Submissions for variant NM_000298.6(PKLR):c.1456C>T (p.Arg486Trp)

gnomAD frequency: 0.00270  dbSNP: rs116100695

Total submissions: 20

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Knight Diagnostic Laboratories, Oregon Health and Sciences University	RCV000001577	SCV000223943	likely pathogenic	Pyruvate kinase deficiency of red cells	2016-01-27	criteria provided, single submitter	clinical testing	The c.1456C>T (p.Arg486Trp) (NM_ 000298.5) missense variant has been reported in several unrelated individuals diagnosed with PK deficiency. These families have a well-documented clinical history of anemia (Zarza et al. 1998). Case-control studies have reported this variant as a common disease causing variant accounting for 9%-32% of diagnosed cases (Zarza et al., 1998; Zanella et al., 2001; Kedar et al., 2009). This variant has often been reported in trans with several pathogenic variants, and functional studies have shown that patients harboring this variant, in a compound heterozygous state, have reduced PK activity relative to normal controls (Zarza et al., 1998; Zanella et al., 2001; Valentini et al. 2002; Kedar et al., 2009). This c.1456C>T variant is reported at low frequency in the population databases (ESP = 0.291%; 1000 Genomes = 1%; ExAC = 0.298%), and multiple in silico algorithms predict this variant to have a deleterious effect (GERP = 4.85; CADD = 18.75; PolyPhen = 1; SIFT = 0). Therefore, this collective evidence supports the classification of the c.1456C>T (p.Arg486Trp) variant as a recessive Likely Pathogenic variant for PK deficiency.
Eurofins Ntd Llc (ga)	RCV000724015	SCV000331623	likely pathogenic	not provided	2017-04-14	criteria provided, single submitter	clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000001577	SCV000713497	likely pathogenic	Pyruvate kinase deficiency of red cells	2020-03-30	criteria provided, single submitter	clinical testing	proposed classification - variant undergoing re-assessment, contact laboratory
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000724015	SCV000885966	pathogenic	not provided	2023-10-20	criteria provided, single submitter	clinical testing	The PKLR c.1456C>T; p.Arg486Trp variant (rs116100695), is reported in the literature as both a homozygous and compound heterozygous variant in several individuals affected with pyruvate kinase deficiency (Baronciani 1993, Kedar 2009, Manco 2000, Zanella 2001, Zarza 1998). This variant is reported in ClinVar (Variation ID: 1513). This variant is found in the general population with an overall allele frequency of 0.3% (833/282498 alleles, including two homozygotes) in the Genome Aggregation Database. Additionally, an alternative change at the same amino acid location (c.1457G>T, p.Arg486Leu) that is known to affect the PK activity has also been reported in an individual with hemolytic anemia (Pissard 2006). The arginine at codon 486 is moderately conserved and computational analyses predict that this variant is deleterious (REVEL 0.91). Based on available information, this variant is considered to be pathogenic. References: Baronciani L et al. Analysis of pyruvate kinase-deficiency mutations that produce nonspherocytic hemolytic anemia. Proc Natl Acad Sci U S A. 1993 90:4324-4327. Kedar P et al. Spectrum of novel mutations in the human PKLR gene in pyruvate kinase-deficient Indian patients with heterogeneous clinical phenotypes. Clin Genet. 2009 75:157-162. Manco L et al. A new PKLR gene mutation in the R-type promoter region affects the gene transcription causing pyruvate kinase deficiency. Br J Haematol. 2000 110:993-997. Pissard S et al. Pyruvate kinase deficiency in France: a 3-year study reveals 27 new mutations. Br J Haematol. 2006 133:683-689. Zanella A et al. Molecular characterization of the PK-LR gene in sixteen pyruvate kinase-deficient patients. Br J Haematol. 2001 113:43-48. Zarza R et al. Molecular characterization of the PK-LR gene in pyruvate kinase deficient Spanish patients. Red Cell Pathology Group of the Spanish Society of Haematology (AEHH). Br J Haematol. 1998 103:377-382.
