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LMDRA (leucine rich melanocyte differentiation associated)

Written2016-04Kunal Ray, Mainak Sengupta, Sampurna Ghosh
Academy of Scientific and Innovative Research (AcSIR), Campus at CSIR - Central Road Research Institute, Mathura Road, New Delhi - 110 025, kunalray@gmail.com (KR); University of Calcutta, Department of Genetics, 35, Ballygunge Circular Road, Kolkata - 700 019, sengupta.mainak@gmail.com); sampurna_ghosh@yahoo.in (MS, SG) India.

Abstract C10orf11 encodes a leucine-rich repeat protein having a role in melanocyte differentiation. Mutations in this gene have been associated with autosomal recessive oculocutaneous albinism 7 (OCAVII).

Keywords OCAVII, albinism, C10orf11

(Note : for Links provided by Atlas : click)

Identity

Alias_namesC10orf11
chromosome 10 open reading frame 11
Alias_symbol (synonym)CDA017
OCA7
Other aliasOculocutaneous Albinism 7
C10orf11 (Chromosome 10 Open Reading Frame 11)
HGNC (Hugo) LRMDA
LocusID (NCBI) 83938
Atlas_Id 60852
Location 10q22.3  [Link to chromosome band 10q22]
Location_base_pair Starts at 75431646 and ends at 76557376 bp from pter ( according to hg19-Feb_2009)  [Mapping LRMDA.png]
 
  Cytogenetic band showing C10orf11 locus (http://www.genecards.org/cgi-bin/carddisp.pl?gene=C10orf11&keywords= C10orf11).
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

DNA/RNA

Description In Chromosome: 10, the 1,128,715 bases long gene starts from 75,431,453bp from pter and ends 76,560,167 bp from pter; Orientation: Plus strand. It contains 6 exons.
Transcription C10orf11 encodes 16 splice variants of which 4 are protein coding and the remaining are processed transcripts.

Protein

Description The gene encodes a 198 amino acids long leucine-rich repeat-containing protein of molecular mass 22568 Da.
Expression The gene is expressed in embryonic melanoblasts and fetal melanocyte and has not been detected in retinal pigment epithelial cells. In addition the expression of the gene in the following tissue types are evident by its existence in the corresponding cDNA libraries: adrenal cortex, brain, cartilage, cerebellum, endocrine, eye, fetus, heart, kidney, liver, lung, muscle, nervous, pancreas, pancreatic islet, placenta, pooled tissue, prostate, skin, stem cell, testis and uterus (http://cgap.nci.nih.gov/Genes/GeneInfo?ORG=Hs&CID=118161&LLNO=83938).
Localisation 10q22.3
Function The precise function of C10ORF11 is not yet known. However, there is some evidence that the protein might have a role in melanocyte differentiation.

Mutations

Germinal C10orf11 mutations are responsible for Oculocutaneous Albinism type 7 (OCA7). Nine Faroese patients and one Danish patient of Lithuanian origin were found to have mutations in C10orf11 gene representing OCAVII (Gronskov et al., 2014). These patients have a light skin pigmentation that is reported to be lighter than their relatives. Hair color ranges from light blond to dark brown. Eye findings include nystagmus, iris transillumination, visual acuity ranging from 6/9 to 3/60 and very sparse peripheral ocular fundus pigmentation.

Implicated in

Note
  
Entity Breast Cancer
Note To identify genetic polymorphisms associated with clinical outcomes of breast cancer patients with tamoxifen treatment, genome-wide association study was conducted using 462 Japanese patients with hormone receptor-positive, invasive breast cancer receiving adjuvant tamoxifen therapy. The study revealed that rs10509373 in C10orf11 gene to be significantly associated with recurrence-free survival in the replication study (log-rank P= 2.02 ◊ 10-4). Hazard ratio per C allele of rs10509373 was found to be 4.51 [95% confidence interval (CI), 2.727.51; P= 6.29 ◊ 10-9]. In a combined analysis of rs10509373 genotype with previously identified genetic makers, CYP2D6 and ABCC2, the number of risk alleles of these three genes was reported to have cumulative effect on recurrence-free survival among 345 patients receiving tamoxifen monotherapy (log-rank P= 2.28 ◊ 10-12) (Kiyotani et al., 2011).
  

Bibliography

Mutations in c10orf11, a melanocyte-differentiation gene, cause autosomal-recessive albinism
Grnskov K, Dooley CM, stergaard E, Kelsh RN, Hansen L, Levesque MP, Vilhelmsen K, Mllgård K, Stemple DL, Rosenberg T
Am J Hum Genet 2013 Mar 7;92(3):415-21
PMID 23395477
 
A genome-wide association study identifies locus at 10q22 associated with clinical outcomes of adjuvant tamoxifen therapy for breast cancer patients in Japanese
Kiyotani K, Mushiroda T, Tsunoda T, Morizono T, Hosono N, Kubo M, Tanigawara Y, Imamura CK, Flockhart DA, Aki F, Hirata K, Takatsuka Y, Okazaki M, Ohsumi S, Yamakawa T, Sasa M, Nakamura Y, Zembutsu H
Hum Mol Genet 2012 Apr 1;21(7):1665-72
PMID 22180457
 

Citation

This paper should be referenced as such :
Ray K, Sengupta M, Ghosh S
LMDRA (leucine rich melanocyte differentiation associated);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/C10orf11ID60852ch10q22.html


Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Oculocutaneous Albinism


External links

Nomenclature
HGNC (Hugo)LRMDA   23405
Cards
AtlasC10orf11ID60852ch10q22.txt
Entrez_Gene (NCBI)LRMDA  83938  leucine rich melanocyte differentiation associated
AliasesC10orf11; CDA017
GeneCards (Weizmann)LRMDA
Ensembl hg19 (Hinxton)ENSG00000148655 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000148655 [Gene_View]  chr10:75431646-76557376 [Contig_View]  LRMDA [Vega]
ICGC DataPortalENSG00000148655
TCGA cBioPortalLRMDA
AceView (NCBI)LRMDA
Genatlas (Paris)LRMDA
WikiGenes83938
SOURCE (Princeton)LRMDA
Genetics Home Reference (NIH)LRMDA
Genomic and cartography
GoldenPath hg38 (UCSC)LRMDA  -     chr10:75431646-76557376 +  10q22.2-q22.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LRMDA  -     10q22.2-q22.3   [Description]    (hg19-Feb_2009)
EnsemblLRMDA - 10q22.2-q22.3 [CytoView hg19]  LRMDA - 10q22.2-q22.3 [CytoView hg38]
Mapping of homologs : NCBILRMDA [Mapview hg19]  LRMDA [Mapview hg38]
OMIM614537   615179   
Gene and transcription
Genbank (Entrez)AF267860 AK125328 BM720401 BX105111 CR933639
RefSeq transcript (Entrez)NM_001305581 NM_032024
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LRMDA
Cluster EST : UnigeneHs.690504 [ NCBI ]
CGAP (NCI)Hs.690504
Alternative Splicing GalleryENSG00000148655
Gene ExpressionLRMDA [ NCBI-GEO ]   LRMDA [ EBI - ARRAY_EXPRESS ]   LRMDA [ SEEK ]   LRMDA [ MEM ]
Gene Expression Viewer (FireBrowse)LRMDA [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)83938
GTEX Portal (Tissue expression)LRMDA
Human Protein AtlasENSG00000148655-LRMDA [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9H2I8   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9H2I8  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9H2I8
Splice isoforms : SwissVarQ9H2I8
PhosPhoSitePlusQ9H2I8
Domaine pattern : Prosite (Expaxy)LRR (PS51450)   
Domains : Interpro (EBI)L_dom-like    Leu-rich_rpt   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)LRMDA
DMDM Disease mutations83938
Blocks (Seattle)LRMDA
SuperfamilyQ9H2I8
Human Protein Atlas [tissue]ENSG00000148655-LRMDA [tissue]
Peptide AtlasQ9H2I8
IPIIPI00012461   IPI00639880   
Protein Interaction databases
DIP (DOE-UCLA)Q9H2I8
IntAct (EBI)Q9H2I8
FunCoupENSG00000148655
BioGRIDLRMDA
STRING (EMBL)LRMDA
ZODIACLRMDA
Ontologies - Pathways
QuickGOQ9H2I8
Ontology : AmiGOmelanocyte differentiation  
Ontology : EGO-EBImelanocyte differentiation  
NDEx NetworkLRMDA
Atlas of Cancer Signalling NetworkLRMDA
Wikipedia pathwaysLRMDA
Orthology - Evolution
OrthoDB83938
GeneTree (enSembl)ENSG00000148655
Phylogenetic Trees/Animal Genes : TreeFamLRMDA
HOVERGENQ9H2I8
HOGENOMQ9H2I8
Homologs : HomoloGeneLRMDA
Homology/Alignments : Family Browser (UCSC)LRMDA
Gene fusions - Rearrangements
Tumor Fusion PortalLRMDA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLRMDA [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LRMDA
dbVarLRMDA
ClinVarLRMDA
1000_GenomesLRMDA 
Exome Variant ServerLRMDA
ExAC (Exome Aggregation Consortium)ENSG00000148655
GNOMAD BrowserENSG00000148655
Genetic variants : HAPMAP83938
Genomic Variants (DGV)LRMDA [DGVbeta]
DECIPHERLRMDA [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLRMDA 
Mutations
ICGC Data PortalLRMDA 
TCGA Data PortalLRMDA 
Broad Tumor PortalLRMDA
OASIS PortalLRMDA [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDLRMDA
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 LRMDA
DgiDB (Drug Gene Interaction Database)LRMDA
DoCM (Curated mutations)LRMDA (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LRMDA (select a term)
intoGenLRMDA
Cancer3DLRMDA(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM614537    615179   
Orphanet
DisGeNETLRMDA
MedgenLRMDA
Genetic Testing Registry LRMDA
NextProtQ9H2I8 [Medical]
TSGene83938
GENETestsLRMDA
Target ValidationLRMDA
Huge Navigator LRMDA [HugePedia]
snp3D : Map Gene to Disease83938
BioCentury BCIQLRMDA
ClinGenLRMDA
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD83938
Chemical/Pharm GKB GenePA134899373
Clinical trialLRMDA
Miscellaneous
canSAR (ICR)LRMDA (select the gene name)
Probes
Litterature
PubMed12 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLRMDA
EVEXLRMDA
GoPubMedLRMDA
iHOPLRMDA
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:45:41 CET 2017

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