ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.280G>A (p.Asp94Asn)

gnomAD frequency: 0.00128  dbSNP: rs73167107
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000319000 SCV000439005 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000375961 SCV000439006 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 2 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV000520922 SCV000616805 uncertain significance not provided 2021-02-18 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV000319000 SCV000835176 likely benign Alpha-N-acetylgalactosaminidase deficiency type 1 2024-01-31 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000764402 SCV000895456 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 2; Alpha-N-acetylgalactosaminidase deficiency type 1 2018-10-31 criteria provided, single submitter clinical testing
Baylor Genetics RCV000375961 SCV001527155 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 2 2018-01-18 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Mayo Clinic Laboratories, Mayo Clinic RCV000520922 SCV001713918 uncertain significance not provided 2020-01-13 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004530382 SCV004756244 likely benign NAGA-related disorder 2022-02-08 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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