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PRF1 perforin 1 [ Homo sapiens (human) ]

Gene ID: 5551, updated on 11-Apr-2024

Summary

Official Symbol
PRF1provided by HGNC
Official Full Name
perforin 1provided by HGNC
Primary source
HGNC:HGNC:9360
See related
Ensembl:ENSG00000180644 MIM:170280; AllianceGenome:HGNC:9360
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
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Genomic context

See PRF1 in Genome Data Viewer
Location:
10q22.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (70597348..70602741, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (71467050..71472469, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (72357104..72362497, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72194899-72195400 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72197102-72197282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72199683-72200292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72200293-72200900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72200901-72201510 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72202121-72202730 Neighboring gene Sharpr-MPRA regulatory region 10829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72210316-72210984 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:72214954-72215480 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72215481-72216006 Neighboring gene nodal growth differentiation factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72232724-72233490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72239853-72240495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72240496-72241137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72242631-72243178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2450 Neighboring gene phosphatase domain containing paladin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72253375-72254035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72258695-72259456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72259457-72260216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72273197-72273732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72273733-72274267 Neighboring gene Sharpr-MPRA regulatory region 14353 Neighboring gene YY1 transcription factor pseudogene 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:72288493-72289410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72297349-72298033 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72298034-72298719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72301641-72302141 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72318935-72319878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72319879-72320822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72344798-72345298 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72345790-72345956 Neighboring gene Sharpr-MPRA regulatory region 12376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72356137-72356637 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:72385043-72385632 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72391517-72392148 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72396829-72397014 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17237 Neighboring gene Sharpr-MPRA regulatory region 11165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3511 Neighboring gene CRISPRi-validated cis-regulatory element chr10.2252 Neighboring gene Sharpr-MPRA regulatory region 4371 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72442365-72443210 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:72447939-72448583 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72453261-72453762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72453763-72454262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72461609-72462110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72462111-72462610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72465820-72466320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72497279-72497778 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17283 Neighboring gene Sharpr-MPRA regulatory region 12298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72502823-72503626 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72516391-72517350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72521542-72522311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72536007-72536834 Neighboring gene thymus, brain and testes associated

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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Aplastic anemia
MedGen: C0002874 OMIM: 609135 GeneReviews: Not available
not available
Familial hemophagocytic lymphohistiocytosis 2
MedGen: C1863727 OMIM: 603553 GeneReviews: Not available
Compare labs
Lymphoma, non-Hodgkin, familial
MedGen: C4721532 OMIM: 605027 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Common body mass index-associated variants confer risk of extreme obesity.
EBI GWAS 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 PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC65093

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables pore-forming activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables wide pore channel activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables wide pore channel activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in T cell mediated cytotoxicity IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in T cell mediated cytotoxicity ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in apoptotic process TAS
Traceable Author Statement
more info
PubMed 
involved_in cellular defense response TAS
Traceable Author Statement
more info
PubMed 
involved_in defense response to tumor cell ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in defense response to virus IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in defense response to virus ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in granzyme-mediated programmed cell death signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in immune response to tumor cell ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in immunological synapse formation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in immunological synapse formation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in killing of cells of another organism IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of killing of cells of another organism IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein homooligomerization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein import IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in protein transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in cytolytic granule IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytolytic granule ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cytolytic granule lumen TAS
Traceable Author Statement
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in endosome lumen IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
is_active_in immunological synapse ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in membrane HDA PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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
    B2R6X4, P14222, Q59F57, Q86WX7
    UniProtKB/TrEMBL
    E6Y8C6
    Related
    ENSP00000398568.1, ENST00000441259.2
    Conserved Domains (2) summary
    cd04032
    Location:388514
    C2_Perforin; C2 domain of Perforin
    smart00457
    Location:167369
    MACPF; membrane-attack complex / perforin
  2. NM_005041.6NP_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, X13224
    Consensus CDS
    CCDS7305.1
    UniProtKB/Swiss-Prot
    B2R6X4, P14222, Q59F57, Q86WX7
    UniProtKB/TrEMBL
    E6Y8C6
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    70597348..70602741 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    71467050..71472469 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)