ClinVar Miner

Submissions for variant NM_001370466.1(NOD2):c.1553C>T (p.Pro518Leu)

dbSNP: rs777949388
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001782812 SCV000397230 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.
Illumina Laboratory Services, Illumina RCV000355684 SCV000397231 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001812846 SCV002048352 uncertain significance not provided 2020-12-16 criteria provided, single submitter clinical testing The NOD2 c.1634C>T; p.Pro545Leu variant (rs777949388), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 319448). This variant is found in the South Asian population with an overall allele frequency of 0.09% (27/30614 alleles, including one homozygote) in the Genome Aggregation Database. The proline at codon 545 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.238). However, given the lack of clinical and functional data, the significance of the p.Pro545Leu variant is uncertain at this time.
Invitae RCV002522859 SCV002405740 benign Blau syndrome; Regional enteritis 2021-06-22 criteria provided, single submitter clinical testing

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