rs116100695
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 12P and 1B. PM1PM5PP5_Very_StrongBP4
The NM_000298.6(PKLR):c.1456C>T(p.Arg486Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00295 in 1,613,440 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R486Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_000298.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PKLR | ENST00000342741.6 | c.1456C>T | p.Arg486Trp | missense_variant | Exon 10 of 11 | 1 | NM_000298.6 | ENSP00000339933.4 | ||
| PKLR | ENST00000392414.7 | c.1363C>T | p.Arg455Trp | missense_variant | Exon 10 of 11 | 1 | ENSP00000376214.3 |
Frequencies
GnomAD3 genomes 0.00277 AC: 421AN: 152186Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00305 AC: 765AN: 251132Hom.: 2 AF XY: 0.00334 AC XY: 453AN XY: 135782
GnomAD4 exome AF: 0.00297 AC: 4345AN: 1461136Hom.: 7 Cov.: 33 AF XY: 0.00307 AC XY: 2231AN XY: 726892
GnomAD4 genome 0.00276 AC: 421AN: 152304Hom.: 1 Cov.: 31 AF XY: 0.00308 AC XY: 229AN XY: 74464
ClinVar
Submissions by phenotype
Pyruvate kinase deficiency of red cells Pathogenic:11
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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. -
PM3_VeryStrong+PP1+PS3 -
The p.Arg486Trp variant in PKLR has been reported in >30 compound heterozygous individuals with pyruvate kinase deficiency and segregated in 1 affected relative (PKD; Baronciani 1993 PMID:8483951, Zarza 1998 PMID:9827908, Manco 2000 PMID:11054094, Zanella 2001 PMID:11328279, Kedar 2009 PMID:18759866, Kager 2016 PMID:26728349, Jaouani 2017 PMID:28133914, Canu 2020 PMID:32974842, Milanesio 2021, Jamwal 2020 PMIDL32036089). It has also been identified in 0.812% (204/25114) of Finnish (unknown frequency of PKD) and 0.29% (375/128890) of European chromosomes (1:20,000 frequency of PKD) by gnomAD (http://gnomad.broadinstitute.org). This variant has been reported in ClinVar (Variation ID 1513). Enzymatic studies suggest that the p.Arg486Trp variant may be a mild mutation with reduced activity (Zarza 1998 PMID:9827908, Zanella 2001 PMID:11328279, Valentini 2002 PMID:11960989, and Kedar 2009 PMID:18759866). In summary, although additional studies are required to fully establish its clinical significance, the p.Arg486Trp variant meets criteria to be classified as likely pathogenic for autosomal recessive pyruvate kinase deficiency. ACMG/AMP Criteria applied: PM3_VeryStrong, PS3_Moderate. -
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The observed missense c.1456C>T(p.Arg486Trp) variant in PKLR gene has been reported previously in homozygous or compound heterozygous state in individual(s) affected with Pyruvate kinase deficiency (PKD) (Dongerdiye et al., 2023). Experimental studies have shown that this variant moderately affects PKLR function (Valentini et al., 2002). This variant is reported with the allele frequency of 0.3% in the gnomAD Exomes. This variant has been reported to the ClinVar database as Likely Pathogenic / Pathogenic (multiple submitters). 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. The amino acid change p.Arg486Trp in PKLR is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Multiple lines of computational evidence (Polyphen - Possibly Damaging, SIFT - Damaging, and MutationTaster - Disease causing automatic) predict a damaging effect on protein structure and function for this variant. For these reasons, this variant has been classified as Pathogenic. -
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. -
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. -
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Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as pathogenic. The following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with pyruvate kinase deficiency (MIM#266200). (I) 0108 - This gene is associated with both recessive and dominant disease. Both dominant elevated adenosine triphosphate of erythrocytes (MIM#102900) and recessive pyruvate kinase deficiency (MIM#266200) have been associated with PKLR. However, most of the literature reports associate with the recessive condition. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to tryptophan. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (829 heterozygotes, 2 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (10 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and poorly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated pyruvate kinase C-terminal domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant is one of the most common variants reported in individuals with pyruvate kinase deficiency (ClinVar, PMIDs: 16704447, 32036089, 34093240). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
