ClinVar Miner

Submissions for variant NM_020975.6(RET):c.3020A>C (p.Lys1007Thr)

gnomAD frequency: 0.00001  dbSNP: rs759798237
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001307727 SCV001497150 uncertain significance Multiple endocrine neoplasia, type 2 2023-04-20 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 1007 of the RET protein (p.Lys1007Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with RET-related conditions. ClinVar contains an entry for this variant (Variation ID: 1010142). 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 disruptive. 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.
All of Us Research Program, National Institutes of Health RCV001307727 SCV004835517 uncertain significance Multiple endocrine neoplasia, type 2 2023-11-20 criteria provided, single submitter clinical testing This missense variant replaces lysine with threonine at codon 1007 of the RET protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with RET-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Ambry Genetics RCV004034136 SCV004939255 uncertain significance Hereditary cancer-predisposing syndrome 2023-11-02 criteria provided, single submitter clinical testing The c.3020A>C (p.K1007T) alteration is located in exon 18 (coding exon 18) of the RET gene. This alteration results from a A to C substitution at nucleotide position 3020, causing the lysine (K) at amino acid position 1007 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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