ClinVar Genomic variation as it relates to human health

neurodegenerative syndrome; cerebellar ataxia; epilepsy; tremor

This variant is interpreted as a Pathogenic, for Neurodegeneration with brain iron accumulation 1, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PP1 => Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease. PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS4-Moderate => Recurrent mutation. (PMID:11479594,15834858,24075960) (PMID:12510040). PS3 => Well-established functional studies show a deleterious effect (PMID:16272150,15659606).

Functional studies show G521R leads to loss of protein catalytic activity (Zhang et al., 2006); This variant is associated with the following publications: (PMID: 25131622, 22221393, 11479594, 24215330, 22416811, 26828213, 26795593, 23968566, 29590070, 28708303, 16450344, 31628766, 30363918, 32654475, 33144682, 33098801, 31589614, 28252636, 16272150)

PS3, PS4, PP3, PP5

Variant summary: PANK2 c.1561G>A (p.Gly521Arg) results in a non-conservative amino acid change in 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 8.7e-05 in 251484 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in PANK2 causing Pantothenate Kinase-Associated Neurodegeneration (8.7e-05 vs 0.0011), allowing no conclusion about variant significance. c.1561G>A has been reported in the literature in multiple bi-allelic individuals affected with Pantothenate Kinase-Associated Neurodegeneration/Hallervorden-Spatz syndrome (example: Zhou_2001). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 11479594). Eleven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 521 of the PANK2 protein (p.Gly521Arg). This variant is present in population databases (rs137852959, gnomAD 0.02%). This missense change has been observed in individuals with atypical and typical pantothenate kinase-associated neurodegeneration (PMID: 11479594, 16450344, 22221393, 26795593). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 4548). 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 expected to disrupt PANK2 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects PANK2 function (PMID: 15659606, 16272150). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

The c.1561G>A (p.G521R) alteration is located in coding exon 6 of the PANK2 gene. This alteration results from a G to A substitution at nucleotide position 1561, causing the glycine (G) at amino acid position 521 to be replaced by an arginine (R). Based on data from gnomAD, the A allele has an overall frequency of 0.01% (36/282886) total alleles studied, with a frequency of 0.02% (28/129190) in the European (non-Finnish) subpopulation. This alteration has been reported previously in the homozygous and compound heterozygous state in multiple individuals with pantothenate kinase-associated neurodegeneration (Zhou, 2001; Leoni, 2012; Wu, 2013; Chérot, 2018; Santambrogio, 2020). This amino acid position is highly conserved in available vertebrate species. Functional analyses in HEK293 cells demonstrated that the p.G521R alteration causes marked instability of the intermediate PANK2, and reduced production of the mature protein. In vitro enzymatic activity assay of mutant and wild type proteins revealed that p.G521R results in more than 90% reduction in enzyme activity compared to wild-type (Kotzbauer, 2005). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

Converted during submission to Pathogenic.

Variant confirmed as disease-causing by referring clinical team

Variant confirmed as disease-causing by referring clinical team

The PANK2 p.Gly521Arg variant in homozygosity consistently presents as classic PKAN in the literature (Li_2013_22416811, Wu_2013_23968566, Zhang_2006_16272150). The variant was identified in dbSNP (ID: rs137852959) “with Pathogenic allele”, ClinVar classified as pathogenic (submitters: Ambry Genetics, Center for Pediatric Genomic Medicine (Children's Mercy Hospital and Clinics), GeneDx, OMIM, Undiagnosed Diseases Program Translational Research Laboratory (NIH) and Groupe Hospitalier Pitie Salpetriere (Paris)), and in control databases in 35 of 277234 chromosomes at a frequency of 0.0001 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include Other in 2 of 6468 chromosomes (freq: 0.0003), Latino in 3 of 34420 chromosomes (freq: 0.00009), European Non-Finnish in 28 of 126718 chromosomes (freq: 0.0002), African in 1 of 24030 chromosomes (freq: 0.00004), and South Asian in 1 of 30782 chromosomes (freq: 0.00003), while not observed in the Ashkenazi Jewish, East Asian and European Finnish populations. The p.Gly521 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact of the variant Arg to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as pathogenic.

The most frequent PANK2 pathogenic variant, p.Gly521Arg, leads to a protein that is misfolded and devoid of activity [Zhang et al 2006].