rs28933973

Positions:

chr10-70599048-G-A

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong

The NM_001083116.3(PRF1):c.673C>T(p.Arg225Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

PRF1
NM_001083116.3 missense

Scores

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:11

Conservation

PhyloP100: 0.273

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:

PALD1 (HGNC:):

PALD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP3

MetaRNN computational evidence supports a deleterious effect, 0.994

PP5

Variant 10-70599048-G-A is Pathogenic according to our data. Variant chr10-70599048-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 13711.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-70599048-G-A is described in Lovd as [Likely_pathogenic]. Variant chr10-70599048-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRF1	NM_001083116.3 linkuse as main transcript	c.673C>T	p.Arg225Trp	missense_variant	3/3	ENST00000441259.2	NP_001076585.1	P14222
PRF1	NM_005041.6 linkuse as main transcript	c.673C>T	p.Arg225Trp	missense_variant	3/3		NP_005032.2	P14222

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRF1	ENST00000441259.2 linkuse as main transcript	c.673C>T	p.Arg225Trp	missense_variant	3/3	5	NM_001083116.3	ENSP00000398568.1		P14222

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000120

AC:

AN:

249622

Hom.:

AF XY:

0.0000222

AC XY:

AN XY:

134962

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000178

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000479

AC:

AN:

1461136

Hom.:

Cov.:

AF XY:

0.00000413

AC XY:

AN XY:

726754

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000450

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000459

Hom.:

ExAC

AF:

0.0000247

AC:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.0000593

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Familial hemophagocytic lymphohistiocytosis 2

Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 24, 2023	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 225 of the PRF1 protein (p.Arg225Trp). This variant is present in population databases (rs28933973, gnomAD 0.006%). This missense change has been observed in individuals with familial hemophagocytic lymphohistiocytosis (PMID: 10583959, 11565555, 14757862, 27271812). ClinVar contains an entry for this variant (Variation ID: 13711). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PRF1 protein function. Experimental studies have shown that this missense change affects PRF1 function (PMID: 15365097). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	a substitution of Tryptophan for Arginine in codon 225. This variant’s frequency is reported as A=0.00002 (3/120924, ExAC) and A=0.00001 (3/244444, GnomAD). It is reported in ClinVar as pathogenic and not reported in LOVD. Homozygous or compound heterozygous pathogenic mutations in the PRF1 gene are known to cause Hemophagocytic lymphohistiocytosis (HLH, OMIM 603553). Heterozygous germline pathogenic mutations in the PRF1 gene maybe associated with increased risk of non-Hodgkin Lymphoma (OMIM 605027), Wiernik et al. (2000) and Altieri et al. (2005). -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The observed missense variant c.673C>Tp.Arg225Trp in PRF1 gene has been reported in homozygous/compound heterozygous state in individuals with familial hemophagocytic lymphohistiocytosis Blincoe A, et al., 2020, Tesi B, et al., 2015. Experimental studies have shown that this missense change affects PRF1 function Voskoboinik I, et al., 2004. The p.Arg225Trp variant is reported with 0.002% allele frequency in gnomAD Exomes. The amino acid Arg at position 225 is changed to a Trp changing protein sequence and it might alter its composition and physico-chemical properties. This variant has been reported to the ClinVar database as Pathogenic multiple submissions. Multiple lines of computational evidence Polyphen-probably damaging, SIFT-damaging and Mutation Taster-disease causing predict a damaging effect on protein structure and function for this variant. The reference amino acid p.Arg225Trp in PRF1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 01, 2013	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Sep 01, 2022	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). Missense changes are a common disease-causing mechanism. Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000013711). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 23443029 , 26184781 , 26684649 , 27271812). Different missense changes at the same codon (p.Arg225Gln, p.Arg225Pro) have been reported to be associated with PRF1-related disorder (PMID: 17674359 , 29357941). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The PRF1 c.673C>T (p.Arg225Trp) missense variant has been described in at least eight studies in which it is found in a total of 16 patients with familial hemophagocytic lymphohistiocytosis including in 11 in a homozygous state, in three in a compound heterozygous state, and in two of unknown zygosity (Stepp et al. 1999; Clementi et al. 2001; Molleran et al. 2004; Trizzino et al. 2008; Chiapparini et al. 2011; Dias et al. 2013; Tesi et al. 2015; Madkaikar et al. 2016). The variant was also found in a heterozygous state in four unaffected related individuals. The p.Arg225Trp was absent from at least 100 control chromosomes but is reported at a frequency of 0.00035 in the European American population of the Exome Sequencing Project. Functional studies demonstrated that the variant results in decreased or absent perforin expression and reduced NK cell cytolytic activity (Stepp et al. 1999; Risma et al. 2004; Voskoboinik et al. 2004; Trizzino et al. 2008). Based on the evidence, the p.Arg225Trp variant 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. -

