ClinVar Miner

Submissions for variant NM_000222.3(KIT):c.2104C>G (p.Leu702Val)

gnomAD frequency: 0.00004  dbSNP: rs768847037
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000458317 SCV000550120 uncertain significance Gastrointestinal stromal tumor 2025-01-05 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 702 of the KIT protein (p.Leu702Val). This variant is present in population databases (rs768847037, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with KIT-related conditions. ClinVar contains an entry for this variant (Variation ID: 409779). 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.
Fulgent Genetics, Fulgent Genetics RCV000764545 SCV000895631 uncertain significance Gastrointestinal stromal tumor; Mastocytosis; Piebaldism; Malignant tumor of testis; Acute myeloid leukemia 2018-10-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV001014447 SCV001175154 benign Hereditary cancer-predisposing syndrome 2024-10-28 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GeneDx RCV004722787 SCV005333760 uncertain significance not provided 2024-02-02 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
PreventionGenetics, part of Exact Sciences RCV004748776 SCV005349032 uncertain significance KIT-related disorder 2024-07-11 no assertion criteria provided clinical testing The KIT c.2104C>G variant is predicted to result in the amino acid substitution p.Leu702Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.020% of alleles in individuals of Latino descent in gnomAD and is interpreted as a variant of uncertain significance in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/409779/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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