Fulgent Genetics, Fulgent Genetics	RCV000762857	SCV000893217	pathogenic	Pyruvate kinase hyperactivity; Pyruvate kinase deficiency of red cells	2022-05-28	criteria provided, single submitter	clinical testing
Invitae	RCV000724015	SCV001035168	pathogenic	not provided	2024-01-18	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 486 of the PKLR protein (p.Arg486Trp). This variant is present in population databases (rs116100695, gnomAD 0.8%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with pyruvate kinase deficiency (PMID: 9057665, 9657767, 9827908, 11054094, 17574881, 27871768, 32974842). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. This variant is commonly associated with mild to asymptomatic disease when observed in the homozygous state. However, this variant in conjunction with another pathogenic variant is a common cause of mild chronic hemolytic anemia, particularly in populations of southern Europe. Instances of moderate to severe disease in association with this variant have also been reported (PMID: 17360088, 9482576, 11328279, 10354117). ClinVar contains an entry for this variant (Variation ID: 1513). 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) performed at Invitae indicates that this missense variant is not expected to disrupt PKLR protein function with a negative predictive value of 80%. Experimental studies have shown that this variant moderately affects PKLR function (PMID: 11960989). For these reasons, this variant has been classified as Pathogenic.
Mayo Clinic Laboratories, Mayo Clinic	RCV000724015	SCV001713042	pathogenic	not provided	2021-05-10	criteria provided, single submitter	clinical testing	PS4, PM1, PM3, PP4, PP5
CeGaT Center for Human Genetics Tuebingen	RCV000724015	SCV001746867	pathogenic	not provided	2021-04-01	criteria provided, single submitter	clinical testing
GeneDx	RCV000724015	SCV001792018	likely pathogenic	not provided	2023-05-01	criteria provided, single submitter	clinical testing	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30681718, 29555771, 27871768, 32279356, 31980526, 29549173, 32165483, 11960989, 20981092, 8483951, 11054094, 24533562, 29349879, 29519373, 29519369, 11328279, 9827908, 18759866, 27346685, 29396846, 30358897, 28133914, 9482576, 32036089, 32543069, 32043619, 30609409, 31974203, 32974842, 26728349, 18708292, 33054133, 33054047, 23770304, 33054048, 34426522, 34662886, 33631127)
Revvity Omics, Revvity	RCV000724015	SCV002024662	pathogenic	not provided	2023-11-27	criteria provided, single submitter	clinical testing
Mendelics	RCV000991156	SCV002518869	pathogenic	Pyruvate kinase hyperactivity	2022-05-04	criteria provided, single submitter	clinical testing
3billion	RCV000001577	SCV002521511	likely pathogenic	Pyruvate kinase deficiency of red cells	2022-05-22	criteria provided, single submitter	clinical testing	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000001513). A different missense change at the same codon (p.Arg486Leu) has been reported to be associated with PKLR related disorder (PMID: 16704447). It is observed in the gnomAD v2.1.1 (https://gnomad.broadinstitute.org/) dataset at total allele frequency of 0.305%. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.91; 3Cnet: 0.83). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	RCV002251854	SCV002523854	pathogenic	See cases	2020-11-13	criteria provided, single submitter	clinical testing	ACMG classification criteria: PS3, PS4, PM3, PP1, PP3, PP4, BS2
Institute of Human Genetics, Heidelberg University	RCV000001577	SCV002757812	pathogenic	Pyruvate kinase deficiency of red cells	2022-09-16	criteria provided, single submitter	clinical testing
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine	RCV000001577	SCV004171978	pathogenic	Pyruvate kinase deficiency of red cells	2023-01-24	criteria provided, single submitter	clinical testing	The missense c.1456C>T (p.Arg486Trp) variant in PKLR gene has been reported previously (as the most common variant) in compound heterozygous state in multiple individuals affected with pyruvate kinase deficiency (Montllor et al. 2017; Jaouani et al. 2017; Canu et al. 2020). Experimental evidence shows that this variant is more thermoresistant than the wild type, did not induce significant conformational changes in the overall protein conformation, and leads to a drastic reduction in catalytic efficiency, which is consistent with a moderate phenotype (Valentini et al. 2002). The p.Arg486Trp variant is reported