HCP5

Summary

HCP5 (HLA complex P5, HGNC:21659) is a long non-coding RNA gene on chromosome 6p21.33.

At a glance

• Gene type: non-coding (lncRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21659
Approved symbol	HCP5
Name	HLA complex P5
Location	6p21.33
Locus type	RNA, long non-coding
Status	Approved
Aliases	D6S2650E, P5-1
Ensembl gene	ENSG00000206337
Ensembl biotype	lncRNA
OMIM	604676
Entrez	10866
RNAcentral	URS000075AF59 — lncRNA, 2547 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 14 lncRNA

ENST00000414046, ENST00000460889, ENST00000467369, ENST00000541196, ENST00000666495, ENST00000670109, ENST00000674016, ENST00000718209, ENST00000718210, ENST00000718211, ENST00000718212, ENST00000718213, ENST00000718214, ENST00000718215

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000414046 — 2 exons

Exon	Start	End
ENSE00001826870	31463371	31472408
ENSE00004034430	31463170	31463279

Expression profiles

Bgee: expression breadth ubiquitous, 230 present calls, max score 96.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.7206 / max 638.6518, expressed in 972 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66884	12.7206	972

Top tissues by expression

272 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	96.07	gold quality
spleen	UBERON:0002106	93.33	gold quality
lymph node	UBERON:0000029	92.19	gold quality
rectum	UBERON:0001052	92.11	gold quality
mucosa of transverse colon	UBERON:0004991	91.65	gold quality
blood	UBERON:0000178	91.53	gold quality
cervix squamous epithelium	UBERON:0006922	90.47	gold quality
leukocyte	CL:0000738	89.72	gold quality
vermiform appendix	UBERON:0001154	89.35	gold quality
monocyte	CL:0000576	89.12	gold quality
mononuclear cell	CL:0000842	89.03	gold quality
gall bladder	UBERON:0002110	88.71	gold quality
skin of abdomen	UBERON:0001416	88.33	gold quality
skin of leg	UBERON:0001511	88.08	gold quality
tonsil	UBERON:0002372	87.23	gold quality
apex of heart	UBERON:0002098	87.11	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.01	gold quality
type B pancreatic cell	CL:0000169	86.40	gold quality
small intestine Peyer’s patch	UBERON:0003454	86.04	gold quality
olfactory bulb	UBERON:0002264	86.00	gold quality
caecum	UBERON:0001153	85.75	gold quality
zone of skin	UBERON:0000014	85.59	gold quality
transverse colon	UBERON:0001157	85.00	gold quality
upper lobe of left lung	UBERON:0008952	85.00	gold quality
right adrenal gland	UBERON:0001233	84.95	gold quality
pancreatic ductal cell	CL:0002079	84.81	silver quality
left adrenal gland	UBERON:0001234	84.77	gold quality
smooth muscle tissue	UBERON:0001135	84.59	gold quality
small intestine	UBERON:0002108	84.54	gold quality
bone marrow cell	CL:0002092	84.45	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.78

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 40)

