rs374304304 — ASL ASL Arg94Cys

ASL Arg94Cys — A Pathogenic Variant in the Urea Cycle's Second Recycling Step

Every gram of protein you eat generates ammonia as a byproduct of amino acid catabolism. Left unchecked, ammonia is neurotoxic — even modest elevations cause brain swelling, seizures, and coma. The urea cycle exists specifically to neutralize this threat, converting ammonia into urea for renal excretion across five enzymatic steps. Step four is catalysed by argininosuccinate lyase¹¹ argininosuccinate lyase
ASL — encoded by the ASL gene on chromosome 7q11.21. The enzyme cleaves argininosuccinate into arginine and fumarate, regenerating the arginine used by arginase in the final urea cycle step. The rs374304304 variant (c.280C>T) swaps a cysteine for an arginine at position 94 of the ASL protein, reducing enzyme activity to approximately 12% of normal and placing the gene squarely in the category of established pathogenic variants for argininosuccinic aciduria²² argininosuccinic aciduria
ASLD — also called argininosuccinate lyase deficiency. The second most common urea cycle disorder, with a prevalence of ~1 in 70,000 live births globally (ASLD).

The Mechanism

The p.Arg94Cys substitution replaces a positively charged arginine with a cysteine at a structurally conserved residue of the ASL tetramer interface. Cell-based assays³³ Cell-based assays
Inauen KV et al. Effect of cysteamine on mutant ASL proteins with cysteine for arginine substitutions. Mol Diagn Ther, 2016 showed that the Arg94Cys enzyme retains only approximately 12% of wild-type catalytic activity. The substitution introduces a free thiol group where none normally exists, disrupting the active-site geometry required for argininosuccinate cleavage. Interestingly, treatment with cysteamine — a compound that chemically reacts with free cysteines — increased Arg94Cys ASL activity by 64% in these assays, pointing toward the cysteine residue as the proximate functional defect and suggesting a potential avenue for pharmacological rescue.

Beyond its role in ureagenesis, ASL also participates in endothelial nitric oxide synthesis. The enzyme channels arginine directly to nitric oxide synthase (NOS) through a protein–protein interaction. In ASLD, this channelling defect⁴⁴ channelling defect
Kho J et al. Argininosuccinate lyase deficiency causes an endothelial-dependent form of hypertension. Am J Hum Genet, 2018 reduces local NO production in blood vessel walls independently of circulating arginine levels, causing endothelial dysfunction and a form of hypertension that does not respond reliably to arginine supplementation alone.

The Evidence

ASLD was classified in GeneReviews and ClinVar as an established pathogenic condition decades before rs374304304 was formally catalogued. ClinVar (VCV000092359) lists the Arg94Cys variant as Pathogenic/Likely pathogenic with criteria provided by ten independent diagnostic laboratories — Baylor Genetics, Fulgent, GeneDx, Labcorp Genetics (Invitae), LabCorp Women's Health, Natera, Myriad Genetics, Revvity Omics, Eurofins Ntd, and Sinai Health System — with no classification conflicts. The variant is associated exclusively with argininosuccinic aciduria.

Nagamani et al.⁵⁵ Nagamani et al.
Nagamani SC, Erez A, Lee B. Argininosuccinate lyase deficiency. Genet Med, 2012 reviewed the full clinical spectrum of ASLD: neonatal-onset with life-threatening hyperammonemia (ammonia ≥1000 µmol/L without treatment) in the most severe genotypes, and late-onset with episodic hyperammonemia triggered by illness or stress in milder cases. Critically, there is no reliable genotype–phenotype correlation — enzyme activity alone does not predict disease severity, making the clinical course difficult to forecast from the variant alone.

Long-term complications extend well beyond hyperammonemia. Burrage et al.⁶⁶ Burrage et al.
Burrage LC et al. Chronic liver disease and impaired hepatic glycogen metabolism in argininosuccinate lyase deficiency. JCI Insight, 2020 found elevated ALT in 37% of ASLD patients and documented liver fibrosis on histology even when aminotransferases were normal. A 2023 retrospective study⁷⁷ 2023 retrospective study
Elkhateeb N et al. Natural history of epilepsy in argininosuccinic aciduria. Epilepsia, 2023 found epilepsy in 60% of ASLD patients, with 27% showing pharmacoresistant seizures. Systemic hypertension was characterised mechanistically in an endothelial-specific mouse model⁸⁸ endothelial-specific mouse model
Kho J et al., Am J Hum Genet, 2018 as a direct consequence of impaired endothelial nitric oxide production — a systemic manifestation that is not corrected by conventional dietary management.

Practical Actions

For biallelic ASLD (homozygous or compound heterozygous), long-term management requires protein restriction — dietary protein is typically limited to the minimum requirement for age, with the remainder of energy needs supplied as non-protein calories. Arginine base supplementation (100–300 mg/kg/day in children; 2.2–5.5 g/m²/day in adults) replenishes the arginine that would normally be released by the intact urea cycle. Arginine base is preferred over arginine hydrochloride to avoid metabolic acidosis with chronic use.

Affected individuals require metabolic monitoring every 2–4 weeks in the first year, tapering to every 3–4 months in stable older children and adults: plasma ammonia, plasma amino acids (particularly argininosuccinate and citrulline), liver function tests (ALT, AST, albumin, INR), blood pressure, and serum potassium. Liver ultrasound every 1–2 years is recommended given the high rate of subclinical liver disease.

Acute hyperammonemic crises require emergency management — protein is immediately stopped, intravenous glucose and lipids provide energy, and intravenous nitrogen scavengers (sodium benzoate/phenylacetate) are used. Severe cases may require dialysis.

For heterozygous carriers, no metabolic treatment is indicated. The primary significance is reproductive.

Interactions

ASLD is caused by biallelic loss of ASL function — most patients are compound heterozygous for two different pathogenic ASL variants rather than homozygous for a single variant. When a carrier of Arg94Cys (CT genotype) has a partner who also carries any pathogenic ASL variant, each pregnancy faces a 25% risk of ASLD. The combination of two pathogenic ASL alleles — regardless of which specific variants — determines clinical disease. Cascade carrier testing of first-degree relatives of any confirmed ASLD patient is therefore standard practice.