Submissions for variant NM_001083116.3(PRF1):c.673C>T (p.Arg225Trp)

gnomAD frequency: 0.00001  dbSNP: rs28933973

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000014711	SCV000363433	pathogenic	Familial hemophagocytic lymphohistiocytosis 2	2017-04-27	criteria provided, single submitter	clinical testing	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.
Invitae	RCV000014711	SCV002234638	pathogenic	Familial hemophagocytic lymphohistiocytosis 2	2023-11-24	criteria provided, single submitter	clinical testing	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.
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV002260964	SCV002542792	pathogenic	Autoinflammatory syndrome	2018-02-01	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV002281706	SCV002570678	pathogenic	Familial hemophagocytic lymphohistiocytosis	2022-07-13	criteria provided, single submitter	clinical testing	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.
3billion	RCV000014711	SCV002573266	pathogenic	Familial hemophagocytic lymphohistiocytosis 2	2022-09-01	criteria provided, single submitter	clinical testing	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.
Ambry Genetics	RCV002513053	SCV003556362	pathogenic	Inborn genetic diseases	2021-06-18	criteria provided, single submitter	clinical testing	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.
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV000014711	SCV004015267	pathogenic	Familial hemophagocytic lymphohistiocytosis 2	2023-07-07	criteria provided, single submitter	clinical testing	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).
Neuberg Centre For Genomic Medicine, NCGM	RCV000014711	SCV004100919	pathogenic	Familial hemophagocytic lymphohistiocytosis 2		criteria provided, single submitter	clinical testing	The missense variant p.R225W in PRF1 (NM_001083116.3) has been previously reported in affected patients (Madkaikar M et al). Functional studies reveal a damaging effect (Trizzino et al, 2008). It has been submitted to ClinVar as Pathogenic. The p.R225W variant is observed in 1/18,386 (0.0054%) alleles from individuals of East Asian background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics	RCV003473102	SCV004204187	pathogenic	Aplastic anemia	2023-10-11	criteria provided, single submitter	clinical testing
OMIM	RCV000014711	SCV000034966	pathogenic	Familial hemophagocytic lymphohistiocytosis 2	2013-11-01	no assertion criteria provided	literature only