ClinVar Miner

Submissions for variant NM_004517.4(ILK):c.590C>T (p.Thr197Met)

dbSNP: rs767383055
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001984975 SCV002212760 uncertain significance Primary familial hypertrophic cardiomyopathy 2024-10-23 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 197 of the ILK protein (p.Thr197Met). This variant is present in population databases (rs767383055, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with ILK-related conditions. ClinVar contains an entry for this variant (Variation ID: 1435677). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.
New York Genome Center RCV003448436 SCV004176076 uncertain significance ILK-related cardiomyopathy 2023-08-30 criteria provided, single submitter clinical testing The c.590C>T p.(Thr197Met) variant identified in the ILK gene is located on exon 7 of this 13-exon gene and substitutes a Threonine for Methionine at amino acid position 197 of the encoded protein. This variant is absent from population databases (gnomAD v2.1.1, gnomADv3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.590C>T variant has been deposited to ClinVar as Variant of Uncertain Significance (ClinVar ID: 1435677) by a single submitter, and to our current knowledge it has not been reported in affected individuals in the literature. In silico algorithms are supportive of the benign effect of this variant on protein function (REVEL score: 0.220). However, functional studies are not available to provide more information about the variant’s damaging effect. Based on available evidence this c.590C>T (p.Thr197Met) variant identified in the ILK gene is classified as a Variant of Uncertain Significance.

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