ClinVar Genomic variation as it relates to human health

The p.Gly390Arg variant in AAS1 has been reported in >30 individuals with citrullinemia type I (both in the homozygous and compound heterozygous state) and segregated with disease in at least 5 affected relatives from 5 families. It is the most common variant identified in patients with the classical phenotype (Vilaseca 2001 PMID: 11708871, Gao 2003 PMID: 12815590, Berning 2008 PMID: 18473344, Engel 2009 PMID: 19006241, Laróvere 2009 PMID: 19358837, Laróvere 2012 PMID: 23430935). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID: 6329) and has been identified in 0.06% (3/4828) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). In vitro functional studies provide some evidence that this variant impacts protein function, demonstrating less than 2% of wild type argininosuccinate synthetase activity (Berning 2008 PMID: 18473344, Shaheen 1994PMID: 8792870) and computational prediction tools and conservation analyses are consistent with pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive citrullinemia type I. ACMG/AMP Criteria applied: PM3_Very Strong, PP1_Moderate, PS3_Supporting, PP3.

Variant summary: The ASS1 c.1168G>A variant affects a conserved nucleotide, resulting in amino acid change from Gly to Arg. Gly390 is located in a-helix 12 and is important for intermolecular contact of the multimerization tails, and 5/5 in-silico tools predict damaging outcome for this variant. The enzymatic ASS activity of G390R was shown to be below 2% of the wild-type protein (Berning_HM_2008). This variant was found in 45/113324 control chromosomes at a frequency of 0.0003971, which does not exceed maximal expected frequency of a pathogenic ASS1 allele (0.0040825). This variant is reported as the most common mutation in patients with the classic phenotype of citrullinemia. In addition, several clinical laboratories classified this variant as pathogenic. Taken together, this variant was classified as pathogenic.

NM_000050.4(ASS1):c.1168G>A(G390R) is classified as likely pathogenic in the context of citrullinemia type 1. Sources cited for classification include the following: PMID 18473344, 16475226, 12815590, and 7557970. Classification of NM_000050.4(ASS1):c.1168G>A(G390R) is based on the following criteria: There is strong evidence of association with the variant and the relevant disease and there is functional data showing deficient protein function. Please note: this variant was assessed in the context of healthy population screening.

Published functional studies demonstrate less than 2% of wild type argininosuccinate synthetase activity (Berning et al., 2008); 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: 27535533, 31469252, 31980526, 25433810, 7557970, 11941481, 30848473, 11708871, 8792870, 19006241, 12815590, 23430935, 19358837, 2358466, 28741715, 16421053, 28132756, 27287393, 22975760, 25087612, 18473344, 16475226)

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 390 of the ASS1 protein (p.Gly390Arg). This variant is present in population databases (rs121908641, gnomAD 0.1%). This missense change has been observed in individuals with citrullinemia type I (PMID: 11708871, 12815590, 18473344, 19006241, 19358837, 23430935). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 6329). 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 ASS1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects ASS1 function (PMID: 8792870, 18473344). For these reasons, this variant has been classified as Pathogenic.

The c.1168G>A (p.G390R) alteration is located in exon 15 (coding exon 13) of the ASS1 gene. This alteration results from a G to A substitution at nucleotide position 1168, causing the glycine (G) at amino acid position 390 to be replaced by an arginine (R). Based on data from gnomAD, the A allele has an overall frequency of 0.03% (86/282044) total alleles studied. The highest observed frequency was 0.11% (32/30412) of South Asian alleles. This mutation has been reported in the homozygous and compound heterozygous states in patients with citrullinemia and is the most commonly reported mutation in multiple cohorts worldwide (Gao, 2003; Diez-Fernandez, 2017). This amino acid position is highly conserved in available vertebrate species. In vitro studies demonstrate that this mutation results in significantly reduced enzymatic activity in multiple cell types (Berning, 2008; Zielonka, 2019). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PM3,PP3,PP4.

The c.1168G>A (p.Gly390Arg) missense variant in ASS1 gene has been reported in homozygous state in individuals affected with citrullinemia (Laróvere et al., 2012). Experimental studies have shown that this variant disrupts the function and substantially reduces the activity of the encoded enzyme in vitro (Berning et al., 2008). This variant is reported with the allele frequency (0.03%) in the gnomad and novel in 1000 genome database. This variant has been reported to the ClinVar database as Pathogenic/Likely Pathogenic. The amino acid Gly at position 390 is changed to a Arg changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.

The observed variant c.1168G>A (p.Gly390Arg) is not reported in 1000 Genomes and has a minor allele frequency of 0.00040 in ExAC databases. The in silico prediction of the variant is disease causing by MutationTaster2, damaging by SIFT and probably damaging by Polyphen2.