rs1131691916
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000033.4(ABCD1):c.565C>T(p.Arg189Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 11/19 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R189Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000033.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.565C>T | p.Arg189Trp | missense_variant | 1/10 | ENST00000218104.6 | |
ABCD1 | XM_047441916.1 | c.565C>T | p.Arg189Trp | missense_variant | 1/11 | ||
ABCD1 | XM_047441917.1 | c.565C>T | p.Arg189Trp | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.565C>T | p.Arg189Trp | missense_variant | 1/10 | 1 | NM_000033.4 | P1 | |
ABCD1 | ENST00000370129.4 | c.10C>T | p.Arg4Trp | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 26
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 26
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Pathogenic:5
Likely pathogenic, criteria provided, single submitter | clinical testing | 3billion | Jan 03, 2022 | Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000430349, PMID:10737980, PS1_S). A different missense change at the same codon has been reported to be associated with ABCD1 related disorder (PM5_P). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.969, 3CNET: 0.986, PP3_P). A missense variant is a common mechanism associated with Adrenomyeloneuropathy (PP2_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust | Jan 27, 2021 | Criteria Codes: PS4_Mod PM2 PP3 PP4 - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2022 | For these reasons, this variant has been classified as Pathogenic. 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 ABCD1 protein function. ClinVar contains an entry for this variant (Variation ID: 430349). This missense change has been observed in individuals with clinical features of ABCD1-related conditions (PMID: 10737980, 15811009, 30069915). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 189 of the ABCD1 protein (p.Arg189Trp). - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 30, 2023 | - - |
not provided Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jul 06, 2018 | The R189W variant in the ABCD1 gene has been reported previously in at least two individuals with adrenoleukodystrophy, including one individual with Addison disease and one with adrenomyeloneuropathy (Lachtermacher et al., 2000; Coll et al., 2005). The R189W variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R189W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. R189W is reported as pathogenic variant in the ALD Database, as is another missense variant at the same position, supporting the functional importance of this residue. Additionally, missense variants in nearby residues (L190P, D194H, and D194N) have been reported in the Human Gene Mutation Database in association with adrenoleukodystrophy (Stenson et al., 2014). We interpret R189W as a likely pathogenic variant. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 29, 2023 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Oct 23, 2020 | - - |
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 17, 2018 | The p.R189W variant (also known as c.565C>T), located in coding exon 1 of the ABCD1 gene, results from a C to T substitution at nucleotide position 565. The arginine at codon 189 is replaced by tryptophan, an amino acid with dissimilar properties. This variant was identified in one individual with Addison disease and one individual with adrenomyeloneuropathy; both individuals had elevated very long chain fatty acid plasma concentrations (Lachtermacher MB et al. Hum. Mutat., 2000;15:348-53; Coll MJ et al. Clin. Genet., 2005 May;67:418-24). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at