ClinVar Miner

Submissions for variant NM_001875.5(CPS1):c.2809_2810del (p.Ile937fs)

gnomAD frequency: 0.00001  dbSNP: rs1318756445
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000673303 SCV000798487 likely pathogenic Congenital hyperammonemia, type I 2018-03-12 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000673303 SCV000914890 uncertain significance Congenital hyperammonemia, type I 2018-11-01 criteria provided, single submitter clinical testing The CPS1 c.2809_2810delAT (p.Ile937ProfsTer5) variant results in a frameshift, and is predicted to result in premature termination of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. The p.Ile937ProfsTer5 variant is listed in a supplementary table in Haberle et al. (2011) as a novel variant, with no further details given. This variant is not found in the 1000 Genomes Project, the Exome Sequencing Project, the Exome Aggregation Consortium or the Genome Aggregation Database in a region of good coverage, so the variant is presumed to be rare. Based on the predicted truncating nature of the variant and limited evidence, the p.Ile937ProfsTer5 variant is classified as a variant of unknown significance but suspicious for pathogenicity for carbamoylphosphate synthetase I deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Baylor Genetics RCV003465526 SCV004216196 pathogenic Pulmonary hypertension, neonatal, susceptibility to 2022-10-12 criteria provided, single submitter clinical testing
Invitae RCV000673303 SCV004293068 pathogenic Congenital hyperammonemia, type I 2023-02-03 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 557195). This premature translational stop signal has been observed in individual(s) with carbamoyl phosphate synthetase I deficiency (PMID: 21120950). This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change creates a premature translational stop signal (p.Ile937Profs*5) in the CPS1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CPS1 are known to be pathogenic (PMID: 21120950).
GenomeConnect - Invitae Patient Insights Network RCV000673303 SCV004228704 not provided Congenital hyperammonemia, type I no assertion provided phenotyping only Variant interpreted as Likely pathogenic and reported on 04-20-2020 by Lab Natera. 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.

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