rs121434233
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_021628.3(ALOXE3):c.700C>T(p.Arg234*) variant causes a stop gained change. The variant allele was found at a frequency of 0.000142 in 1,614,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
ALOXE3
NM_021628.3 stop_gained
NM_021628.3 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 3.69
Genes affected
ALOXE3 (HGNC:13743): (arachidonate lipoxygenase 3) This gene is a member of the lipoxygenase family, which are catabolized by arachidonic acid-derived compounds. The encoded enzyme is a hydroperoxide isomerase that synthesizes a unique type of epoxy alcohol (8R-hydroxy-11R,12R-epoxyeicosa-5Z,9E,14Z-trienoic acid) from 12R-hydroperoxyeicosatetraenoic acid (12R-HPETE). This epoxy alcohol can activate the the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARalpha), which is implicated in epidermal differentiation. Loss of function of the enzyme encoded by this gene results in ichthyosis, implicating the function of this gene in the differentiation of human skin. This gene is part of a cluster of lipoxygenase genes on 17p13.1. Mutations in this gene result in nonbullous congenital ichthyosiform erythroderma (NCIE). Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-8112177-G-A is Pathogenic according to our data. Variant chr17-8112177-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 3408.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-8112177-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALOXE3 | NM_021628.3 | c.700C>T | p.Arg234* | stop_gained | 7/16 | ENST00000448843.7 | NP_067641.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALOXE3 | ENST00000448843.7 | c.700C>T | p.Arg234* | stop_gained | 7/16 | 1 | NM_021628.3 | ENSP00000400581.2 | ||
ALOXE3 | ENST00000380149.6 | c.700C>T | p.Arg234* | stop_gained | 6/15 | 1 | ENSP00000369494.2 | |||
ALOXE3 | ENST00000318227.4 | c.700C>T | p.Arg234* | stop_gained | 7/16 | 2 | ENSP00000314879.4 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152152Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000147 AC: 37AN: 251482Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135916
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GnomAD4 exome AF: 0.000144 AC: 211AN: 1461850Hom.: 0 Cov.: 31 AF XY: 0.000179 AC XY: 130AN XY: 727224
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GnomAD4 genome AF: 0.000125 AC: 19AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74444
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:9Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:6
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 05, 2024 | This sequence change creates a premature translational stop signal (p.Arg234*) in the ALOXE3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ALOXE3 are known to be pathogenic (PMID: 11773004, 19890349, 27025581). This variant is present in population databases (rs121434233, gnomAD 0.03%). This premature translational stop signal has been observed in individual(s) with autosomal recessive congenital ichthyosis (PMID: 11773004, 27025581). ClinVar contains an entry for this variant (Variation ID: 3408). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 01, 2023 | Several patients who were compound heterozygous for R234* and the pathogenic P630L variant were reported to have self-improving collodion ichthyosis (Vahlquist et al., 2010; Hotz et al., 2021); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 19890349, 25525159, 11773004, 19131948, 31589614, 33435499, 16116617, 34908195, 27025581) - |
Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Autosomal recessive congenital ichthyosis 3 Pathogenic:2Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2009 | - - |
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpretted as Pathogenic and reported on 01-06-2020 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Pathogenic, no assertion criteria provided | clinical testing | Institute for Human Genetics, University Medical Center Freiburg | Jan 07, 2021 | - - |
ALOXE3-related disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 05, 2024 | The ALOXE3 c.700C>T variant is predicted to result in premature protein termination (p.Arg234*). This variant has been reported in the homozygous or compound heterozygous state in at least 2 affected individuals with congenital Ichthyosis (Family A2, Figure 1, Jobard et al. 2002. PubMed ID: 11773004; Patient 91, Table S1, Pigg et al. 2016. PubMed ID: 27025581). This variant is reported in 0.029% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Nonsense variants in ALOXE3 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at