Atlas of Genetics and Cytogenetics in Oncology and Haematology

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HLA-C (major histocompatibility complex, class I, C)

Identity

Alias_namesHLA-JY3
D6S204
PSORS1
psoriasis susceptibility 1
Other aliasHLAC
HLC-C
MHC
HGNC (Hugo) HLA-C
LocusID (NCBI) 3107
Atlas_Id 40831
Location 6p21.33  [Link to chromosome band 6p21]
Location_base_pair Starts at 31268749 and ends at 31272136 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
AES (19p13.3) / HLA-C (6p21.33)BTNL3 (5q35.3) / HLA-C (6p21.33)DAPL1 (2q24.1) / HLA-C (6p21.33)
HLA-A (6p22.1) / HLA-C (6p21.33)HLA-C (6p21.33) / ANP32A (15q23)HLA-C (6p21.33) / CFB (6p21.33)
HLA-C (6p21.33) / FOXP1 (3p13)HLA-C (6p21.33) / HEPH (Xq12)HLA-C (6p21.33) / HLA-B (6p21.33)
HLA-C (6p21.33) / HSP90AA1 (14q32.31)HLA-C (6p21.33) / TCOF1 (5q32)HLA-C (6p21.33) / ZMIZ2 (7p13)
HLA-C (6p21.33) / ZNF664 (12q24.31)HLA-G (6p22.1) / HLA-C (6p21.33)HLA-H (6p22.1) / HLA-C (6p21.33)
HLA-J (6p22.1) / HLA-C (6p21.33)HLA-L (6p22.1) / HLA-C (6p21.33)LIF (22q12.2) / HLA-C (6p21.33)
LOC100507412 (-) / HLA-C (6p21.33)NUMA1 (11q13.4) / HLA-C (6p21.33)S100A11 (1q21.3) / HLA-C (6p21.33)
STX4 (16p11.2) / HLA-C (6p21.33)TGFBI (5q31.1) / HLA-C (6p21.33)HLA-C 6p21.33 / CFB 6p21.33
HLA-C 6p21.33 / FOXP1 3p13HLA-C 6p21.33 / TCOF1 5q32

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(3;6)(p13;p21) HLA-C/FOXP1
t(5;6)(q32;p21) HLA-C/TCOF1
HLA-C/CFB (6p21)

