ClinVar Miner

Submissions for variant NM_000027.4(AGA):c.395-8A>G

gnomAD frequency: 0.00001  dbSNP: rs386833426
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000049354 SCV004020466 pathogenic Aspartylglucosaminuria 2023-06-20 criteria provided, single submitter clinical testing Variant summary: AGA c.395-8A>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Four predict the variant creates a 3' acceptor site, and three of four predict the variant also abolishes/weakens the canonical 3' acceptor site. At least one publication reports experimental evidence that this variant indeed affects mRNA splicing by creating an alternative 3' acceptor site upstream from the canonical 3' acceptor site, resulting in a 7 bp insertion which ultimately leads to a frameshift and premature termination codon. The variant allele was found at a frequency of 8e-06 in 250390 control chromosomes (gnomAD). c.395-8A>G has been reported in the literature in the homozygous state in two siblings affected with Aspartylglucosaminuria (Yoshida_1992). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and found the variant results in an unstable protein with <10% of normal activity when expressed in vitro (Saarela_2001). The following publications have been ascertained in the context of this evaluation (PMID: 11309371, 1427775). No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Baylor Genetics RCV000049354 SCV004217693 likely pathogenic Aspartylglucosaminuria 2023-06-27 criteria provided, single submitter clinical testing
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049354 SCV000081786 probable-pathogenic Aspartylglucosaminuria no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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