ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.759+1_759+8del

dbSNP: rs768761898
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001199313 SCV001370393 likely pathogenic Alpha-N-acetylgalactosaminidase deficiency type 2 2019-10-27 criteria provided, single submitter clinical testing This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2.
Labcorp Genetics (formerly Invitae), Labcorp RCV001863139 SCV002298438 likely pathogenic Alpha-N-acetylgalactosaminidase deficiency type 1 2024-11-05 criteria provided, single submitter clinical testing This sequence change affects a splice site in intron 6 of the NAGA 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 NAGA are known to be pathogenic (PMID: 8782044, 11251574). This variant is present in population databases (rs768761898, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with NAGA-related conditions. ClinVar contains an entry for this variant (Variation ID: 932122). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV002480653 SCV002779119 likely pathogenic Alpha-N-acetylgalactosaminidase deficiency type 2; Alpha-N-acetylgalactosaminidase deficiency type 1 2022-03-30 criteria provided, single submitter clinical testing

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