ClinVar Miner

Submissions for variant NM_000287.4(PEX6):c.1802G>A (p.Arg601Gln)

gnomAD frequency: 0.00294  dbSNP: rs34324426
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Total submissions: 22
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000424129 SCV000232509 likely pathogenic not provided 2018-01-12 criteria provided, single submitter clinical testing
Leeds Amelogenesis Imperfecta Research Group, University of Leeds RCV000201298 SCV000264800 pathogenic Heimler syndrome 2 2015-10-01 criteria provided, single submitter research PMID:26387595 paper details one individual who is heterozygous for c.1802G>A variant with Heimler syndrome; other two detail Zellweger spectrum patients with variant
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000424129 SCV000511457 benign not provided 2017-01-04 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000180127 SCV000596393 uncertain significance not specified 2016-03-29 criteria provided, single submitter clinical testing
Counsyl RCV000675148 SCV000800748 likely benign Peroxisome biogenesis disorder 4A (Zellweger); Peroxisome biogenesis disorder 4B 2017-11-21 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000779504 SCV000916141 likely pathogenic Peroxisome biogenesis disorder 4A (Zellweger) 2017-08-28 criteria provided, single submitter clinical testing The PEX6 c.1802G>A (p.Arg601Gln) missense variant has been reported in at least six studies in which it is found in at least 12 individuals in a compound heterozygous state, including five individuals diagnosed with a mild Zellweger syndrome (ZS) and seven with Heimler syndrome (Yik et al. 2009; Ebberink et al. 2010; Tran et al. 2014; Ratbi et al. 2015; Ferdinandusse et al. 2016; Smith et al. 2016). One of the compound heterozygotes diagnosed with ZS carried a third variant in the PEX6 gene (phase unknown) (Yik et al. 2009). Another of the compound heterozygotes presented with a late-onset form of ZS with a phenotype that mimicked X-linked adrenoleukodystrophy (Tran et al. 2014). The p.Arg601Gln variant was also present in a heterozygous state in an individual with ZS who carried two variants in the PEX1 gene in a compound heterozygous state (Yik et al. 2009). The individuals with Heimler syndrome included a set of twins, three siblings from an unrelated family and two additional individuals from two other unrelated families (Ratbi et al. 2015; Smith et al. 2016). Affected individuals carrying the p.Arg601Gln variant often have a mild phenotype that may include normal intellect, sensorineural hearing loss, amelogenesis imperfecta, Beau's lines, and leukonychia and have been occasionally been misdiagnosed with both X-linked adrenoleukodystrophy and Usher syndrome with amelogenesis imperfecta (Tran et al. 2014; Ratbi et al. 2015; Ferdinandusse et al. 2016; Smith et al. 2016). The p.Arg601Gln variant was absent from 200 control chromosomes and is reported at a frequency of 0.014563 in the Gujarati Indian in Houston population of the 1000 Genomes Project. There are eight homozygotes present in the Genome Aggregation Database, which may be explained by the mild phenotypic presentation caused by the p.Arg601Gln variant and by the variant acting as a hypomorphic allele (Smith et al. 2016). The Arg601 residue is conserved. Transfection of the p.Arg601Gln variant into primary skin fibroblasts cells completely deficient in PEX1 and PEX6 demonstrated that the variant rescued peroxisomal biogenesis in between 35 to 40% of cells indicating a significant residual activity (Ratbi et al. 2015). Based on the collective evidence, the p.Arg601Gln variant is classified as likely pathogenic for Zellweger Syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Baylor Genetics RCV000850505 SCV000992708 pathogenic Peroxisome biogenesis disorder 4A (Zellweger); Peroxisome biogenesis disorder 4B; Heimler syndrome 2 2018-10-12 criteria provided, single submitter clinical testing
Invitae RCV001081170 SCV001122566 uncertain significance Peroxisome biogenesis disorder 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 601 of the PEX6 protein (p.Arg601Gln). This variant is present in population databases (rs34324426, gnomAD 0.5%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with late-onset Zellweger spectrum disorder, also called Heimler syndrome (PMID: 25079599, 26387595, 27302843, 29676688). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 198709). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects PEX6 function (PMID: 26387595). This variant disrupts the p.Arg601 amino acid residue in PEX6. Other variant(s) that disrupt this residue have been observed in individuals with PEX6-related conditions (PMID: 26287655), which suggests that this may be a clinically significant amino acid residue. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
CeGaT Center for Human Genetics Tuebingen RCV000424129 SCV001154747 pathogenic not provided 2023-10-01 criteria provided, single submitter clinical testing PEX6: PM3:Very Strong, PM5, PM2:Supporting, PS3:Supporting
Johns Hopkins Genomics, Johns Hopkins University RCV000779504 SCV001167289 likely pathogenic Peroxisome biogenesis disorder 4A (Zellweger) 2019-09-25 criteria provided, single submitter clinical testing
Blueprint Genetics RCV001075628 SCV001241255 uncertain significance Retinal dystrophy 2019-02-08 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000180127 SCV001370721 uncertain significance not specified 2023-12-14 criteria provided, single submitter clinical testing Variant summary: PEX6 c.1802G>A (p.Arg601Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0027 in 246348 control chromosomes in the gnomAD database, including 7 homozygotes. The observed variant frequency is approximately 1.42 fold of the estimated maximal expected allele frequency for a pathogenic variant in PEX6 causing Peroxisome Biogenesis Disorder phenotype (0.0019), suggesting that the variant is benign. c.1802G>A has been reported in the literature in multiple individuals affected with mild, late-onset Zellweger syndrome in the compound heterozygous state (Ferdinandusse_2016, Tran_2014, Yik_2009) . In one of these patients, late-onset Zellweger syndrome mimicked X-linked adrenoleukodystrophy (Tran_2014). Two patients reported by Yik_2009 also carried additional