ClinVar Miner

Submissions for variant NM_015443.4(KANSL1):c.118G>A (p.Ala40Thr)

gnomAD frequency: 0.00004  dbSNP: rs376632173
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001705001 SCV000241349 likely benign not provided 2018-05-31 criteria provided, single submitter clinical testing
Invitae RCV001041956 SCV001205610 uncertain significance Koolen-de Vries syndrome 2021-08-28 criteria provided, single submitter clinical testing Due to the possible presence of a polymorphic segmental duplication, the location of the variant could not be unambiguously resolved. Variants with ambiguous mapping are still reported relative to the KANSL1 transcript. This sequence change replaces alanine with threonine at codon 40 of the KANSL1 protein (p.Ala40Thr). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and threonine. This variant is present in population databases (rs376632173, ExAC 0.01%). This variant has not been reported in the literature in individuals with KANSL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 205764). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Until the location of this sequence change can be resolved, the clinical significance of this variant remains uncertain. It has been classified as a Variant of Uncertain Significance.

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