ClinVar Miner

Submissions for variant NM_014159.7(SETD2):c.5633T>C (p.Phe1878Ser)

gnomAD frequency: 0.00001  dbSNP: rs587778665
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000557190 SCV000655754 uncertain significance Luscan-Lumish syndrome 2020-06-26 criteria provided, single submitter clinical testing In summary, this variant is a rare missense change with uncertain impact on protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a SETD2-related disease. ClinVar contains an entry for this variant (Variation ID: 135205). This sequence change replaces phenylalanine with serine at codon 1878 of the SETD2 protein (p.Phe1878Ser). The phenylalanine residue is moderately conserved and there is a large physicochemical difference between phenylalanine and serine.
Baylor Genetics RCV000557190 SCV001522173 uncertain significance Luscan-Lumish syndrome 2021-05-21 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000557190 SCV002555431 uncertain significance Luscan-Lumish syndrome 2022-03-15 criteria provided, single submitter clinical testing
ITMI RCV000122017 SCV000086228 not provided not specified 2013-09-19 no assertion provided reference population

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