ClinVar Miner

Submissions for variant NM_000045.4(ARG1):c.57+1G>A

gnomAD frequency: 0.00001  dbSNP: rs587776539
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV000002496 SCV000894375 pathogenic Arginase deficiency 2022-02-10 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000002496 SCV002060238 likely pathogenic Arginase deficiency 2021-11-11 criteria provided, single submitter clinical testing NM_000045.3(ARG1):c.57+1G>A is a canonical splice site variant classified as likely pathogenic in the context of argininemia. c.57+1G>A has been observed in cases with relevant disease (PMID: 7649538). Functional assessments of this variant are not available in the literature. c.57+1G>A has been observed in population frequency databases (gnomAD: NFE 0.001%). In summary, NM_000045.3(ARG1):c.57+1G>A is a canonical splice site variant in a gene where loss of function is a known mechanism of disease, is predicted to disrupt protein function, and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
Labcorp Genetics (formerly Invitae), Labcorp RCV000002496 SCV002247420 pathogenic Arginase deficiency 2024-08-14 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 1 of the ARG1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ARG1 are known to be pathogenic (PMID: 7649538, 12052859). This variant is present in population databases (rs587776539, gnomAD 0.002%). Disruption of this splice site has been observed in individual(s) with arginase deficiency (PMID: 7649538). ClinVar contains an entry for this variant (Variation ID: 2395). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000002496 SCV004208481 pathogenic Arginase deficiency 2024-01-08 criteria provided, single submitter clinical testing
OMIM RCV000002496 SCV000022654 pathogenic Arginase deficiency 1995-09-01 no assertion criteria provided literature only

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