ClinVar Miner

Submissions for variant NM_144687.4(NLRP12):c.779C>T (p.Thr260Met)

gnomAD frequency: 0.00027  dbSNP: rs150280940
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001080546 SCV000414556 benign Familial cold autoinflammatory syndrome 2 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.
GeneDx RCV000481155 SCV000571347 uncertain significance not provided 2018-03-27 criteria provided, single submitter clinical testing The T260M variant in the NLRP12 gene has not been reported previously as a pathogenic, nor as a benign variant in a peer reviewed journal article to our knowledge. The T260M variant is observed in 40/16508 (0.25%) alleles from individuals of South Asian background in the ExAC dataset (Lek et al., 2016). This variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret T260M as a variant of uncertain significance.
Invitae RCV001080546 SCV000767409 likely benign Familial cold autoinflammatory syndrome 2 2024-01-18 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002263584 SCV002542567 uncertain significance Autoinflammatory syndrome 2022-04-25 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000481155 SCV004033701 likely benign not provided 2023-08-01 criteria provided, single submitter clinical testing NLRP12: BP4, BS1
Mayo Clinic Laboratories, Mayo Clinic RCV000481155 SCV004225438 uncertain significance not provided 2022-07-13 criteria provided, single submitter clinical testing BS2, PM6_supporting
PreventionGenetics, part of Exact Sciences RCV003922406 SCV004739331 likely benign NLRP12-related disorder 2021-07-29 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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