PRF1 perforin 1 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 10q22.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (70597348..70602741, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (71467050..71472469, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (72357104..72362497, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Familial hemophagocytic phohistiocytosis induced by PRF1 mutation with neurologic manifestations as the initial clinical presentations: A case report.
Title: Familial hemophagocytic phohistiocytosis induced by PRF1 mutation with neurologic manifestations as the initial clinical presentations: A case report.
Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer's disease.
Title: Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer's disease.
Baseline red blood cell distribution width and perforin, dynamic levels of interleukin 6 and lactate are predictors of mortality in patients with sepsis.
Title: Baseline red blood cell distribution width and perforin, dynamic levels of interleukin 6 and lactate are predictors of mortality in patients with sepsis.
[Gene Polymorphisms of Patients with Lymphoma-Associated Hemophagocytic Syndrome in Longyan area, Fujian Province].
Title: [Gene Polymorphisms of Patients with Lymphoma-Associated Hemophagocytic Syndrome in Longyan area, Fujian Province].
Human intestinal and circulating invariant natural killer T cells are cytotoxic against colorectal cancer cells via the perforin-granzyme pathway.
Title: Human intestinal and circulating invariant natural killer T cells are cytotoxic against colorectal cancer cells via the perforin-granzyme pathway.
Spectrum mutations of PRF1, UNC13D, STX11, and STXBP2 genes in Vietnamese patients with hemophagocytic lymphohistiocytosis.
Title: Spectrum mutations of PRF1, UNC13D, STX11, and STXBP2 genes in Vietnamese patients with hemophagocytic lymphohistiocytosis.
Immunohistochemical study of perforin and apoptosis stimulation fragment ligand (FasL)in active vitiligo.
Title: Immunohistochemical study of perforin and apoptosis stimulation fragment ligand (FasL)in active vitiligo.
Granzyme B and perforin produced by SEC2 mutant-activated human CD4(+) T cells and CD8(+) T cells induce apoptosis of K562 leukemic cells by the mitochondrial apoptotic pathway.
Title: Granzyme B and perforin produced by SEC2 mutant-activated human CD4(+) T cells and CD8(+) T cells induce apoptosis of K562 leukemic cells by the mitochondrial apoptotic pathway.
PRF1 mutation alters immune system activation, inflammation, and risk of autoimmunity.
Title: PRF1 mutation alters immune system activation, inflammation, and risk of autoimmunity.
Associations between PRF1 Ala91Val polymorphism and risk of hemophagocytic lymphohistiocytosis: a meta-analysis based on 1366 subjects.
Title: Associations between PRF1 Ala91Val polymorphism and risk of hemophagocytic lymphohistiocytosis: a meta-analysis based on 1366 subjects.

Submit: New GeneRIF Correction See all GeneRIFs (173)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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	not available
Lymphoma, non-Hodgkin, familial MedGen: C4721532 OMIM: 605027 GeneReviews: Not available	not available

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-L40557 (e-PCR)
- UniSTS:18569

RH78918 (e-PCR)
- UniSTS:7131

G29802 (e-PCR)
- UniSTS:78816

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 more info	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

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Preferred Names: perforin-1

Names: cytolysin; lymphocyte pore-forming protein; perforin 1 (pore forming protein)

NCBI Reference Sequences (RefSeq)

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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

NG_009615.1 RefSeqGene

Range

5001..10428

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_94

mRNA and Protein(s)

NM_001083116.3 → NP_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:388 → 514

C2_Perforin; C2 domain of Perforin

smart00457
Location:167 → 369

MACPF; membrane-attack complex / perforin
NM_005041.6 → NP_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:388 → 514

C2_Perforin; C2 domain of Perforin

smart00457
Location:167 → 369

MACPF; membrane-attack complex / perforin