External links

Nomenclature
HGNC (Hugo)HLA-C   4933
Cards
Entrez_Gene (NCBI)HLA-C  3107  major histocompatibility complex, class I, C
AliasesD6S204; HLA-JY3; HLAC; HLC-C; 
MHC; PSORS1
GeneCards (Weizmann)HLA-C
Ensembl hg19 (Hinxton)ENSG00000204525 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000204525 [Gene_View]  ENSG00000204525 [Sequence]  chr6:31268749-31272136 [Contig_View]  HLA-C [Vega]
ICGC DataPortalENSG00000204525
TCGA cBioPortalHLA-C
AceView (NCBI)HLA-C
Genatlas (Paris)HLA-C
WikiGenes3107
SOURCE (Princeton)HLA-C
Genetics Home Reference (NIH)HLA-C
Genomic and cartography
GoldenPath hg38 (UCSC)HLA-C  -     chr6:31268749-31272136 -  6p21.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HLA-C  -     6p21.33   [Description]    (hg19-Feb_2009)
EnsemblHLA-C - 6p21.33 [CytoView hg19]  HLA-C - 6p21.33 [CytoView hg38]
Mapping of homologs : NCBIHLA-C [Mapview hg19]  HLA-C [Mapview hg38]
OMIM142840   177900   609423   
Gene and transcription
Genbank (Entrez)AF168611 AF196489 AF405691 AJ005199 AJ010748
RefSeq transcript (Entrez)NM_001243042 NM_002117
RefSeq genomic (Entrez)NC_000006 NG_029422 NT_113891 NT_167245 NT_167246 NT_167247 NT_167248 NT_167249
Consensus coding sequences : CCDS (NCBI)HLA-C
Cluster EST : UnigeneHs.743218 [ NCBI ]
CGAP (NCI)Hs.743218
Alternative Splicing GalleryENSG00000204525
Gene ExpressionHLA-C [ NCBI-GEO ]   HLA-C [ EBI - ARRAY_EXPRESS ]   HLA-C [ SEEK ]   HLA-C [ MEM ]
Gene Expression Viewer (FireBrowse)HLA-C [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3107
GTEX Portal (Tissue expression)HLA-C
Human Protein AtlasENSG00000204525-HLA-C [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9TNN7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9TNN7  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9TNN7
Splice isoforms : SwissVarQ9TNN7
PhosPhoSitePlusQ9TNN7
Domaine pattern : Prosite (Expaxy)IG_LIKE (PS50835)    IG_MHC (PS00290)   
Domains : Interpro (EBI)Ig-like_dom    Ig-like_dom_sf    Ig-like_fold    Ig/MHC_CS    Ig_C1-set    MHC_I-like_Ag-recog    MHC_I-like_Ag-recog_sf    MHC_I/II-like_Ag-recog    MHC_I_a_a1/a2    MHC_I_a_C   
Domain families : Pfam (Sanger)C1-set (PF07654)    MHC_I (PF00129)    MHC_I_C (PF06623)   
Domain families : Pfam (NCBI)pfam07654    pfam00129    pfam06623   
Domain families : Smart (EMBL)IGc1 (SM00407)  
Conserved Domain (NCBI)HLA-C
DMDM Disease mutations3107
Blocks (Seattle)HLA-C
PDB (RSDB)5VGD   
PDB Europe5VGD   
PDB (PDBSum)5VGD   
PDB (IMB)5VGD   
Structural Biology KnowledgeBase5VGD   
SCOP (Structural Classification of Proteins)5VGD   
CATH (Classification of proteins structures)5VGD   
SuperfamilyQ9TNN7
Human Protein Atlas [tissue]ENSG00000204525-HLA-C [tissue]
Peptide AtlasQ9TNN7
HPRD00829
Protein Interaction databases
DIP (DOE-UCLA)Q9TNN7
IntAct (EBI)Q9TNN7
FunCoupENSG00000204525
BioGRIDHLA-C
STRING (EMBL)HLA-C
ZODIACHLA-C
Ontologies - Pathways
QuickGOQ9TNN7
Ontology : AmiGOGolgi membrane  positive regulation of T cell mediated cytotoxicity  antigen processing and presentation of peptide antigen via MHC class I  antigen processing and presentation of endogenous peptide antigen via MHC class Ib  antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent  antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent  antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent  signaling receptor binding  protein binding  extracellular space  endoplasmic reticulum  Golgi apparatus  plasma membrane  plasma membrane  immune response  external side of plasma membrane  cell surface  ER to Golgi transport vesicle membrane  phagocytic vesicle membrane  early endosome membrane  peptide antigen binding  peptide antigen binding  MHC class I protein complex  regulation of immune response  recycling endosome membrane  interferon-gamma-mediated signaling pathway  type I interferon signaling pathway  integral component of lumenal side of endoplasmic reticulum membrane  
Ontology : EGO-EBIGolgi membrane  positive regulation of T cell mediated cytotoxicity  antigen processing and presentation of peptide antigen via MHC class I  antigen processing and presentation of endogenous peptide antigen via MHC class Ib  antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent  antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent  antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent  signaling receptor binding  protein binding  extracellular space  endoplasmic reticulum  Golgi apparatus  plasma membrane  plasma membrane  immune response  external side of plasma membrane  cell surface  ER to Golgi transport vesicle membrane  phagocytic vesicle membrane  early endosome membrane  peptide antigen binding  peptide antigen binding  MHC class I protein complex  regulation of immune response  recycling endosome membrane  interferon-gamma-mediated signaling pathway  type I interferon signaling pathway  integral component of lumenal side of endoplasmic reticulum membrane  
