Table 1. Variants identified in PEX6 and PEX1 in individuals with HS.
Family | Gene | Variant | Type of variant (DNA level) | Predicted amino acid change | CADDv1.3a | Reference | Alleles dbSNP142b | Alleles EVSc | AllelesExACd |
---|---|---|---|---|---|---|---|---|---|
1 | PEX6e | c.654C>G | Non-synonymous SNV | p.(F218L) | 23.8 | None | N/A | N/A | N/A |
1, 2 and 3 | PEX6e | c.1802G>A | Non-synonymous SNV | p.(R601Q) | 35 | Yik et al.,8 Ebberink et al.,9 Ratbi et al.6 | rs34324426; 5/5008 | 42/13006 | 316/98988(includes 4 homozygotes) |
2 | PEX6e | c.275T>G | Non-synonymous SNV | p.(V92G) | 22.9 | None | N/A | N/A | N/A |
3 | PEX6e | c.296G>T | Non-synonymous SNV | p.(R99L) | 29.4 | None | N/A | N/A | N/A |
4 | PEX6e | c.1314_1321delGGAGGCCT | Eight nucleotide deletion | p.(E439Gfs*3) | 33 | Krause et al.,22 Ebberink et al.21 | rs267608216; no allele frequency stated | 1/12518 | 4/121224 |
4 | PEX6e | c.2714G>T | Non- synonymous SNV | p.(C905F) | 34 | None | N/A | N/A | N/A |
5 | PEX6e | c.1715C>T | Non- synonymous SNV | p.(T572I) | 23.5 | Raas-Rothschild et al.,23 Ebberink et al. 21 | rs61753224; no allele frequency stated | N/A | N/A |
6 | PEX1f | c.1792delA | Single-nucleotide deletion | p.(Q598Tfs*11) | 35 | None | N/A | N/A | N/A |
6 | PEX1f | c.2966T>C | Non- synonymous SNV | p.(I989T) | 29.6 | Maxwell et al.,24 | rs61750427; 2/10016 | N/A | 6/120686 |
For each variant, its CADDv1.3 score (a measure of deleteriousness) is stated and it is indicated whether the variant has been described before, either in a publication or in a database of human variation. If identified, the frequency of the variant in the database studied is stated as the number of reported variant alleles over the total number of alleles sequenced at that locus.
All databases were accessed 7 March 2016.
Combined Annotation Dependent Depletion (CADD) v1.3 (http://cadd.gs.washington.edu/info).
Database of Single Nucleotide Polymorphisms build ID: 142 (dbSNP142), Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine (http://www.ncbi.nlm.nih.gov/SNP/).
Exon Variant Server (EVS) (http://evs.gs.washington.edu/EVS/) version 0.3
Exome Aggregation Consortium (ExAC), Cambridge, MA (http://exac.broadinstitute.org).
PEX6: Ensembl: ENST00000304611 or GenBank: NM_000287.3.
PEX1: Ensembl: ENST00000248633 or GenBank: NM_000466.2.