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CAD
carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase
CAD is located on the short (p) arm of chromosome 2, at band 2p23.3. Arm ratio per GRCh38 - banding schematic.
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Overview
CAD is located on chromosome 2 and encodes a 2,225 amino acid multifunctional protein critical for cellular nucleotide metabolism. The enzyme catalyses the initial three reactions in the de novo pyrimidine synthesis pathway, converting glutamine, bicarbonate, and aspartate into dihydroorotate. Because pyrimidines are essential components of DNA and RNA, CAD activity is indispensable for cell division, gene expression, and normal development. Pathogenic variants are inherited in an autosomal recessive pattern, meaning affected individuals carry two altered copies of the gene. Loss of CAD function particularly impacts rapidly dividing tissues and the developing nervous system, where demand for nucleotides is highest.
What the gene does
The CAD protein operates as a molecular assembly line, channelling substrates through three consecutive enzymatic domains without releasing intermediates. First, the glutamine amidotransferase (GATase) domain hydrolyses glutamine to release ammonia. This ammonia is then transferred to the carbamoyl phosphate synthase (CPSase) region, which uses two molecules of ATP to combine ammonia with bicarbonate, forming carbamoyl phosphate. The aspartate transcarbamylase (ATCase) domain subsequently condenses carbamoyl phosphate with aspartate to produce carbamoyl aspartate. Finally, the dihydroorotase (DHOase) region cyclises this intermediate into dihydroorotate, the precursor for all pyrimidine nucleotides including cytosine, thymine, and uracil. By housing all three activities within a single polypeptide chain, CAD enhances catalytic efficiency and prevents loss of unstable intermediates. The protein's activity is tightly regulated by feedback inhibition from downstream nucleotides, ensuring balanced nucleotide pools during periods of active cell growth and division.
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Chromosome location
CAD maps to chromosomal band 2p23.3 on the short arm of chromosome 2. The gene spans a substantial genomic region and encodes a transcript that produces the 2,225 amino acid multifunctional enzyme. This chromosomal location places CAD within a region containing several other genes involved in metabolic and developmental processes.
Protein structure
The CAD protein is organised into five major functional regions arrayed along its 2,225 amino acid length. The N-terminal GATase (glutamine amidotransferase) region spans amino acids 2-365 and contains a glutamine amidotransferase type-1 domain (residues 177-363) responsible for ammonia generation. A short linker region (amino acids 366-394) connects this to the CPSase (carbamoyl phosphate synthase) region (residues 395-1455), which is itself divided into CPSase A (amino acids 395-933) and CPSase B (amino acids 934-1455). Within CPSase, two ATP-grasp domains (residues 519-711 and 1052-1243) bind and hydrolyse ATP to drive carbamoyl phosphate formation, while an MGS-like domain (amino acids 1308-1462) assists in substrate binding. The DHOase (dihydroorotase) region (residues 1456-1788) catalyses ring closure to form dihydroorotate. Another linker (amino acids 1789-1917) containing a disordered region (residues 1811-1899) provides structural flexibility before the C-terminal ATCase (aspartate transcarbamylase) region (amino acids 1918-2225), which condenses carbamoyl phosphate with aspartate. This modular architecture allows the protein to coordinate substrate channelling across its three catalytic activities.
Key variants
Pathogenic variants in CAD typically result in reduced or absent enzyme activity, impairing pyrimidine biosynthesis. Both missense changes affecting catalytic residues and loss-of-function variants have been reported. Because CAD is inherited in an autosomal recessive manner, individuals with one pathogenic variant are typically asymptomatic carriers, while those with two pathogenic variants may develop clinical manifestations. The spectrum of variants includes changes distributed across the gene's functional domains, reflecting the critical role of each enzymatic activity.