Pathways : KEGGEndocytosis    Phagosome    Cell adhesion molecules (CAMs)    Antigen processing and presentation    Natural killer cell mediated cytotoxicity    Type I diabetes mellitus    HTLV-I infection    Herpes simplex infection    Epstein-Barr virus infection    Viral carcinogenesis    Autoimmune thyroid disease    Allograft rejection    Graft-versus-host disease    Viral myocarditis   
NDEx NetworkHLA-C
Atlas of Cancer Signalling NetworkHLA-C
Wikipedia pathwaysHLA-C
Orthology - Evolution
OrthoDB3107
GeneTree (enSembl)ENSG00000204525
Phylogenetic Trees/Animal Genes : TreeFamHLA-C
HOGENOMQ9TNN7
Homologs : HomoloGeneHLA-C
Homology/Alignments : Family Browser (UCSC)HLA-C
Gene fusions - Rearrangements
Fusion : MitelmanHLA-C/CFB [6p21.33/6p21.33]  
Fusion : MitelmanHLA-C/FOXP1 [6p21.33/3p13]  [t(3;6)(p13;p21)]  
Fusion : MitelmanHLA-C/TCOF1 [6p21.33/5q32]  [t(5;6)(q32;p21)]  
Fusion PortalHLA-C 6p21.33 CFB 6p21.33 BRCA
Fusion PortalHLA-C 6p21.33 FOXP1 3p13 LUAD
Fusion PortalHLA-C 6p21.33 TCOF1 5q32 HNSC
Fusion Cancer (Beijing)AES [19p13.3]  -  HLA-C [6p21.33]  [FUSC002476]
Fusion Cancer (Beijing)BTNL3 [5q35.3]  -  HLA-C [6p21.33]  [FUSC002563]
Fusion Cancer (Beijing)DAPL1 [2q24.1]  -  HLA-C [6p21.33]  [FUSC002140]  [FUSC002140]
Fusion Cancer (Beijing)HLA-A [6p22.1]  -  HLA-C [6p21.33]  [FUSC002269]  [FUSC002269]  [FUSC002269]  [FUSC002269]  [FUSC002269]  [FUSC002269]  [FUSC002269]  [FUSC002269]  [FUSC002269]  [FUSC002269]
Fusion Cancer (Beijing)HLA-C [6p21.33]  -  ANP32A [15q23]  [FUSC000443]
Fusion Cancer (Beijing)HLA-C [6p21.33]  -  HEPH [Xq12]  [FUSC002572]
Fusion Cancer (Beijing)HLA-C [6p21.33]  -  ZMIZ2 [7p13]  [FUSC002541]
Fusion Cancer (Beijing)HLA-G [6p22.1]  -  HLA-C [6p21.33]  [FUSC003076]
Fusion Cancer (Beijing)HLA-H [6p22.1]  -  HLA-C [6p21.33]  [FUSC002068]  [FUSC002068]  [FUSC002068]  [FUSC002068]  [FUSC002068]  [FUSC002068]  [FUSC002068]  [FUSC002068]
Fusion Cancer (Beijing)HLA-J [6p22.1]  -  HLA-C [6p21.33]  [FUSC003231]  [FUSC003231]  [FUSC003231]
Fusion Cancer (Beijing)HLA-L [6p22.1]  -  HLA-C [6p21.33]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]  [FUSC000654]
Fusion Cancer (Beijing)LIF [22q12.2]  -  HLA-C [6p21.33]  [FUSC003321]
Fusion Cancer (Beijing)NUMA1 [11q13.4]  -  HLA-C [6p21.33]  [FUSC002465]
Fusion Cancer (Beijing)S100A11 [1q21.3]  -  HLA-C [6p21.33]  [FUSC003218]
Fusion Cancer (Beijing)STX4 [16p11.2]  -  HLA-C [6p21.33]  [FUSC002276]
Fusion : QuiverHLA-C
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHLA-C [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HLA-C
dbVarHLA-C
ClinVarHLA-C
1000_GenomesHLA-C 
Exome Variant ServerHLA-C
ExAC (Exome Aggregation Consortium)ENSG00000204525
GNOMAD BrowserENSG00000204525
Varsome BrowserHLA-C
Genetic variants : HAPMAP3107
Genomic Variants (DGV)HLA-C [DGVbeta]
DECIPHERHLA-C [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHLA-C 
Mutations
ICGC Data PortalHLA-C 
TCGA Data PortalHLA-C 
Broad Tumor PortalHLA-C
OASIS PortalHLA-C [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHLA-C  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHLA-C
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 HLA-C
DgiDB (Drug Gene Interaction Database)HLA-C
DoCM (Curated mutations)HLA-C (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HLA-C (select a term)
intoGenHLA-C
Cancer3DHLA-C(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM142840    177900    609423   
Orphanet14433   
DisGeNETHLA-C
MedgenHLA-C
Genetic Testing Registry HLA-C
NextProtQ9TNN7 [Medical]
TSGene3107
GENETestsHLA-C
Target ValidationHLA-C
Huge Navigator HLA-C [HugePedia]
snp3D : Map Gene to Disease3107
BioCentury BCIQHLA-C
ClinGenHLA-C
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3107
Chemical/Pharm GKB GenePA35057
Clinical trialHLA-C
Miscellaneous
canSAR (ICR)HLA-C (select the gene name)
DataMed IndexHLA-C
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHLA-C
EVEXHLA-C
GoPubMedHLA-C
iHOPHLA-C
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Jan 17 18:16:15 CET 2019
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