ClinVar Miner

Submissions for variant NM_001370466.1(NOD2):c.1378G>A (p.Val460Ile)

gnomAD frequency: 0.00003  dbSNP: rs908626604
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002547378 SCV001532110 uncertain significance Blau syndrome; Regional enteritis 2022-09-12 criteria provided, single submitter clinical testing Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on NOD2 protein function. ClinVar contains an entry for this variant (Variation ID: 1035561). This variant has not been reported in the literature in individuals affected with NOD2-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 487 of the NOD2 protein (p.Val487Ile). 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.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002261344 SCV002542658 uncertain significance Autoinflammatory syndrome 2018-02-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002546844 SCV003738403 uncertain significance Inborn genetic diseases 2022-11-03 criteria provided, single submitter clinical testing The c.1459G>A (p.V487I) alteration is located in exon 4 (coding exon 4) of the NOD2 gene. This alteration results from a G to A substitution at nucleotide position 1459, causing the valine (V) at amino acid position 487 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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