PEX "inactivating" mutations (one with a PEX12 variant and one with two additional PEX1 variants). Additionally, several publications report the occurrence of this variant in patients with Heimler syndrome, which has clinical overlap with Usher syndrome with lack of peroxisomal abnormalities on plasma screening, and is stated to represent the mild end of Zellweger syndrome (Smith_2016). Heimler syndrome patients reported with this variant include a set of twins (Gao_2019, Ong_2006, Rabti_2015), and 5 other individuals/families who are compound heterozygotes with other PEX6 variants (Smith_2016, Wangtiraumnuay_2018). The variant was also reported in the heterozygous state (no second allele reported) in a patient who presented with bilateral macular schisis and sensorineural hearing loss with no nail or dental abnormalities and normal blood pipecolic/ plasmalogen levels (Doucette_2021). In experimental studies, when the variant was transfected into primary skin fibroblasts completely deficient in PEX1 and PEX6, cells demonstrated about 40% peroxisome positive cells, indicating significant residual activity of the variant (Rabti_2015). The following publications have been ascertained in the context of this evaluation (PMID: 19105186, 19877282, 27302843, 26387595, 31831025, 26943801, 16530715, 25079577, 33776059, 31216405, 33003980, 29676688, 36785559). 18 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments: 10 classified the variant as pathogenic/likely pathogenic, 6 as VUS, and 2 as benign/likely benign. In summary, while the relatively high allele frequency in the control population (gnomAD) suggests that the variant is benign, the potential for mild phenotypes resulting from this variant suggests the disease may go under-diagnosed. It cannot be ruled out that this variant is a risk allele for mild Peroxisome Biogenesis Disorders including Zellweger and Heimler syndromes. Based on the evidence outlined above, the variant was classified as uncertain significance.
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego RCV001265584 SCV001443749 likely pathogenic PEX6-related disorder 2019-11-19 criteria provided, single submitter clinical testing This variant has been previously reported as a compound heterozygous change with multiple different variants, including c.2579G>A (p.Arg860Gln), in patients with peroxisome biogenesis disorder (Zellweger syndrome) or Heimler Syndrome, including bilateral sensorineural hearing loss, amelogenesis imperfecta, nail abnormalities, and retinal pigmentation (PMID: 19105186, 26387595, 27302843). Functional studies of this variant demonstrate that it has significant residual activity, suggesting that it may be a hypomorphic allele (PMID: 26387595). Haplotype analysis of this variant show that it is consistently associated with a haplotype of two SNPs and a 779 KB microsatellite, suggesting that this variant is a founder variant that may have arisen many generations ago (PMID: 27302843). In the gnomAD population database, it is present in the homozygous state in 7 individuals and it is present in the heterozygous state at a frequency of 0.30% (821/277,712). The c.1802G>A (p.Arg601Gln) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.1802G>A (p.Arg601Gln) variant is classified as Likely Pathogenic.
GeneDx RCV000424129 SCV001872724 likely pathogenic not provided 2023-04-10 criteria provided, single submitter clinical testing Previously reported in patients with a peroxisomal biogenesis disorder who harbored the R601Q variant and a second missense variant in the PEX6 gene; however parental studies to confirm phase of the variants was not reported in these cases (Yik et al., 2009; Tran et al., 2014); Reported in adult twin sisters with a clinical diagnosis of Heimler syndrome who harbored this variant and a frameshift variant in the PEX6 gene; these siblings were reported to have normal intellect, profound bilateral hearing loss, leukonychia, and retinal pigmentation changes (Ratbi et al., 2015); 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: 31216405, 26387595, 27302843, 29676688, 19105186, 31884617, 33776059, 25079577, 31374812, 30409984, 33416279, 34313030, 19877282, 34426522, 34234304, 30675382, 27848944)
Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital RCV000180127 SCV001984589 uncertain significance not specified 2020-03-11 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000424129 SCV003814874 uncertain significance not provided 2020-12-12 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV001265584 SCV004107814 uncertain significance PEX6-related disorder 2024-01-02 criteria provided, single submitter clinical testing The PEX6 c.1802G>A variant is predicted to result in the amino acid substitution p.Arg601Gln. This variant has been reported in patients with peroxisome biogenesis disorders and has been reported to be associated with a milder phenotype (Ebberink et al. 2010. PubMed ID: 19877282; Yik et al. 2009. PubMed ID: 19105186; Ratbi et al. 2015. PubMed ID: 26387595; Wangtiraumnuay et al. 2018; PubMed ID: 29676688). However, this variant has also been reported in a large population database at allele frequencies of up to ~0.47%, including 7 homozygous individuals. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Baylor Genetics RCV000201298 SCV004201518 pathogenic Heimler syndrome 2 2023-10-30 criteria provided, single submitter clinical testing
Institute of Immunology and Genetics Kaiserslautern RCV000850505 SCV004803208 pathogenic Peroxisome biogenesis disorder 4A (Zellweger); Peroxisome biogenesis disorder 4B; Heimler syndrome 2 2024-03-18 criteria provided, single submitter clinical testing ACMG Criteria: PS3, PS4, PM3, PP3, PP5; Individual was compound heterozygous for PEX6 variants c.1314_1321del and c.1802G>A
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV003987426 SCV004804994 likely pathogenic Peroxisome biogenesis disorder 4B 2024-03-17 criteria provided, single submitter research
OMIM RCV000201298 SCV000256087 pathogenic Heimler syndrome 2 2015-10-01 no assertion criteria provided literature only
Mayo Clinic Laboratories, Mayo Clinic RCV000424129 SCV000801833 likely pathogenic not provided 2018-02-07 no assertion criteria provided clinical testing

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