ClinVar Genomic variation as it relates to human health

The p.Ser258Leu variant in ALG1 has been reported in at least 10 homozygous and 14 compound heterozygous individuals with a congenital disorder of glycosylation (Grubenmann 2004, Schwarz 2004, Kranz 2004, Harshman 2016, Ng 2016, Park 2016, Barba 2016, and Bowling 2017), and has also been reported in ClinVar (Variation ID#4724). In vitro functional studies provide evidence that the p.Ser258ZLeu var iant impacts the protein (Grubenmann 2004, Schwarz 2004, Kranz 2004, and Ng 2016 ). This variant has been identified in 0.05% (67/126078) of European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; d bSNP rs28939378). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency . In summary, although additional studies are required to fully establish its c linical significance, the p.Ser258Leu variant is pathogenic for congenital disor ders of glycosylation in an autosomal recessive manner based on functional studi es and its occurrence in individuals with this disease.

Variant summary: ALG1 c.773C>T (p.Ser258Leu) results in a non-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 0.0003 in 250018 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in ALG1 causing Congenital Disorder Of Glycosylation Type 1K (0.0003 vs 0.0011), allowing no conclusion about variant significance. c.773C>T has been reported in the literature in multiple individuals affected with Congenital Disorder Of Glycosylation Type 1K both in the homozygous and compound heterozygous state (Han_2020, Kranz_2004, Ng_2016). Functional studies have shown the variant to disrupt normal ALG1 enzymatic function (eg. Kranz_2004). 12 clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.031%). The variant is in trans with NM_019109.5:c.826C>T. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.61; 3Cnet: 0.25). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000004724). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

Published functional studies demonstrate a damaging effect (Grubenmann et al., 2004); 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: 21228398, 14709599, 26931382, 14973782, 27325525, 28554332, 30609409, 31618474, 31994750, 32573669)

This variant has been previously reported as a compound heterozygous and homozygous change in patients with Congenital disorder of glycosylation, type Ik (PMID: 14709599, 27325525, 26931382), and as a compound heterozygous change in patients with seizure disorders (PMID: 28554332, 31618474). This variant could not rescue growth in an alg-1 deficient yeast strain, suggesting that the variant affects protein function (PMID: 14709599, 26931382). It is present in the heterozygous state in the gnomAD population database at a frequency of .03% (87/281390) and thus is presumed to be rare. The c.773C>T (p.Ser258Leu) variant is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.773C>T (p.Ser258Leu) variant is classified as Pathogenic.

This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 258 of the ALG1 protein (p.Ser258Leu). This variant is present in population databases (rs28939378, gnomAD 0.05%). This missense change has been observed in individuals with congenital disorder of glycosylation (PMID: 14709599, 14973778, 14973782, 20679665, 22966035, 26931382, 27172925, 27325525, 28554332). ClinVar contains an entry for this variant (Variation ID: 4724). 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 not expected to disrupt ALG1 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects ALG1 function (PMID: 14973778, 22966035, 26931382). For these reasons, this variant has been classified as Pathogenic.

The ALG1 c.773C>T; p.Ser258Leu variant (rs28939378) is reported in the literature in the compound heterozygous or homozygous state in individuals affected with congenital disorders of glycosylation (Barba 2016, Bell 2011, Bowling 2017, Grubenmann 2004, Han 2020, Harshman 2016, Kranz 2004, Lipinski 2021, Ng 2016, Schwarz 2004). Functional analyses demonstrate reduced enzyme function (Grubenmann 2004, Kranz 2004, Ng 2016, Schwarz 2004). This variant is also reported in ClinVar (Variation ID: 4724), and is found in the general population with an overall allele frequency of 0.031% (87/281390 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.615). Based on available information, this variant is considered to be pathogenic. References: Barba C et al. Congenital disorders of glycosylation presenting as epileptic encephalopathy with migrating partial seizures in infancy. Dev Med Child Neurol. 2016 Oct;58(10):1085-91. PMID: 27172925. Bell CJ et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med. 2011 Jan 12;3(65):65ra4. PMID: 21228398. Bowling KM et al. Genomic diagnosis for children with intellectual disability and/or developmental delay. Genome Med. 2017 May 30;9(1):43. PMID: 28554332. Grubenmann CE et al. Deficiency of the first mannosylation step in the N-glycosylation pathway causes congenital disorder of glycosylation type Ik. Hum Mol Genet. 2004 Mar 1;13(5):535-42. PMID: 14709599. Han J et al. Rapid prenatal diagnosis of skeletal dysplasia using medical trio exome sequencing: Benefit for prenatal counseling and pregnancy management. Prenat Diagn. 2020 Apr;40(5):577-584. PMID: 31994750. Harshman LA et al. Congenital nephrotic syndrome in an infant with ALG1-congenital disorder of glycosylation. Pediatr Int. 2016 Aug;58(8):785-8. PMID: 27325525. Kranz C et al. Congenital disorder of glycosylation type Ik (CDG-Ik): a defect of mannosyltransferase I. Am J Hum Genet. 2004 Mar;74(3):545-51. PMID: 14973782. Lipinski P et al. Congenital disorders of glycosylation: Prevalence, incidence and mutational spectrum in the Polish population. Mol Genet Metab Rep. 2021 Feb 11;27:100726. PMID: 33643843. Ng BG et al. ALG1-CDG: Clinical and Molecular Characterization of 39 Unreported Patients. Hum Mutat. 2016 Jul;37(7):653-60. PMID: 26931382. Schwarz M et al. Deficiency of GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase causes congenital disorder of glycosylation type Ik. Am J Hum Genet. 2004 Mar;74(3):472-81. PMID: 14973778.

The c.773C>T (p.S258L) alteration is located in exon 7 (coding exon 7) of the ALG1 gene. This alteration results from a C to T substitution at nucleotide position 773, causing the serine (S) at amino acid position 258 to be replaced by a leucine (L). Based on data from gnomAD, the T allele has an overall frequency of 0.03% (87/281390) total alleles studied. The highest observed frequency was 0.05% (68/128302) of European (non-Finnish) alleles. This alteration was detected in the homozygous state and in conjunction with another alteration in ALG1 in multiple individuals with ALG1-related congenital disorder of glycosylation (Grubenmann, 2004; Kranz, 2004; Schwarz, 2004; Dupre, 2010; Morava, 2012; Barba, 2016; Ng, 2016; Han, 2020). This amino acid position is well conserved in available vertebrate species. Functional assays in yeast and patient-derived fibroblasts show <10% enzymatic activity in the biosynthesis of lipid-linked oligosaccharides (Kranz, 2004; Schwarz, 2004; Grubenmann, 2004; Dupre, 2010). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with congenital disorder of glycosylation, type Ik (MIM#608540). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from serine to leucine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (87 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported as homozygous or compound heterozygous in many individuals with type I congenital disorder of glycosylation (PMID: 26931382). It has also been reported as likely pathogenic/pathogenic many times in ClinVar. (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Variant interpreted as Pathogenic and reported on 01-08-2021 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.