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LMCD1 (LIM and cysteine rich domains 1)

Identity

Other alias-
HGNC (Hugo) LMCD1
LocusID (NCBI) 29995
Atlas_Id 41165
Location 3p26.1  [Link to chromosome band 3p26]
Location_base_pair Starts at 8543493 and ends at 8609811 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
LMCD1 (3p26.1) / PBX3 (9q33.3)NUDCD3 (7p13) / LMCD1 (3p26.1)THRB (3p24.2) / LMCD1 (3p26.1)
THRB 3p24.2 / LMCD1 3p26.1

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)LMCD1   6633
Cards
Entrez_Gene (NCBI)LMCD1  29995  LIM and cysteine rich domains 1
Aliases
GeneCards (Weizmann)LMCD1
Ensembl hg19 (Hinxton)ENSG00000071282 [Gene_View]  chr3:8543493-8609811 [Contig_View]  LMCD1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000071282 [Gene_View]  chr3:8543493-8609811 [Contig_View]  LMCD1 [Vega]
ICGC DataPortalENSG00000071282
TCGA cBioPortalLMCD1
AceView (NCBI)LMCD1
Genatlas (Paris)LMCD1
WikiGenes29995
SOURCE (Princeton)LMCD1
Genetics Home Reference (NIH)LMCD1
Genomic and cartography
GoldenPath hg19 (UCSC)LMCD1  -     chr3:8543493-8609811 +  3p26.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)LMCD1  -     3p26.1   [Description]    (hg38-Dec_2013)
EnsemblLMCD1 - 3p26.1 [CytoView hg19]  LMCD1 - 3p26.1 [CytoView hg38]
Mapping of homologs : NCBILMCD1 [Mapview hg19]  LMCD1 [Mapview hg38]
OMIM604859   
Gene and transcription
Genbank (Entrez)AF169284 AF216709 AI693011 AI951010 AK022176
RefSeq transcript (Entrez)NM_001278233 NM_001278234 NM_001278235 NM_014583
RefSeq genomic (Entrez)NC_000003 NC_018914 NT_022517 NW_004929309
Consensus coding sequences : CCDS (NCBI)LMCD1
Cluster EST : UnigeneHs.732705 [ NCBI ]
CGAP (NCI)Hs.732705
Alternative Splicing GalleryENSG00000071282
Gene ExpressionLMCD1 [ NCBI-GEO ]   LMCD1 [ EBI - ARRAY_EXPRESS ]   LMCD1 [ SEEK ]   LMCD1 [ MEM ]
Gene Expression Viewer (FireBrowse)LMCD1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)29995
GTEX Portal (Tissue expression)LMCD1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NZU5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NZU5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NZU5
Splice isoforms : SwissVarQ9NZU5
PhosPhoSitePlusQ9NZU5
Domaine pattern : Prosite (Expaxy)LIM_DOMAIN_1 (PS00478)    LIM_DOMAIN_2 (PS50023)    PET (PS51303)   
Domains : Interpro (EBI)PET_domain    Znf_LIM   
Domain families : Pfam (Sanger)LIM (PF00412)    PET (PF06297)   
Domain families : Pfam (NCBI)pfam00412    pfam06297   
Domain families : Smart (EMBL)LIM (SM00132)  
Conserved Domain (NCBI)LMCD1
DMDM Disease mutations29995
Blocks (Seattle)LMCD1
SuperfamilyQ9NZU5
Human Protein AtlasENSG00000071282
Peptide AtlasQ9NZU5
HPRD06891
IPIIPI00303258   IPI00910942   IPI00927828   IPI00926221   IPI00927275   IPI00926626   
Protein Interaction databases
DIP (DOE-UCLA)Q9NZU5
IntAct (EBI)Q9NZU5
FunCoupENSG00000071282
BioGRIDLMCD1
STRING (EMBL)LMCD1
ZODIACLMCD1
Ontologies - Pathways
QuickGOQ9NZU5
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  positive regulation of defense response to virus by host  transcription corepressor activity  transcription corepressor activity  extracellular space  nucleus  nucleoplasm  cytoplasm  transcription, DNA-templated  zinc ion binding  regulation of cardiac muscle hypertrophy  extracellular matrix  cellular protein metabolic process  positive regulation of calcineurin-NFAT signaling cascade  mitophagy in response to mitochondrial depolarization  xenophagy  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  positive regulation of defense response to virus by host  transcription corepressor activity  transcription corepressor activity  extracellular space  nucleus  nucleoplasm  cytoplasm  transcription, DNA-templated  zinc ion binding  regulation of cardiac muscle hypertrophy  extracellular matrix  cellular protein metabolic process  positive regulation of calcineurin-NFAT signaling cascade  mitophagy in response to mitochondrial depolarization  xenophagy  
NDEx NetworkLMCD1
Atlas of Cancer Signalling NetworkLMCD1
Wikipedia pathwaysLMCD1
Orthology - Evolution
OrthoDB29995
GeneTree (enSembl)ENSG00000071282
Phylogenetic Trees/Animal Genes : TreeFamLMCD1
HOVERGENQ9NZU5
HOGENOMQ9NZU5
Homologs : HomoloGeneLMCD1
Homology/Alignments : Family Browser (UCSC)LMCD1
Gene fusions - Rearrangements
Fusion : MitelmanTHRB/LMCD1 [3p24.2/3p26.1]  [t(3;3)(p24;p26)]  
Fusion: TCGATHRB 3p24.2 LMCD1 3p26.1 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLMCD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LMCD1
dbVarLMCD1
ClinVarLMCD1
1000_GenomesLMCD1 
Exome Variant ServerLMCD1
ExAC (Exome Aggregation Consortium)LMCD1 (select the gene name)
Genetic variants : HAPMAP29995
Genomic Variants (DGV)LMCD1 [DGVbeta]
DECIPHER (Syndromes)3:8543493-8609811  ENSG00000071282
CONAN: Copy Number AnalysisLMCD1 
Mutations
ICGC Data PortalLMCD1 
TCGA Data PortalLMCD1 
Broad Tumor PortalLMCD1
OASIS PortalLMCD1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLMCD1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLMCD1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LMCD1
DgiDB (Drug Gene Interaction Database)LMCD1
DoCM (Curated mutations)LMCD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LMCD1 (select a term)
intoGenLMCD1
Cancer3DLMCD1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604859   
Orphanet
MedgenLMCD1
Genetic Testing Registry LMCD1
NextProtQ9NZU5 [Medical]
TSGene29995
GENETestsLMCD1
Huge Navigator LMCD1 [HugePedia]
snp3D : Map Gene to Disease29995
BioCentury BCIQLMCD1
ClinGenLMCD1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD29995
Chemical/Pharm GKB GenePA30401
Clinical trialLMCD1
Miscellaneous
canSAR (ICR)LMCD1 (select the gene name)
Probes
Litterature
PubMed20 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLMCD1
EVEXLMCD1
GoPubMedLMCD1
iHOPLMCD1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Mar 30 15:07:13 CEST 2017

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