ClinVar Miner

Submissions for variant NM_001370466.1(NOD2):c.1922C>T (p.Pro641Leu)

gnomAD frequency: 0.00024  dbSNP: rs5743275
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000339948 SCV000397248 benign Blau syndrome 2018-01-12 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Laboratory Services, Illumina RCV001782818 SCV000397249 uncertain significance Inflammatory bowel disease 1 2018-01-12 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.
Invitae RCV002522864 SCV001038654 benign Blau syndrome; Regional enteritis 2024-01-26 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001812848 SCV001472397 uncertain significance not provided 2021-03-16 criteria provided, single submitter clinical testing The NOD2 c.2003C>T; p.Pro668Leu variant (rs5743275), to our knowledge, is not reported in the medical literature but is reported in the Infevers database (see link). This variant is reported in ClinVar (Variation ID: 319456) and is found in the Ashkenazi Jewish population with an allele frequency of 1% (99/10108 alleles) in the Genome Aggregation Database. The proline at codon 668 is moderately conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.385). However, given the lack of clinical and functional data, the significance of the p.Pro668Leu variant is uncertain at this time. References: Link to Infevers database: https://infevers.umai-montpellier.fr/web/search.php?n=6
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002261060 SCV002542671 likely benign Autoinflammatory syndrome 2021-03-16 criteria provided, single submitter clinical testing

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