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PRF1 perforin 1 [ Homo sapiens (human) ]

Gene ID: 5551, updated on 6-Jan-2019

Summary

Official Symbol
PRF1provided by HGNC
Official Full Name
perforin 1provided by HGNC
Primary source
HGNC:HGNC:9360
See related
Ensembl:ENSG00000180644 MIM:170280
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
P1; PFP; HPLH2
Summary
This gene encodes a protein with structural similarities to complement component C9 that is important in immunity. This protein forms membrane pores that allow the release of granzymes and subsequent cytolysis of target cells. Whether pore formation occurs in the plasma membrane of target cells or in an endosomal membrane inside target cells is subject to debate. Mutations in this gene are associated with a variety of human disease including diabetes, multiple sclerosis, lymphomas, autoimmune lymphoproliferative syndrome (ALPS), aplastic anemia, and familial hemophagocytic lymphohistiocytosis type 2 (FHL2), a rare and lethal autosomal recessive disorder of early childhood. [provided by RefSeq, Aug 2017]
Expression
Biased expression in spleen (RPKM 24.2), bone marrow (RPKM 10.6) and 12 other tissues See more
Orthologs

Genomic context

See PRF1 in Genome Data Viewer
Location:
10q22.1
Exon count:
3
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (70597348..70602788, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (72357104..72362531, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10859 Neighboring gene nodal growth differentiation factor Neighboring gene phosphatase domain containing paladin 1 Neighboring gene YY1 transcription factor pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 11165 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 14 Neighboring gene Sharpr-MPRA regulatory region 12298

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Aplastic anemia
MedGen: C0002874 OMIM: 609135 GeneReviews: Not available
Compare labs
Hemophagocytic lymphohistiocytosis, familial, 2 Compare labs
Non-Hodgkin lymphoma
MedGen: C0024305 OMIM: 605027 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Common body mass index-associated variants confer risk of extreme obesity.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Stimulation of CD8+ T cells with HIV-1 Nef peptides upregulates perforin and TNF-alpha expression PubMed
Pr55(Gag) gag Stimulation of CD8+ T cells with HIV-1 Gag peptides upregulates perforin and TNF-alpha expression PubMed
Tat tat Upregulation of intracellular perforin accumulation by IL-7 in CD8 T-cells is inhibited by HIV-1 Tat PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Allograft Rejection, organism-specific biosystem (from WikiPathways)
    Allograft Rejection, organism-specific biosystemThis pathway illustrates molecular interactions involved in the fundamental adaptive immune response for allograft destruction. This pathway was adapted in large part from the KEGG pathway http://www...
  • Allograft rejection, organism-specific biosystem (from KEGG)
    Allograft rejection, organism-specific biosystemAllograft rejection is the consequence of the recipient's alloimmune response to nonself antigens expressed by donor tissues. After transplantation of organ allografts, there are two pathways of anti...
  • Allograft rejection, conserved biosystem (from KEGG)
    Allograft rejection, conserved biosystemAllograft rejection is the consequence of the recipient's alloimmune response to nonself antigens expressed by donor tissues. After transplantation of organ allografts, there are two pathways of anti...
  • Apoptosis, organism-specific biosystem (from KEGG)
    Apoptosis, organism-specific biosystemApoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled...
  • Apoptosis, organism-specific biosystem (from WikiPathways)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Apoptosis, conserved biosystem (from KEGG)
    Apoptosis, conserved biosystemApoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled...
  • Autoimmune thyroid disease, organism-specific biosystem (from KEGG)
    Autoimmune thyroid disease, organism-specific biosystemThe classification of autoimmune throid disease (AITD) includes Hashimoto's thyroiditis (HT) or chronic autoimmune thyroiditis and its variants, Graves' disease (GD) and autoimmune atrophic thyroidi...
  • Autoimmune thyroid disease, conserved biosystem (from KEGG)
    Autoimmune thyroid disease, conserved biosystemThe classification of autoimmune throid disease (AITD) includes Hashimoto's thyroiditis (HT) or chronic autoimmune thyroiditis and its variants, Graves' disease (GD) and autoimmune atrophic thyroidi...
  • Caspase cascade in apoptosis, organism-specific biosystem (from Pathway Interaction Database)
    Caspase cascade in apoptosis, organism-specific biosystem
    Caspase cascade in apoptosis
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Downstream signaling in naive CD8+ T cells, organism-specific biosystem (from Pathway Interaction Database)
    Downstream signaling in naive CD8+ T cells, organism-specific biosystem
    Downstream signaling in naive CD8+ T cells
  • Graft-versus-host disease, organism-specific biosystem (from KEGG)
    Graft-versus-host disease, organism-specific biosystemGraft-versus-host disease (GVHD) is a lethal complication of allogeneic hematopoietic stem cell transplantation (HSCT) where immunocompetent donor T cells attack the genetically disparate host cells....
  • Graft-versus-host disease, conserved biosystem (from KEGG)
    Graft-versus-host disease, conserved biosystemGraft-versus-host disease (GVHD) is a lethal complication of allogeneic hematopoietic stem cell transplantation (HSCT) where immunocompetent donor T cells attack the genetically disparate host cells....
  • IL12 signaling mediated by STAT4, organism-specific biosystem (from Pathway Interaction Database)
    IL12 signaling mediated by STAT4, organism-specific biosystem
    IL12 signaling mediated by STAT4
  • IL2 signaling events mediated by STAT5, organism-specific biosystem (from Pathway Interaction Database)
    IL2 signaling events mediated by STAT5, organism-specific biosystem
    IL2 signaling events mediated by STAT5
  • Nanomaterial induced apoptosis, organism-specific biosystem (from WikiPathways)
    Nanomaterial induced apoptosis, organism-specific biosystemApotosis caused by nanomaterials, such as single-walled carbon nanohorns, titanium oxide, and polystyrene nanoparticles, may be induced through lysosomal impairment. For example, PAMAMs have been fou...
  • Natural killer cell mediated cytotoxicity, organism-specific biosystem (from KEGG)
    Natural killer cell mediated cytotoxicity, organism-specific biosystemNatural killer (NK) cells are lymphocytes of the innate immune system that are involved in early defenses against both allogeneic (nonself) cells and autologous cells undergoing various forms of stre...
  • Natural killer cell mediated cytotoxicity, conserved biosystem (from KEGG)
    Natural killer cell mediated cytotoxicity, conserved biosystemNatural killer (NK) cells are lymphocytes of the innate immune system that are involved in early defenses against both allogeneic (nonself) cells and autologous cells undergoing various forms of stre...
  • TCR signaling in naive CD8+ T cells, organism-specific biosystem (from Pathway Interaction Database)
    TCR signaling in naive CD8+ T cells, organism-specific biosystem
    TCR signaling in naive CD8+ T cells
  • Type I diabetes mellitus, organism-specific biosystem (from KEGG)
    Type I diabetes mellitus, organism-specific biosystemType I diabetes mellitus is a disease that results from autoimmune destruction of the insulin-producing beta-cells. Certain beta-cell proteins act as autoantigens after being processed by antigen-pre...
  • Type I diabetes mellitus, conserved biosystem (from KEGG)
    Type I diabetes mellitus, conserved biosystemType I diabetes mellitus is a disease that results from autoimmune destruction of the insulin-producing beta-cells. Certain beta-cell proteins act as autoantigens after being processed by antigen-pre...
  • Viral myocarditis, organism-specific biosystem (from KEGG)
    Viral myocarditis, organism-specific biosystemMyocarditis is a cardiac disease associated with inflammation and injury of the myocardium. It results from various etiologies, both noninfectious and infectious, but coxsackievirus B3 (CVB3) is stil...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC65093

