Fetal anomalies
Gene: CPS1 Red List (low evidence)Red List (low evidence)
Presents post-natally.Created: 10 Feb 2022, 1:27 a.m. | Last Modified: 10 Feb 2022, 1:27 a.m.
Panel Version: 0.3235
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Carbamoylphosphate synthetase I deficiency MIM#237300
Red List (low evidence)
Metabolic disorder with two main forms: a lethal neonatal type and a less severe, delayed-onset type. Carbamoyl phosphate synthetase I deficiency is an autosomal recessive inborn error of metabolism of the urea cycle which causes hyperammonemia.
PMID:8486760
Identified a homozygous missense mutation in a newborn Japanese girl with CPS I deficiency.
PMID:17310273
Identified 25 different mutations in the CPS1 gene, including 19 novel mutations n 16 of 18 in Japanese patients with a clinical diagnosis of CPS I deficiency. Two patients with confirmed CPS I deficiency had later onset at ages 13 and 31 years, respectively. Genotype/phenotype correlations were not observed.
PMID:21120950
By analyzing tissue and DNA samples from 205 individuals with CPS I deficiency spanning 24 years, Haberle et al. (2011) identified 192 different pathogenic mutations in the CPS1 gene, including 130 novel mutations. When combined with previously reported mutations, it was clear that most mutations (90%) were private, occurring in only 1 family each. The few recurrent mutations tended to occur at CpG dinucleotides. Most missense mutations occurred around exon 24, at the boundary between both homologous halves of the region encoding the 120-kD catalytic moiety of the enzyme. Mutations also clustered at the bicarbonate and carbamate phosphorylation domains, at the NAG cofactor binding domain, and at the interface between the large and small subunit-like moieties. Comparative modeling using the E. coli enzyme showed that the location of missense mutations correlated with evolutionary importance and included internal residues, suggesting that they affect protein folding.Created: 9 Feb 2022, 11:46 p.m. | Last Modified: 9 Feb 2022, 11:46 p.m.
Panel Version: 0.3235
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Carbamoylphosphate synthetase I deficiency MIM#237300
Publications
Variants in this GENE are reported as part of current diagnostic practice
Gene: cps1 has been classified as Red List (Low Evidence).
Phenotypes for gene: CPS1 were changed from CARBAMOYL PHOSPHATE SYNTHETASE 1 DEFICIENCY to Carbamoylphosphate synthetase I deficiency MIM#237300
Publications for gene: CPS1 were set to
gene: CPS1 was added gene: CPS1 was added to Fetal anomalies. Sources: Expert Review Red,Genomics England PanelApp Mode of inheritance for gene: CPS1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: CPS1 were set to CARBAMOYL PHOSPHATE SYNTHETASE 1 DEFICIENCY
If promoting or demoting a gene, please provide comments to justify a decision to move it.
Genes included in a Genomics England gene panel for a rare disease category (green list) should fit the criteria A-E outlined below.
These guidelines were developed as a combination of the ClinGen DEFINITIVE evidence for a causal role of the gene in the disease(a), and the Developmental Disorder Genotype-Phenotype (DDG2P) CONFIRMED DD Gene evidence level(b) (please see the original references provided below for full details). These help provide a guideline for expert reviewers when assessing whether a gene should be on the green or the red list of a panel.
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.
AND
D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic setting(iv).
AND
E. No convincing evidence exists or has emerged that contradicts the role of the gene in the specified phenotype.
(i)Plausible disease-causing mutations: Recurrent de novo mutations convincingly affecting gene function. Rare, fully-penetrant mutations - relevant genotype never, or very rarely, seen in controls. (ii) Interpretable functional region: ORF in protein coding genes miRNA stem or loop. (iii) Phenotype: the rare disease category, as described in the eligibility statement. (iv) Intermediate penetrance genes should not be included.
It’s assumed that loss-of-function variants in this gene can cause the disease/phenotype unless an exception to this rule is known. We would like to collect information regarding exceptions. An example exception is the PCSK9 gene, where loss-of-function variants are not relevant for a hypercholesterolemia phenotype as they are associated with increased LDL-cholesterol uptake via LDLR (PMID: 25911073).
If a curated set of known-pathogenic variants is available for this gene-phenotype, please contact us at panelapp@genomicsengland.co.uk
We classify loss-of-function variants as those with the following Sequence Ontology (SO) terms:
Term descriptions can be found on the PanelApp homepage and Ensembl.
If you are submitting this evaluation on behalf of a clinical laboratory please indicate whether you report variants in this gene as part of your current diagnostic practice by checking the box
Standardised terms were used to represent the gene-disease mode of inheritance, and were mapped to commonly used terms from the different sources. Below each of the terms is described, along with the equivalent commonly-used terms.
A variant on one allele of this gene can cause the disease, and imprinting has not been implicated.
A variant on the paternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on the maternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on one allele of this gene can cause the disease. This is the default used for autosomal dominant mode of inheritance where no knowledge of the imprinting status of the gene required to cause the disease is known. Mapped to the following commonly used terms from different sources: autosomal dominant, dominant, AD, DOMINANT.
A variant on both alleles of this gene is required to cause the disease. Mapped to the following commonly used terms from different sources: autosomal recessive, recessive, AR, RECESSIVE.
The disease can be caused by a variant on one or both alleles of this gene. Mapped to the following commonly used terms from different sources: autosomal recessive or autosomal dominant, recessive or dominant, AR/AD, AD/AR, DOMINANT/RECESSIVE, RECESSIVE/DOMINANT.
A variant on one allele of this gene can cause the disease, however a variant on both alleles of this gene can result in a more severe form of the disease/phenotype.
A variant in this gene can cause the disease in males as they have one X-chromosome allele, whereas a variant on both X-chromosome alleles is required to cause the disease in females. Mapped to the following commonly used term from different sources: X-linked recessive.
A variant in this gene can cause the disease in males as they have one X-chromosome allele. A variant on one allele of this gene may also cause the disease in females, though the disease/phenotype may be less severe and may have a later-onset than is seen in males. X-linked inactivation and mosaicism in different tissues complicate whether a female presents with the disease, and can change over their lifetime. This term is the default setting used for X-linked genes, where it is not known definitately whether females require a variant on each allele of this gene in order to be affected. Mapped to the following commonly used terms from different sources: X-linked dominant, x-linked, X-LINKED, X-linked.
The gene is in the mitochondrial genome and variants within this can cause this disease, maternally inherited. Mapped to the following commonly used term from different sources: Mitochondrial.
Mapped to the following commonly used terms from different sources: Unknown, NA, information not provided.
For example, if the mode of inheritance is digenic, please indicate this in the comments and which other gene is involved.