ClinVar Miner

Submissions for variant NM_015443.4(KANSL1):c.316A>G (p.Thr106Ala)

gnomAD frequency: 0.00001  dbSNP: rs371450753
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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 RCV000476833 SCV000548808 uncertain significance Koolen-de Vries syndrome 2023-10-13 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 threonine with alanine at codon 106 of the KANSL1 protein (p.Thr106Ala). The threonine residue is highly conserved and there is a small physicochemical difference between threonine and alanine. The frequency data for this variant in the population databases (gnomAD) is considered unreliable due to the presence of homologous sequence, such as pseudogenes or paralogs, in the genome. This variant has not been reported in the literature in individuals with KANSL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 408956). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt KANSL1 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.
Fulgent Genetics, Fulgent Genetics RCV000476833 SCV002775976 uncertain significance Koolen-de Vries syndrome 2022-05-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV004984898 SCV005603947 uncertain significance Inborn genetic diseases 2024-10-08 criteria provided, single submitter clinical testing The c.316A>G (p.T106A) alteration is located in exon 2 (coding exon 1) of the KANSL1 gene. This alteration results from a A to G substitution at nucleotide position 316, causing the threonine (T) at amino acid position 106 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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