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
wide pore channel activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
T cell mediated cytotoxicity IEA
Inferred from Electronic Annotation
more info
 
apoptotic process TAS
Traceable Author Statement
more info
PubMed 
cellular defense response TAS
Traceable Author Statement
more info
PubMed 
cytolysis ISS
Inferred from Sequence or Structural Similarity
more info
 
defense response to tumor cell ISS
Inferred from Sequence or Structural Similarity
more info
 
defense response to virus ISS
Inferred from Sequence or Structural Similarity
more info
 
immune response to tumor cell ISS
Inferred from Sequence or Structural Similarity
more info
 
immunological synapse formation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of killing of cells of other organism IDA
Inferred from Direct Assay
more info
PubMed 
protein homooligomerization IDA
Inferred from Direct Assay
more info
PubMed 
transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytolytic granule IDA
Inferred from Direct Assay
more info
PubMed 
cytolytic granule ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
endosome lumen IEA
Inferred from Electronic Annotation
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
membrane HDA PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
perforin-1
Names
cytolysin
lymphocyte pore-forming protein
perforin 1 (pore forming protein)

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009615.1 RefSeqGene

    Range
    5001..10428
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_94

mRNA and Protein(s)

  1. NM_001083116.3NP_001076585.1  perforin-1 precursor

    See identical proteins and their annotated locations for NP_001076585.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC047695, BQ654088, DA941244, X13224
    Consensus CDS
    CCDS7305.1
    UniProtKB/Swiss-Prot
    P14222
    Related
    ENSP00000398568.1, ENST00000441259.1
    Conserved Domains (2) summary
    cd04032
    Location:388514
    C2_Perforin; C2 domain of Perforin
    smart00457
    Location:167369
    MACPF; membrane-attack complex / perforin
  2. NM_005041.5NP_005032.2  perforin-1 precursor

    See identical proteins and their annotated locations for NP_005032.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC047695, BQ654088, DA816891, HY075867, X13224
    Consensus CDS
    CCDS7305.1
    UniProtKB/Swiss-Prot
    P14222
    Related
    ENSP00000362305.1, ENST00000373209.2
    Conserved Domains (2) summary
    cd04032
    Location:388514
    C2_Perforin; C2 domain of Perforin
    smart00457
    Location:167369
    MACPF; membrane-attack complex / perforin

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    70597348..70602788 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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