Total submissions: 13
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Counsyl | RCV000005832 | SCV000792595 | pathogenic | ALG6-congenital disorder of glycosylation 1C | 2017-07-05 | criteria provided, single submitter | clinical testing | |
Fulgent Genetics, |
RCV000005832 | SCV000894082 | pathogenic | ALG6-congenital disorder of glycosylation 1C | 2021-12-07 | criteria provided, single submitter | clinical testing | |
Illumina Laboratory Services, |
RCV000005832 | SCV000915431 | pathogenic | ALG6-congenital disorder of glycosylation 1C | 2018-08-09 | criteria provided, single submitter | clinical testing | The ALG6 c.998C>T (p.Ala333Val) missense variant is reported to be the most common cause of congenital disorders of glycosylation (CDG) (Drijvers et al. 2010; Ichikawa et al. 2013). Across a selection of the available literature, the p.Ala333Val variant has been reported in a total of eight individuals with CDG, including in four homozygotes, comprised of two sibling pairs who are cousins, and in four unrelated compound heterozygotes. This variant was also identified in a heterozygous state in five unaffected parents of the probands (Imbach et al. 1999; Westphal et al. 2000; Drijvers et al. 2010; Ichikawa et al. 2013; Dercksen et al. 2013). The p.Ala333Val variant was absent from controls but is reported at a frequency of 0.000075 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies in yeast with a hypoglycosylation phenotype showed that the p.Ala333Val variant was able to only partially restore glycosylation, whereas glycosylation was fully restored with the wild type protein (Imbach et al. 1999; Westphal et al. 2000). Based on the collective evidence, the p.Ala333Val variant is classified as pathogenic for congenital disorders of glycosylation. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. |
Labcorp Genetics |
RCV000005832 | SCV001213979 | pathogenic | ALG6-congenital disorder of glycosylation 1C | 2023-12-18 | criteria provided, single submitter | clinical testing | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 333 of the ALG6 protein (p.Ala333Val). This variant is present in population databases (rs121908443, gnomAD 0.006%). This missense change has been observed in individual(s) with ALG6-congenital disorder of glycosylation (CDG-Ic) (PMID: 10359825, 10914684, 11106564, 20447155, 23430515, 27287710). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 5497). 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 ALG6 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects ALG6 function (PMID: 10359825, 10914684, 11106564). For these reasons, this variant has been classified as Pathogenic. |
Gene |
RCV001547693 | SCV001767459 | pathogenic | not provided | 2022-02-27 | criteria provided, single submitter | clinical testing | Published functional studies demonstrate that the A333V variant severely impairs ALG6 protein function and leads to incomplete CPY glycosylation (Imbach et al., 2000; Westphal et al., 2003); Not observed at a significant frequency in large population cohorts (gnomAD); 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: 23430515, 27287710, 10852543, 12855228, 11106564, 20447155, 10359825, 10914684, 14517965, 23044053, 15771971, 31589614, 33413482, 31991610) |
Prevention |
RCV003407284 | SCV004114863 | pathogenic | ALG6-related disorder | 2023-04-21 | criteria provided, single submitter | clinical testing | The ALG6 c.998C>T variant is predicted to result in the amino acid substitution p.Ala333Val. This variant has been reported to be causative for congenital disorder of glycosylation 1c when present in the homozygous or compound heterozygous state (Imbach et al. 1999. PubMed ID: 10359825; Westphal et al. 2000. PubMed ID: 11106564). This variant is reported in 0.0062% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-63885051-C-T). This variant is interpreted as pathogenic. |
Baylor Genetics | RCV000005832 | SCV004197188 | pathogenic | ALG6-congenital disorder of glycosylation 1C | 2024-03-02 | criteria provided, single submitter | clinical testing | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000005832 | SCV005395145 | pathogenic | ALG6-congenital disorder of glycosylation 1C | 2024-09-09 | criteria provided, single submitter | clinical testing | Variant summary: ALG6 c.998C>T (p.Ala333Val) results in a non-conservative amino acid change in the encoded protein sequence. Three of three in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.4e-05 in 249886 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in ALG6 causing Congenital Disorder Of Glycosylation Type 1C (4.4e-05 vs 0.0011), allowing no conclusion about variant significance. c.998C>T has been reported in the literature in the homozygous and compound heterozygous states in multiple individuals affected with Congenital Disorder Of Glycosylation Type 1C and segregated with disease in at least one family (vandenBoogert_2019, Imbach_1999). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence that this variant impacts protein function in yeast (Imbach_1999). The following publications have been ascertained in the context of this evaluation (PMID: 10359825, 31117816). ClinVar contains an entry for this variant (Variation ID: 5497). Based on the evidence outlined above, the variant was classified as pathogenic. |
OMIM | RCV000005832 | SCV000026014 | pathogenic | ALG6-congenital disorder of glycosylation 1C | 1999-06-08 | no assertion criteria provided | literature only | |
Natera, |
RCV000005832 | SCV001456284 | pathogenic | ALG6-congenital disorder of glycosylation 1C | 2020-09-16 | no assertion criteria provided | clinical testing | |
Genome Diagnostics Laboratory, |
RCV001547693 | SCV001809161 | pathogenic | not provided | no assertion criteria provided | clinical testing | ||
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, |
RCV001547693 | SCV001957079 | pathogenic | not provided | no assertion criteria provided | clinical testing | ||
Clinical Genetics DNA and cytogenetics Diagnostics Lab, |
RCV001547693 | SCV001964941 | likely pathogenic | not provided | no assertion criteria provided | clinical testing |