HLA-C
major histocompatibility complex, class I, C | D6S204, HLA-JY3, PSORS1

HLA-C belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domain, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. About 6000 HLA-C alleles have been described. The HLA system plays an important role in the occurrence and outcome of infectious diseases, including those caused by the malaria parasite, the human immunodeficiency virus (HIV), and the severe acute respiratory syndrome coronavirus (SARS-CoV). The structural spike and the nucleocapsid proteins of the novel coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19), are reported to contain multiple Class I epitopes with predicted HLA restrictions. Individual HLA genetic variation may help explain different immune responses to a virus across a population.[provided by RefSeq, Aug 2020]

Member of: DE-7 DE-7.5
Biological processes 46 terms
ER to Golgi transport vesicle membrane (GO:0012507)ER to Golgi transport vesicle membrane (GO:0012507)Golgi apparatus (GO:0005794)Golgi membrane (GO:0000139)Golgi membrane (GO:0000139)MHC class I protein complex (GO:0042612)TAP binding (GO:0046977)antigen processing and presentation (GO:0019882)antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent (GO:0002486)antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent (GO:0002486)antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)antigen processing and presentation of exogenous peptide antigen via MHC class Ib (GO:0002477)beta-2-microglobulin binding (GO:0030881)cell surface (GO:0009986)cell surface (GO:0009986)early endosome membrane (GO:0031901)early endosome membrane (GO:0031901)endoplasmic reticulum (GO:0005783)endoplasmic reticulum membrane (GO:0005789)external side of plasma membrane (GO:0009897)extracellular exosome (GO:0070062)extracellular region (GO:0005576)extracellular region (GO:0005576)immune response (GO:0006955)immune response (GO:0006955)immune response (GO:0006955)lumenal side of endoplasmic reticulum membrane (GO:0098553)lumenal side of endoplasmic reticulum membrane (GO:0098553)membrane (GO:0016020)peptide antigen binding (GO:0042605)peptide antigen binding (GO:0042605)phagocytic vesicle membrane (GO:0030670)phagocytic vesicle membrane (GO:0030670)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)positive regulation of T cell mediated cytotoxicity (GO:0001916)positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)protein binding (GO:0005515)receptor ligand activity (GO:0048018)recycling endosome membrane (GO:0055038)recycling endosome membrane (GO:0055038)regulation of natural killer cell mediated immunity (GO:0002715)secretory granule membrane (GO:0030667)signal transduction (GO:0007165)signaling receptor binding (GO:0005102)
Expression (TPM)
HLA-C — as a Regulated Gene

TFs regulating HLA-C 0 TFs

Transcription factors with Perturb-seq knockdown data for HLA-C. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = HLA-C upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to HLA-C

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HLA-C, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr6:31,157,467–31,159,255 113.8 kb Distal (>10kb) Multiome 740
chr6:31,171,796–31,173,419 100.1 kb Distal (>10kb) Multiome 178
chr6:31,272,062–31,272,280 at TSS At TSS 286
chr6:31,307,823–31,308,922 36.1 kb Distal (>10kb) Multiome 248
chr6:31,366,884–31,367,398 95.0 kb Distal (>10kb) Multiome 433
chr6:31,399,631–31,400,231 127.7 kb Distal (>10kb) Multiome 678
chr6:31,403,046–31,404,269 131.4 kb Distal (>10kb) Multiome 796
chr6:31,441,682–31,442,105 169.7 kb Distal (>10kb) Multiome 316
chr6:31,462,703–31,463,323 190.9 kb Distal (>10kb) Multiome 352
chr6:31,497,638–31,498,615 225.9 kb Distal (>10kb) Multiome 613
chr6:31,541,205–31,542,816 270.0 kb Distal (>10kb) Multiome 1073
chr6:31,546,485–31,547,136 274.6 kb Distal (>10kb) Multiome 589
chr6:31,547,301–31,547,742 275.5 kb Distal (>10kb) Multiome 762

Genome Browser

Genomic view of the HLA-C locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr6:31,147,467 – 31,557,742
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq