rs35947132

chr10-70600631-G-Achr10-70600631-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The NM_001083116.3(PRF1):c.272C>T(p.Ala91Val) variant causes a missense change. The variant allele was found at a frequency of 0.0354 in 1,613,234 control chromosomes in the GnomAD database, including 1,259 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity,risk factor (no stars). Synonymous variant affecting the same amino acid position (i.e. A91A) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.029 (99 hom., cov: 32)
  • Exomes 𝑓: 0.036 (1160 hom.)
• Consequence: PRF1 NM_001083116.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity; risk factor criteria provided, conflicting classifications P:1 U:3 B:9 O:2
• Conservation: PhyloP100: 6.74

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]

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0071359873).
• BP6: Variant 10-70600631-G-A is Benign according to our data. Variant chr10-70600631-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity, risk_factor]. Clinvar id is 13718.We mark this variant Likely_benign, oryginal submissions are: {Pathogenic=1, risk_factor=1, Benign=3, Likely_benign=3, Uncertain_significance=2, not_provided=1}. Variant chr10-70600631-G-A is described in Lovd as [Benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0287 (4365/152350) while in subpopulation NFE AF= 0.0448 (3046/68034). AF 95% confidence interval is 0.0434. There are 99 homozygotes in gnomad4. There are 2024 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 99 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRF1	NM_001083116.3	c.272C>T	p.Ala91Val	missense_variant	2/3	ENST00000441259.2
PRF1	NM_005041.6	c.272C>T	p.Ala91Val	missense_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRF1	ENST00000441259.2	c.272C>T	p.Ala91Val	missense_variant	2/3	5	NM_001083116.3	P1

Frequencies

GnomAD3 genomes AF: 0.0287 AC: 4362 AN: 152232 Hom.: 99 Cov.: 32

Gnomad AFR AF: 0.00724

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00311

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0349

GnomAD3 exomes AF: 0.0293 AC: 7315 AN: 249508 Hom.: 158 AF XY: 0.0299 AC XY: 4042 AN XY: 135150

Gnomad AFR exome AF: 0.00574

Gnomad AMR exome AF: 0.0230

Gnomad ASJ exome AF: 0.0267

Gnomad EAS exome AF: 0.000163

Gnomad SAS exome AF: 0.00432

Gnomad FIN exome AF: 0.0262

Gnomad NFE exome AF: 0.0466

Gnomad OTH exome AF: 0.0360

GnomAD4 exome AF: 0.0361 AC: 52738 AN: 1460884 Hom.: 1160 Cov.: 34 AF XY: 0.0357 AC XY: 25949 AN XY: 726634

Gnomad4 AFR exome AF: 0.00535

Gnomad4 AMR exome AF: 0.0248

Gnomad4 ASJ exome AF: 0.0261

Gnomad4 EAS exome AF: 0.000176

Gnomad4 SAS exome AF: 0.00384

Gnomad4 FIN exome AF: 0.0305

Gnomad4 NFE exome AF: 0.0422

Gnomad4 OTH exome AF: 0.0301

GnomAD4 genome AF: 0.0287 AC: 4365 AN: 152350 Hom.: 99 Cov.: 32 AF XY: 0.0272 AC XY: 2024 AN XY: 74514

Gnomad4 AFR AF: 0.00721

Gnomad4 AMR AF: 0.0276

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00311

Gnomad4 FIN AF: 0.0221

Gnomad4 NFE AF: 0.0448

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0399 Hom.: 164

Bravo AF: 0.0291

TwinsUK AF: 0.0345 AC: 128

ALSPAC AF: 0.0413 AC: 159

ESP6500AA AF: 0.00931 AC: 41

ESP6500EA AF: 0.0463 AC: 398

ExAC AF: 0.0305 AC: 3707

Asia WGS AF: 0.00318 AC: 11 AN: 3478

EpiCase AF: 0.0489

EpiControl AF: 0.0517

ClinVar

Significance: Conflicting classifications of pathogenicity; risk factor

Submissions summary: Pathogenic:1 Uncertain:3 Benign:9 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial hemophagocytic lymphohistiocytosis 2 Uncertain:1 Benign:3 Other:1

Likely benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 06, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided, no classification provided	literature only	GeneReviews	-	Variant assoc w/late-onset (adult) fHLH [Carvelli et al 2020, Miller et al 2020]. Common variant in population studies of healthy persons; functional effects were studied [Chia et al 2009]. -
Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Uncertain significance, criteria provided, single submitter	research	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 25, 2024	- -

not specified Benign:4

Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 13, 2022	Variant summary: PRF1 c.272C>T (p.Ala91Val) 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 0.029 in 280896 control chromosomes (gnomAD), predominantly at a frequency of 0.046 within the Non-Finnish European subpopulation in the gnomAD database, including 129 homozygotes. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 17 fold of the estimated maximal expected allele frequency for a pathogenic variant in PRF1 causing Familial Hemophagocytic Lymphohistiocytosis phenotype (0.0027), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. Experimental evidence using transiently transfected RBL-2H4 cells showed that the variant had approximately half the lytic activity as cells transfected with wild-type, which was further reduced to less than 10-fold activity when using purified A91V protein (Voskoboinik_2007). Primary natural killer cells from otherwise healthy heterozygous volunteers showed that natural killer cells from A91V/WT individuals had >35% reduction in cell killing efficiency compared with WT/WT individuals (House_2015). Six ClinVar submitters have assessed the variant since 2014: one classified the variant as pathogenic, two as likey benign, two as benign, and one as a risk factor. Based on the evidence outlined above, the variant was classified as likely benign. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 29, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided Pathogenic:1 Benign:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Aug 26, 2014	- -
Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The PRF1 p.Ala91Val variant was identified in the literature, however the role of its pathogenicity has been debated. The variant was identified in 15 of 320 proband chromosomes (frequency: 0.053) from individuals or families with haemophagocytic lymphohistiocytosis (HLH), acquired aplastic anemia, and Dianzani Autoimmune Lymphoproliferative Disease (Molleran_2004_PMID: 14757862, Solomou_2007_PMID: 17311987 & Clementi_2006_PMID: 16720836). The variant has also been reported in control population in multiple studies at frequencies of 0.046, 0.010, 0.0174 and 0.087 (Lek_2016_PMID: 27535533, Zur Stadt_2004_PMID: 15342365; Solomou_2007_PMID: 17311987 & Clementi_2006_PMID: 16720836). The variant was identified in dbSNP (ID: rs35947132) as “With Pathogenic allele”. In ClinVar, there are conflicting interpretations of pathogenicity from six submitters: 1x pathogenic (Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics), 2x likely benign (Illumina Clinical Services Laboratory and Invitae), 1x benign (Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine), and 2x uncertain significance (GeneDx and OMIM). The associated conditions are Hemophagocytic lymphohistiocytosis, familial, 2 and Familial hemophagocytic lymphohistiocytosis. The variant was also identified in LOVD 3.0 but was not found in Cosmic. The variant was identified in control databases in 8191 of 280896 chromosomes (171 homozygous) at a frequency of 0.02916 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 5912 of 128018 chromosomes (freq: 0.04618), Other in 252 of 7176 chromosomes (freq: 0.03512), Ashkenazi Jewish in 273 of 10298 chromosomes (freq: 0.02651), European (Finnish) in 655 of 24848 chromosomes (freq: 0.02636), Latino in 811 of 35320 chromosomes (freq: 0.02296), African in 153 of 24738 chromosomes (freq: 0.006185), South Asian in 132 of 30580 chromosomes (freq: 0.004317), and East Asian in 3 of 19918 chromosomes (freq: 0.000151). Perforin plays a key role in the cytotoxicity of natural killer (NK) cells and cytotoxic T lymphocytes (CTLs). A functional study of the p.A91V variant showed that the variant resulted in impaired cleavage of perforin to its active form, resulting in loss of CTL and NK-cell cytotoxicity against targets (Trambas_2005_PMID: 15741215). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, and GeneSplicer) do not predict a difference in splicing. The p.Ala91 residue is not highly conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, and MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this varaint. This variant is classified as a variant of likely benign. -
risk factor, criteria provided, single submitter	clinical testing	GeneDx	Mar 18, 2021	Identified in individuals with familial hemophagocytic lymphohistiocytosis and acute lymophoblastic leukemia; however, the A91V variant has also been identified in both unaffected relatives and unaffected controls (Zur Stadt et al., 2004; Santoro et al., 2005; An et al., 2013); Functional studies suggest that the A91V variant results in decreased levels of perforin expression, with partial loss of protein function and stability (Voskoboinik et al., 2005; House et al., 2015); This variant is associated with the following publications: (PMID: 33256384, 32150605, 32198610, 32342501, 32542393, 32300447, 31932842, 30957677, 29263817, 30343897, 30287596, 14757862, 24916509, 27622035, 28863861, 27153395, 27872624, 15342365, 23592409, 26597256, 24632576, 22970278, 25937001, 25121636, 24309606, 22437823, 16611257, 25776844, 23073290, 25354579, 18496551, 17311987, 17475905, 15741215, 12229880, 21881043, 15755897, 15921391) -

PRF1-related condition Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 30, 2024

The PRF1 c.272C>T variant is predicted to result in the amino acid substitution p.Ala91Val. This variant has been studied extensively, but its clinical significance remains unclear. The PRF1 gene variant c.272C>T is found at a high frequency among several control populations (up to 4.6% and in many homozygous individuals; and has been classified as a “neutral polymorphism” (Molleran Lee et al. 2004. PubMed ID: 14757862; Zur Stadt et al. 2004. PubMed ID: 15342365). However, considerable clinical and experimental data support a functional role of the p.Ala91Val variant resulting in reduced cytotoxic activity that may be significant for the pathogenesis of hemophagocytic lymphohistiocytosis and other disorders, including NK/T-Cell lymphomas, in both heterozygous and homozygous carriers of the p.Ala91Val substitution (Voskoboinik et al. 2005. PubMed ID: 15755897; Voskoboinik et al. 2007. PubMed ID: 17475905; Martínez-Pomar et al. 2013. PubMed ID: 23073290; Trambas et al. 2005. PubMed ID: 15741215; Clementi et al. 2002. PubMed ID: 12229880; Santoro et al. 2005. PubMed ID: 15921391; Zhang et al. 2011. PubMed ID: 21881043; Mancebo et al. 2006. PubMed ID: 16956828; House et al. 2015. PubMed ID: 25776844; Manso et al. 2014. PubMed ID: 24632576; Willig et al. 2015. PubMed ID: 25937001, Palterer et al. 2017. PubMed ID: 28863861). Consequently, this allele has also been categorized as either a functional polymorphism or as a risk allele. Due to conflicting reports, the significance of this variant remains uncertain. -

Hemophagocytic lymphohistiocytosis, familial, 2, susceptibility to Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

OMIM

Aug 15, 2007

- -

Autoinflammatory syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Jan 29, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.12
Cadd	Uncertain	24
Dann	Uncertain	1.0
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.35
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.66	T;.;T
MetaRNN	Benign	0.0071	T;T;T
MetaSVM	Uncertain	0.12	D
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Benign	0.44	T
Polyphen		1.0	.;D;D
Vest4		0.23, 0.25
MPC		0.43
ClinPred		0.019	T
GERP RS		4.8
Varity_R		0.32
gMVP		0.77

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

Other links and lift over

dbSNP: rs35947132; hg19: chr10-72360387;