with an allele frequency of 0.3% in the gnomAD exomes database and is novel (not in any individuals) in 1000 Genomes database. This variant has been reported to the ClinVar database as Likely Pathogenic / Pathogenic (multiple submissions). The amino acid change p.Arg486Trp in PKLR is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 486 is changed to a Trp changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000001577	SCV004223638	pathogenic	Pyruvate kinase deficiency of red cells	2023-11-10	criteria provided, single submitter	clinical testing	Variant summary: PKLR c.1456C>T (p.Arg486Trp) results in a non-conservative amino acid change located in the Pyruvate Kinase C terminal domain (IPR015795) 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 0.003 in 251132 control chromosomes in the gnomAD database, including 2 homozygotes. c.1456C>T has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with moderate to severe Pyruvate Kinase Deficiency Of Red Cells (examples: Zanella_1997, Pastore_1998, Pissard_2006 ). These data indicate that the variant is very likely to be associated with disease. One publication reports experimental evidence that this variant moderately affects PKLR function (example: Valentini_2002). Fifteen submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000724015	SCV004243293	pathogenic	not provided	2024-02-06	criteria provided, single submitter	clinical testing
OMIM	RCV000001577	SCV000021733	pathogenic	Pyruvate kinase deficiency of red cells	2009-02-01	no assertion criteria provided	literature only
Reproductive Health Research and Development, BGI Genomics	RCV000991156	SCV001142310	pathogenic	Pyruvate kinase hyperactivity	2020-01-06	no assertion criteria provided	curation	NM_000298.5:c.1456C>T in the PKLR gene has an allele frequency of 0.008 in European (Finnish) subpopulation in the gnomAD database. This variant has been reported in multiple individuals with Pyruvate kinase deficiency, in a compound heterozygous state: 1190A>T/1456C>T, 1042-1044del/1456C>T, 992A>G/1456C>T, 1436G>A/1456C>T (PMID: 18759866); 1456C>T/1675C>T, 1456C>T/1010G>A, 1456C>T/1223C>T, 1456C>T/1070T>C, 1456C>T/721G>T(PMID: 9827908). Functional studies suggest that the p.Arg486Trp variant may be a mild mutation with reduced enzyme activity (PMID: 11960989).Taken together, we interprete this variant as Pathogenic/Likely pathogenic variant. ACMG/AMP Criteria applied: PM3_VeryStrong, PS3, PP4.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000724015	SCV001550687	pathogenic	not provided		no assertion criteria provided	clinical testing	The PKLR p.R486W variant was identified in over 30 individuals with pyruvate kinase deficiency and haemolytic anemia as a compound heterozygous variant; phenotypes ranged from mild to severe (Russo_2018_PMID:29396846; Jaouani_2017_PMID:28133914; Montllor_2016_PMID:27871768; Kedar_2009_PMID:18759866; Zanella_2001_PMID:11328279; Manco_2000_PMID:11054094; Zarza_1998_PMID:9827908; Baronciani_1993_PMID:8483951; Marcello_2008_PMID:18708292). The variant was identified in dbSNP (ID: rs116100695) and ClinVar (classified as pathogenic by Fulgent Genetics, ARUP Laboratories and Reproductive Health Research and Development, BGI Genomics, as likely pathogenic by Laboratory of Molecular Medicine, EGL Genetics and Knight Diagnostic Laboratories, Oregon Health and Services University, and as likely benign by Invitae). The variant was identified in control databases in 833 of 282498 chromosomes (2 homozygous) at a frequency of 0.002949 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (Finnish) in 204 of 25114 chromosomes (freq: 0.008123), South Asian in 113 of 30616 chromosomes (freq: 0.003691), European (non-Finnish) in 375 of 128890 chromosomes (freq: 0.002909), Other in 20 of 7218 chromosomes (freq: 0.002771), Ashkenazi Jewish in 28 of 10360 chromosomes (freq: 0.002703), Latino in 80 of 35424 chromosomes (freq: 0.002258) and African in 13 of 24926 chromosomes (freq: 0.000522), but was not observed in the East Asian population. Although the p.R486 residue is not conserved in mammals and other organisms, computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein. The variant occurs outside of the splicing consensus sequence and 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. Functional data suggests that this variant results in decreased catalytic efficiency (Valentini_2002_PMID:11960989). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.