rs34324426

chr6-42967450-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM5 PP3 BP4_Moderate BS2

The NM_000287.4(PEX6):c.1802G>A(p.Arg601Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00309 in 1,612,580 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R601W) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0028 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0031 (16 hom.)
• Consequence: PEX6 NM_000287.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:13 U:7 B:2
• Conservation: PhyloP100: 6.99

Genes affected

PEX6 (HGNC:8859): (peroxisomal biogenesis factor 6) This gene encodes a member of the AAA (ATPases associated with diverse cellular activities) family of ATPases. This member is a predominantly cytoplasmic protein, which plays a direct role in peroxisomal protein import and is required for PTS1 (peroxisomal targeting signal 1, a C-terminal tripeptide of the sequence ser-lys-leu) receptor activity. Mutations in this gene cause peroxisome biogenesis disorders of complementation group 4 and complementation group 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM5: Other missense variant is known to change same aminoacid residue: Variant chr6-42967451-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 632484.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Likely_pathogenic=4, Pathogenic=1}.
• PP3: Multiple lines of computational evidence support a deleterious effect 7: BayesDel_noAF, Cadd, Dann, Eigen, M_CAP, MutationAssessor, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• BP4: Computational evidence support a benign effect (MetaRNN=0.11544728).
• BS2: High Homozygotes in GnomAdExome at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PEX6	NM_000287.4	c.1802G>A	p.Arg601Gln	missense_variant	8/17	ENST00000304611.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEX6	ENST00000304611.13	c.1802G>A	p.Arg601Gln	missense_variant	8/17	1	NM_000287.4	P1
PEX6	ENST00000244546.4	c.1802G>A	p.Arg601Gln	missense_variant	8/15	1

Frequencies

GnomAD3 genomes AF: 0.00281 AC: 428 AN: 152160 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000651

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.000458

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00517

Gnomad OTH AF: 0.00192

GnomAD3 exomes AF: 0.00275 AC: 677 AN: 246348 Hom.: 7 AF XY: 0.00294 AC XY: 392 AN XY: 133458

Gnomad AFR exome AF: 0.000633

Gnomad AMR exome AF: 0.00144

Gnomad ASJ exome AF: 0.00111

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00317

Gnomad FIN exome AF: 0.00125

Gnomad NFE exome AF: 0.00423

Gnomad OTH exome AF: 0.00249

GnomAD4 exome AF: 0.00312 AC: 4554 AN: 1460302 Hom.: 16 Cov.: 32 AF XY: 0.00319 AC XY: 2314 AN XY: 726306

Gnomad4 AFR exome AF: 0.000329

Gnomad4 AMR exome AF: 0.00132

Gnomad4 ASJ exome AF: 0.000959

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00281

Gnomad4 FIN exome AF: 0.00173

Gnomad4 NFE exome AF: 0.00356

Gnomad4 OTH exome AF: 0.00273

GnomAD4 genome AF: 0.00281 AC: 428 AN: 152278 Hom.: 1 Cov.: 31 AF XY: 0.00254 AC XY: 189 AN XY: 74438

Gnomad4 AFR AF: 0.000650

Gnomad4 AMR AF: 0.000458

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00186

Gnomad4 FIN AF: 0.00207

Gnomad4 NFE AF: 0.00517

Gnomad4 OTH AF: 0.00190

Alfa AF: 0.00414 Hom.: 4

Bravo AF: 0.00225

TwinsUK AF: 0.00216 AC: 8

ALSPAC AF: 0.00311 AC: 12

ESP6500AA AF: 0.00136 AC: 6

ESP6500EA AF: 0.00419 AC: 36

ExAC AF: 0.00268 AC: 326

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:13 Uncertain:7 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:4 Uncertain:1 Benign:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 12, 2018	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 07, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2023	PEX6: PM3:Very Strong, PM5, PM2:Supporting, PS3:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 12, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Jan 04, 2017	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 10, 2023	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) -

Heimler syndrome 2 Pathogenic:3

Pathogenic, no assertion criteria provided	literature only	OMIM	Oct 01, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 30, 2023	- -
Pathogenic, criteria provided, single submitter	research	Leeds Amelogenesis Imperfecta Research Group, University of Leeds	Oct 01, 2015	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 -

not specified Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Mar 29, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 14, 2023	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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital	Mar 11, 2020	- -

Peroxisome biogenesis disorder 4A (Zellweger);C3553937:Peroxisome biogenesis disorder 4B;C4225267:Heimler syndrome 2 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Institute of Immunology and Genetics Kaiserslautern	Mar 18, 2024	ACMG Criteria: PS3, PS4, PM3, PP3, PP5; Individual was compound heterozygous for PEX6 variants c.1314_1321del and c.1802G>A -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 12, 2018	- -

Peroxisome biogenesis disorder 4A (Zellweger) Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Aug 28, 2017	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	Sep 25, 2019	- -

PEX6-related disorder Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Jan 02, 2024	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	Nov 19, 2019	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. -

Peroxisome biogenesis disorder 4B Pathogenic:1

Likely pathogenic, criteria provided, single submitter

research

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Mar 17, 2024

- -

Peroxisome biogenesis disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Nov 01, 2022

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. -

Retinal dystrophy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Blueprint Genetics

Feb 08, 2019

- -

Peroxisome biogenesis disorder 4A (Zellweger);C3553937:Peroxisome biogenesis disorder 4B Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Counsyl

Nov 21, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.34
BayesDel_addAF	Uncertain	0.10	D
BayesDel_noAF	Pathogenic	0.38
Cadd	Pathogenic	29
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.55	D;.
Eigen	Pathogenic	0.96
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.92	D;D
M_CAP	Pathogenic	0.49	D
MetaRNN	Benign	0.12	T;T
MetaSVM	Pathogenic	0.81	D
MutationAssessor	Pathogenic	3.3	M;M
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.52	T
PROVEAN	Uncertain	-3.3	D;D
REVEL	Pathogenic	0.85
Sift	Uncertain	0.0010	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;.
Vest4		0.96
MVP		0.94
MPC		0.66
ClinPred		0.083	T
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.92
gMVP		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs34324426; hg19: chr6-42935188; COSMIC: COSV104547784; COSMIC: COSV104547784;