSTS
SHGC-155428  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,442,137 - 8,442,452UniSTSGRCh37
Build 3638,417,137 - 8,417,452RGDNCBI36
Celera38,378,893 - 8,379,208RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,376,739 - 8,377,054UniSTS
TNG Radiation Hybrid Map35288.0UniSTS
SHGC-155429  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3738,440,417 - 8,440,727UniSTSGRCh37
Build 3638,415,417 - 8,415,727RGDNCBI36
Celera38,377,173 - 8,377,483RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,375,019 - 8,375,329UniSTS
TNG Radiation Hybrid Map35292.0UniSTS
REN69886  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375131,682,098 - 131,682,351UniSTSGRCh37
Build 365131,709,997 - 131,710,250RGDNCBI36
Celera5127,812,171 - 127,812,424RGD
Cytogenetic Map3p26.1UniSTS
HuRef38,351,439 - 8,351,693UniSTS
HuRef5126,874,349 - 126,874,602UniSTS


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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 1 1 11
Low 42 174 137 26 39 25 833 33 1546 62 344 211 11 1 47 593 2 2
Below cutoff 2330 2231 1520 545 1011 388 3479 2108 2175 334 1098 1385 162 1156 2159 4

Sequence


Reference Sequences
RefSeq Acc Id: NR_110131
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3837,952,805 - 8,016,307 (-)NCBI
T2T-CHM13v2.037,943,713 - 8,007,235 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LMCD1-AS1 COSMIC
Ensembl Genes ENSG00000227110 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000441861 ENTREZGENE
GTEx ENSG00000227110 GTEx
Human Proteome Map LMCD1-AS1 Human Proteome Map
NCBI Gene LOC101927394 ENTREZGENE
RNAcentral URS00005848BA RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-03-27 LMCD1-AS1  LMCD1 antisense RNA 1    LMCD1 antisense RNA 1 (head to head)  Symbol and/or name change 5135510 APPROVED