ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.280G>A (p.Asp94Asn) (rs73167107)

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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 RCV000764402 SCV000895456 uncertain significance Kanzaki disease; Schindler disease, type 1 2018-10-31 criteria provided, single submitter clinical testing
GeneDx RCV000520922 SCV000616805 uncertain significance not provided 2017-07-25 criteria provided, single submitter clinical testing The D94N variant in the NAGA gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is observed in 131/66698 (0.196%) alleles from individuals of non-Finnish European background, and is observed in the homozygous state in one individual, in the ExAC dataset (Lek et al., 2016). The D94N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret D94N as a variant of uncertain significance.
Illumina Clinical Services Laboratory,Illumina RCV000319000 SCV000439005 uncertain significance Schindler disease, type 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000375961 SCV000439006 uncertain significance Kanzaki disease 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000319000 SCV000835176 uncertain significance Schindler disease, type 1 2018-05-30 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid with asparagine at codon 94 of the NAGA protein (p.Asp94Asn). The aspartic acid residue is highly conserved and there is a small physicochemical difference between aspartic acid and asparagine. This variant is present in population databases (rs73167107, ExAC 0.2%). This variant has not been reported in the literature in individuals with NAGA-related disease. ClinVar contains an entry for this variant (Variation ID: 341912). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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