rs147035858

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong

The NM_001083116.3(PRF1):c.50delT(p.Leu17ArgfsTer34) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,609,230 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★).

Frequency

Genomes: 𝑓 0.00088 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000089 ( 0 hom. )

Consequence

PRF1
NM_001083116.3 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:16O:1

Conservation

PhyloP100: -2.80

Variant links:

Genes affected

PRF1 (HGNC:9360): (perforin 1) 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]

PRF1 links:

PALD1 (HGNC:23530): (phosphatase domain containing paladin 1) Predicted to enable protein tyrosine phosphatase activity. Predicted to be involved in peptidyl-tyrosine dephosphorylation. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

PALD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PVS1

Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 11 pathogenic variants in the truncated region.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 10-70600852-CA-C is Pathogenic according to our data. Variant chr10-70600852-CA-C is described in ClinVar as [Pathogenic]. Clinvar id is 468305.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-70600852-CA-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRF1	NM_001083116.3 link	c.50delT	p.Leu17ArgfsTer34	frameshift_variant	Exon 2 of 3	ENST00000441259.2	NP_001076585.1	P14222
PRF1	NM_005041.6 link	c.50delT	p.Leu17ArgfsTer34	frameshift_variant	Exon 2 of 3		NP_005032.2	P14222

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRF1	ENST00000441259.2 link	c.50delT	p.Leu17ArgfsTer34	frameshift_variant	Exon 2 of 3	5	NM_001083116.3	ENSP00000398568.1		P14222

Frequencies

GnomAD3 genomes

AF:

0.000881

AC:

134

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00314

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000237

AC:

AN:

231966

Hom.:

AF XY:

0.000158

AC XY:

AN XY:

126318

show subpopulations

Gnomad AFR exome

AF:

0.00324

Gnomad AMR exome

AF:

0.000212

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000975

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000892

AC:

130

AN:

1456928

Hom.:

Cov.:

AF XY:

0.0000745

AC XY:

AN XY:

724418

show subpopulations

Gnomad4 AFR exome

AF:

0.00326

Gnomad4 AMR exome

AF:

0.000228

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000117

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.000133

GnomAD4 genome

AF:

0.000880

AC:

134

AN:

152302

Hom.:

Cov.:

AF XY:

0.000819

AC XY:

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00313

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000454

Hom.:

Bravo

AF:

0.00107

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:16Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Familial hemophagocytic lymphohistiocytosis 2

Pathogenic:6Other:1

Dec 03, 1999

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This frameshifting variant in exon 2 of 3 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. Loss-of-function variation in PRF1 is an established mechanism of disease (PMID:17873118). This variant has been previously reported as a homozygous and compound heterozygous change in individuals with familial hemophagocytic lymphohistiocytosis (PMID: 10583959, 22437823, 23255033, 29239076, 34083498). The c.50del (p.Leu17ArgfsTer34) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.03% (87/263362) and thus is presumed to be rare. Based on the available evidence, c.50del (p.Leu17ArgfsTer34) is classified as Pathogenic. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Leu17Argfs*34) in the PRF1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PRF1 are known to be pathogenic (PMID: 1156555, 16860143). This variant is present in population databases (rs147035858, gnomAD 0.3%). This premature translational stop signal has been observed in individual(s) with familial hemophagocytic lymphohistiocytosis (FHL) (PMID: 10583959, 14757862, 16860143, 17873118, 22437823, 23255033). It is commonly reported in individuals of African ancestry (PMID: 10583959, 14757862, 16860143, 17873118, 22437823, 23255033). ClinVar contains an entry for this variant (Variation ID: 468305). For these reasons, this variant has been classified as Pathogenic. -

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

High frequency in African American population [Lee et al 2006] -

Oct 03, 2018

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The PRF1 c.50delT (p.Leu17ArgfsTer34) variant results in a frameshift and is predicted to result in premature termination of the protein. The p.Leu17ArgfsTer34 variant has been described in four studies in which it is found in a homozygous state in 36 probands and in a compound heterozygous state in 11 probands (Stepp et al. 1999; Lee et al. 2006; Trizzino et al. 2008; Higa et al. 2013). The p.Leu17ArgfsTer34 variant was reported in seven of 58 control chromosomes and is reported at a reported frequency of 0.003926 in the African population of the Exome Aggregation Consortium. Individuals who were homozygous for the variant were found to have absent NK cytolytic activity, individuals who were compound heterozygotes for the variant were shown to have activity levels of between 1 - 5% of wild type. Perforin expression was severely reduced or undetectable (Stepp et al. 1999; Lee et al. 2006; Trizzino et al. 2008; Higa et al. 2013). Haplotype analysis showed that the p.Leu17ArgfsTer34 variant is inherited as part of a common haplotype, commonly seen in affected individuals of African descent associated with an earlier age of onset compared to other variants in the PRF1 gene (Lee et al. 2006). Based on the potential impact of truncating variants and collective evidence, the p.Leu17ArgfsTer34variant is classified as pathogenic for familial hemophagocytic lymphohistiocytosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Oct 01, 2021

New York Genome Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 30, 2017

Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

- -

not provided

Pathogenic:5

Jan 25, 2022

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 04, 2021

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 22, 2015

Clinical Genetics and Genomics, Karolinska University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 09, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 16860143, 10583959, 29239076, 17873118, 23255033, 22437823, 24916509, 30487145, 31395954, 29625052, 32542393, 34083498, 33570715, 14757862, 31589614) -

Jan 29, 2024

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2, PM3_very_strong, PS4, PVS1 -

Aplastic anemia

Pathogenic:1

Mar 24, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial hemophagocytic lymphohistiocytosis

Pathogenic:1

Jun 25, 2020

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: PRF1 c.50delT (p.Leu17ArgfsX34) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 0.00024 in 231966 control chromosomes and at a frequency of 0.0032 among individuals of African descent. c.50delT has been reported in the literature in multiple individuals affected with Familial Hemophagocytic Lymphohistiocytosis (example, Stepp_1999, Sanchez_2012, Higa_2013, Zhang_2014, Wojcik_2019). At-least one of these reports suggests a potential digenic mode of inheritance of FHL as a result of a synergistic function effect within genes involved in cytotoxic lymphocyte degranulation (Zhang_2014). It has also been reported as a well recognized cause of Familial Hemophagocytic Lymphohistiocytosis among individuals of African descent (Lee_2006). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

PRF1-related disorder

Pathogenic:1

Feb 22, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The PRF1 c.50delT variant is predicted to result in a frameshift and premature protein termination (p.Leu17Argfs*34). This variant has been reported to be causative for recessive familial hemophagocytic lymphohistiocytosis (FHL) in several studies (Stepp et al. 1999. PubMed ID: 10583959; Molleran Lee et al. 2004. PubMed ID: 14757862). This variant has been reported to be found at a high frequency among FHL patients of African descent (Lee et al. 2006. PubMed ID: 16860143), and is reported in 0.34% of alleles in individuals of African descent in gnomAD. Frameshift variants in PRF1 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Aplastic anemia;C1863727:Familial hemophagocytic lymphohistiocytosis 2;C4721532:Lymphoma, non-Hodgkin, familial

Pathogenic:1

May 07, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autoinflammatory syndrome

Pathogenic:1

Apr 17, 2018

Genome Diagnostics Laboratory, The Hospital for Sick Children

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over