Aplastic anemia

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 11, 2024

- -

Inborn genetic diseases

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 18, 2021

The c.673C>T (p.R225W) alteration is located in exon 3 (coding exon 2) of the PRF1 gene. This alteration results from a C to T substitution at nucleotide position 673, causing the arginine (R) at amino acid position 225 to be replaced by a tryptophan (W). Based on data from the Genome Aggregation Database (gnomAD) database, the PRF1 c.673C>T alteration was observed in <0.01% (3/249622) of total alleles studied, with a frequency of 0.01% (1/18386) in the East Asian subpopulation. This alteration has been reported in the homozygous and compound heterozygous states in multiple unrelated patients with features of familial hemophagocytic lymphohistiocytosis (Stepp, 1999; Molleran Lee, 2004; Clementi, 2001; Trizzino, 2008; Dias, 2013; Tesi, 2015). This amino acid position is not well conserved in available vertebrate species. Cells from an affected patient showed nearly complete absence of perforin and greatly reduced cytolytic activity (Stepp, 1999; Feldmann, 2002). In addition, in vitro functional studies of the p.R225W alteration demonstrated abnormal protein function including loss of cytolytic activity, failure to traffic to rat basophil leukemia secretory granules, diminished perforin detection, and no apparent proteolytic maturation. In one study, immunohistochemistry analysis of transfected cells indicated mislocalization whereas another demonstrated punctate staining on immunohistochemistry similar to wildtype (Voskoboinik, 2004; Risma, 2006). The in silico prediction for the p.R225W alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -

Familial hemophagocytic lymphohistiocytosis

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Jul 13, 2022

Variant summary: PRF1 c.673C>T (p.Arg225Trp) results in a non-conservative amino acid change located in the membrane attack complex component/perforin (MACPF) domain (IPR020864) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 249622 control chromosomes (gnomAD). c.673C>T has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with Familial Hemophagocytic Lymphohistiocytosis (e.g. Stepp_1999, Clementi_2001, Molleran Lee_2004, Steinburg_2006, Trizzino_2008, Blincoe_2020). These data indicate that the variant is very likely to be associated with disease. Experimental studies have shown that the variant is associated with reduced or absent expression of the mature protein and severely impaired NK function (e.g. Stepp_1999, Voskoboinik_2004, Risma_2006). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Autoinflammatory syndrome

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Feb 01, 2018

- -

Familial hemophagocytic lymphohistiocytosis type 1

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Neuberg Centre For Genomic Medicine, NCGM

Jun 22, 2023

The observed missense variant c.673C>T p.Arg225Trp in the PRF1 gene has been reported in individuals with familial hemophagocytic lymphohistiocytosis Blincoe A, et al., 2020, Tesi B, et al., 2015. Experimental studies have shown that this missense change affects PRF1 function Voskoboinik I, et al., 2004. The variant is reported with 0.001% allele frequency in gnomAD Exomes. This variant has been reported to the ClinVar database as Pathogenic multiple submissions.The amino acid Arginine at position 225 is changed to a Tryptophan changing protein sequence and it might alter its composition and physico-chemical properties. Multiple lines of computational evidence Polyphen-probably damaging, SIFT-damaging and Mutation Taster-disease causing predict a damaging effect on protein structure and function for this variant. The reference amino acid p.Arg225Trp in PRF1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Uncertain

0.045

BayesDel_noAF

Uncertain

0.0

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.74

D;D

Eigen

Benign

0.093

Eigen_PC

Benign

-0.052

FATHMM_MKL

Benign

0.14

LIST_S2

Uncertain

0.87

.;D

M_CAP

Uncertain

0.094

MetaRNN

Pathogenic

0.99

D;D

MetaSVM

Uncertain

0.52

MutationAssessor

Uncertain

2.7

M;M

PrimateAI

Benign

0.33

PROVEAN

Uncertain

-3.2

D;D

REVEL

Uncertain

0.58

Sift

Uncertain

0.025

D;D

Sift4G

Uncertain

0.0070

D;D

Polyphen

1.0

D;D

Vest4

0.79

MutPred

0.91

Loss of methylation at R225 (P = 0.0393);Loss of methylation at R225 (P = 0.0393);

MVP

0.88

MPC

0.14

ClinPred

0.90

GERP RS

2.3

Varity_R

0.30

gMVP

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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