• HCP5 single nucleotide polymorphism genotyping can serve as a simple screening tool for prediction of hypersensitivity reactions to abacavir. (PMID:18684101)
• Data demonstrate that the influence of ZNRD1 alleles on disease progression rates are attributable to HLA-A10, help clarify the relationship between the HCP5, HLA-C and HLA-B*57 alleles, and reaffirm a critical role of HLA-B*57 alleles in HIV disease. (PMID:18982067)
• No significant HIV-1 restriction was observed in the cells throughout HIV-1 life cycle, suggesting that the association of HCP5 variant with viral control is likely due to HLA-B*5701-related effect or other functional variants in the haplotype or both (PMID:19935381)
• HLA-B44 allele is prevalent in Polish patients with chronic spontaneous urticaria (PMID:20559009)
• Haplotype analysis revealed that HLA-B*5701 and the HCP5 rs2395029(G) allele are in complete LD (r(2) = 1) in this Mexican Mestizos sample. (PMID:21510768)
• assessed whether increases in viral load set points are associated with genetic markers in CCR5, HCP5, and HLA-C genes (PMID:21860345)
• confirms the MICA/HCP5 region as a susceptibility locus for HCV-related hepatocellular carcinoma and identifies rs2244546 in HCP5 as a novel tagging SNP (PMID:23665287)
• We confirmed the association of HCP5 with the Stevens Johnsons Syndrome/Toxic Epidermal Necrolysis susceptibility in a population from Mozambique treated with nevirapine (PMID:24322967)
• The aim of this study was to investigate whether the HCP5, TNIP1, TNFAIP3, SPATA2 and COG6 genes were genetic risk factors for psoriasis in Chinese population. (PMID:25264125)
• Genome-wide association analyses in 22,981 participants (2280 shingles cases) from the electronic Medical Records and Genomics Network identified a genomic region in the combined and European ancestry groups that has an age of onset effect reaching genome-wide significance region tags the non-coding gene HCP5 (HLA Complex P5). (PMID:25297839)
• Evidence of a higher risk to develop pericarditis with STAT4 genotypes, and an association between HCP5 rs3099844 and anti-Ro/SSA antibodies in Italian systemic lupus erythematosus patients. (PMID:25369137)
• The minor alleles of rs2395029, rs9264942, and rs3689068 in the HCP5 and HLA-C, and ZNRD1 genes associate with lower viral loads (VL) among antiretroviral-naive individuals and with shorter time to first VL less 51 copies/ml during anti-HIV therapy. (PMID:27083073)
• Six single-nucleotide polymorphisms (SNPs) in three loci were associated significantly with Kawasaki disease (KD) susceptibility, including the previously reported BLK locus. The other two loci were newly identified: NMNAT2 on chromosome 1q25.3 and the human leukocyte antigen (HLA) region on chromosome 6p21.3 (HLA-C, HLA-B, MICA and HCP5). (PMID:28855716)
• This study showed that polymorphisms in MICA, but not in DEPDC5, HCP5 or PNPLA3, are associated with with chronic hepatitis C-related hepatocellular carcinoma development in Japanese patients with chronic hepatitis C virus infection. (PMID:28928439)
• The results of this study confirms the minor allele HCP5 is positively associated with allopurinol-induced drug hypersensitivity. (PMID:29193002)
• we confirmed that SP1-induced upregulation of long non-coding RNA HCP5 promotes the development of osteosarcoma. (PMID:30554864)
• We confirmed the association of Sjogren’s syndrome with the STAT4 and IL10 genes and we describe a novel association with HCP5. (PMID:30882006)
• HCP5 promotes colon cancer development by activating AP1G1 via PI3K/AKT pathway. (PMID:31002129)
• HCP5 is a SMAD3-responsive long non-coding RNA that promotes lung adenocarcinoma metastasis via miR-203/SNAI axis. (PMID:31131047)
• HCP5 is a unique human-specific gene within the MHC class I genomic region that encodes a hybrid HLA class I endogenous retroviral lncRNA with peptide coding potential. (PMID:31137555)
• Results observed that long noncoding RNA HCP5 was upregulated in triple-negative breast cancer (TNBC) cell lines and specimens. HCP5 promotes TNBC progression as a competing endogenous RNA to regulate BIRC3 by sponging miR-219a. (PMID:31215169)
• High HCP5 expression is associated with childhood obesity. (PMID:31622249)
• HCP5 was found to be highly expressed in prostate cancer. Mechanistically, HCP5 was found to promote the proliferation of prostate cancer cells via sponging miR4656 to upregulate the expression of CEMIP. These results provide novel insight into clarifying the critical function of HCP5 in regulating the progression of prostate cancer. (PMID:31746434)
• LncRNA HCP5 promotes LAML progression via PSMB8-mediated PI3K/AKT pathway activation. (PMID:31836918)
• LncRNA HCP5 promotes cell proliferation and inhibits apoptosis via miR-27a-3p/IGF-1 axis in human granulosa-like tumor cell line KGN. (PMID:31891769)
• Decreased expression of HCP5 in biochemical premature ovarian insufficiency (bPOI) contributed to dysfunctional granulosa cells by regulating MSH5 transcription and DNA damage repair via the interaction with YB1, providing a novel epigenetic mechanism for POI pathogenesis. (PMID:32112110)
• Gene expression of indoleamine and tryptophan dioxygenases and three long non-coding RNAs in breast cancer. (PMID:32165090)
• Long non-coding RNA HCP5 promotes proliferation and metastasis of clear cell renal cell carcinoma via targeting miR-140-5p/IGF1R pathway. (PMID:32271414)
• MSC-induced lncRNA HCP5 drove fatty acid oxidation through miR-3619-5p/AMPK/PGC1alpha/CEBPB axis to promote stemness and chemo-resistance of gastric cancer. (PMID:32300102)
• The Effect of Long Non-Coding RNA (lncRNA) HCP5 on Regulating Epithelial-Mesenchymal Transition (EMT)-Related Markers in Gastric Carcinoma Is Partially Reversed by miR-27b-3p. (PMID:32357145)
• LncRNA HCP5 Regulates Pancreatic Cancer Progression by miR-140-5p/CDK8 Axis. (PMID:32407143)
• An Intronic HCP5 Variant Is Associated With Age of Onset and Susceptibility to Graves Disease in UK and Polish Cohorts. (PMID:32501499)
• Knockdown of lncRNA HCP5 protects against cerebral ischemia/reperfusion injury by regulating miR-652-3p. (PMID:32657103)
• HCP5 rs2395029 is a rapid and inexpensive alternative to HLA-B*57:01 genotyping to predict abacavir hypersensitivity reaction in Spain. (PMID:33044391)
• Long non-coding RNA HCP5 in cancer. (PMID:33245911)
• Silencing of long non-coding RNA HCP5 inhibits proliferation, invasion, migration, and promotes apoptosis via regulation of miR-299-3p/SMAD5 axis in gastric cancer cells. (PMID:33371778)
• T Cell Factor 4 Is Involved in Papillary Thyroid Carcinoma via Regulating Long Non-Coding RNA HCP5. (PMID:33371788)
• Down-regulation of HCP5 inhibits cell proliferation, migration, and invasion through regulating EPHA7 by competitively binding miR-101 in osteosarcoma. (PMID:33439936)
• MEF2A-mediated lncRNA HCP5 Inhibits Gastric Cancer Progression via MiR-106b-5p/p21 Axis. (PMID:33613117)
• Knockdown of long noncoding RNA HCP5 suppresses the malignant behavior of retinoblastoma by sponging miR36195p to target HDAC9. (PMID:33693951)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.