Sample of pathogenic variants
10 pathogenic / likely-pathogenic variants from ClinVar, ranked by review status (expert-panel-reviewed first). This is a sample; recurrent founder variants in a specific population may not appear here - see the full ClinVar listing via the link above.
| Variant (HGVS) | Protein change | Classification | Evidence | Associated condition |
|---|---|---|---|---|
c.5296_5308del | p.Phe1766fs | Pathogenic | ★★☆☆ | not provided |
c.5365C>T | p.Arg1789Ter | Pathogenic | ★★☆☆ | Developmental and epileptic encephalopathy, 50 |
c.5429G>A | p.Arg1810Gln | Pathogenic/Likely pathogenic | ★★☆☆ | Infantile epileptic dyskinetic encephalopathy |
c.571C>T | p.Arg191Ter | Pathogenic | ★★☆☆ | Developmental and epileptic encephalopathy, 50 |
c.5737dup | p.Gln1913fs | Pathogenic/Likely pathogenic | ★★☆☆ | Developmental and epileptic encephalopathy, 50 |
c.98T>G | p.Met33Arg | Pathogenic | ★★☆☆ | Developmental and epileptic encephalopathy, 50 |
c.3596del | p.Phe1199fs | Pathogenic | ★☆☆☆ | Infantile epileptic dyskinetic encephalopathy |
c.4396G>T | p.Gly1466Ter | Pathogenic | ★☆☆☆ | not provided |
c.5441_5442del | p.Gln1814fs | Pathogenic | ★☆☆☆ | not provided |
c.736del | p.Arg246fs | Pathogenic | ★☆☆☆ | not provided |
Evidence stars indicate ClinVar review status. Individual variant interpretation should always be performed by a qualified clinical laboratory - many variants remain classified as Variants of Uncertain Significance (VUS) pending more research.
Associated conditions
Biallelic pathogenic variants in CAD are associated with a spectrum of neurodevelopmental phenotypes. Clinical features often include early-onset epilepsy, intellectual disability of varying severity, developmental delay, and cerebellar abnormalities such as ataxia or hypoplasia. The severity and specific combination of features can vary between affected individuals, even within the same family. These conditions reflect the essential role of pyrimidine metabolism in supporting normal brain development and function, where high rates of cell division and RNA synthesis are required during critical developmental windows.
No disease links recorded for this gene in our reference set.
Inheritance pattern
Conditions caused by pathogenic CAD variants typically follow autosomal recessive inheritance.
When both parents are carriers, each child has a 25% chance of being affected, 50% of being a carrier, and 25% of being unaffected.
UK clinical status
CAD is classified with green (high confidence) status on multiple NHS Genomic Medicine Service gene panels. It appears on the Ataxia and cerebellar anomalies - narrow panel, the DDG2P (Developmental Disorders Genotype-to-Phenotype) database, the Early onset or syndromic epilepsy panel (R59), and the Intellectual disability panel (R29). This inclusion reflects robust clinical and research evidence supporting the gene's role in these neurodevelopmental conditions, and CAD testing may be offered through NHS pathways when a patient's clinical presentation aligns with these phenotypes.
Sources: NHS GMS PanelApp · Genomics England PanelApp · NHS National Genomic Test Directory
Frequently asked questions
What does it mean to be a carrier of a CAD variant?
A carrier has one pathogenic variant in CAD and one normal copy. Carriers typically have no symptoms because the remaining functional copy produces sufficient enzyme activity. However, if both parents are carriers, each pregnancy has a 25% chance of inheriting two pathogenic variants and being affected.
How is CAD-related developmental disorder diagnosed?
Diagnosis involves clinical evaluation of developmental milestones, neurological examination, brain imaging to assess for cerebellar changes, and genetic testing to identify biallelic pathogenic variants in CAD. Testing is typically coordinated through specialist genetic or neurology services within the NHS.
Can pyrimidine synthesis disorders be treated?
Management is generally supportive, focusing on controlling seizures with appropriate antiepileptic medications, physiotherapy for motor difficulties, and educational support for intellectual disability. There is no current cure, and treatment aims to optimise quality of life and manage specific symptoms as they arise.