not provided Pathogenic:10
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The PKLR c.1456C>T; p.Arg486Trp variant (rs116100695, ClinVar Variation ID: 1513) is commonly reported in the literature as compound heterozygous variant in individuals with pyruvate kinase deficiency (Baronciani 1993, Baronciani 1995, Canu 2020, Jamwal 2020, Kedar 2009, Lenzner 1997, Manco 2000, Zanella 2001, Zarza 1998). This variant is found in the general population with an overall allele frequency of 0.3% (833/282,498 alleles, including two homozygotes) in the Genome Aggregation Database (v2.1.1.). Structural and functional analysis of the variant protein show a moderate decrease in the catalytic efficiency (Valentini 2002). Computational analyses predict that this variant is deleterious (REVEL 0.914). 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 May 1. PMID: 8483951. Baronciani L et al. Molecular study of pyruvate kinase deficient patients with hereditary nonspherocytic hemolytic anemia. J Clin Invest. 1995 Apr. PMID: 7706479. Canu G et al. Identification and in silico characterization of a novel PKLR genotype in a Turkish newborn. Mol Biol Rep. 2020 Oct. PMID: 32974842. Jamwal M et al. Next-Generation Sequencing-Based Diagnosis of Unexplained Inherited Hemolytic Anemias Reveals Wide Genetic and Phenotypic Heterogeneity. J Mol Diagn. 2020 Apr. PMID: 32036089. 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 Feb. PMID: 18759866. Lenzner C et al. Molecular analysis of 29 pyruvate kinase-deficient patients from central Europe with hereditary hemolytic anemia. Blood. 1997 Mar 1. PMID: 9057665. Milanesio B et al. Six novel variants in the PKLR gene associated with pyruvate kinase deficiency in Argentinian patients. Clin Biochem. 2021 May. PMID: 33631127. Valentini G et al. Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia. J Biol Chem. 2002 Jun 28. PMID: 11960989. Zanella A et al. Molecular characterization of the PK-LR gene in sixteen pyruvate kinase-deficient patients. Br J Haematol. 2001 Apr. PMID: 11328279. 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 Nov. PMID: 9827908. -
PKLR: PM3:Very Strong, PP4:Moderate, PM2:Supporting, PM5:Supporting, PS3:Supporting -
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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. -
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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). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) 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. -
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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, 32279356, 37895316, 31980526, 29549173, 32165483, 11960989, 20981092, 8483951, 11054094, 24533562, 29349879, 29519373, 29519369, 9827908, 18759866, 27346685, 29396846, 30358897, 28133914, 32543069, 32043619, 30609409, 31974203, 32974842, 26728349, 33054133, 33054047, 23770304, 33054048, 34426522, 34662886, 11328279, 18708292, 32036089, 27871768, 9482576, 33631127, 37188156, 36892591, 38434380, 38581917, 37671043, 35989577, 38811201, 36825813) -
Pyruvate kinase hyperactivity Pathogenic:2
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. -
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PKLR-related disorder Pathogenic:1
The PKLR c.1456C>T variant is predicted to result in the amino acid substitution p.Arg486Trp. This variant is one of the most common disease causing PKLR variants and has been reported in the homozygous and compound heterozygous state in many individuals with pyruvate kinase deficiency (OMIM #266200; Baronciani et al. 1993. PubMed ID: 8483951; Zarza et al. 1998. PubMed ID: 9827908; Valentini et al. 2002. PubMed ID: 11960989; Kedar et al. 2008. PubMed ID: 18759866). Functional studies indicate this variant disrupts protein function (Valentini et al. 2002. PubMed ID: 11960989). This variant is reported in 0.81% of alleles in individuals of European (Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -
See cases Pathogenic:1
ACMG classification criteria: PS3, PS4, PM3, PP1, PP3, PP4, BS2 -
Pyruvate kinase deficiency of red cells;C1863224:Pyruvate kinase hyperactivity Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at