ClinVar Miner

Submissions for variant NM_015443.4(KANSL1):c.619A>G (p.Asn207Asp)

gnomAD frequency: 0.00007  dbSNP: rs372601814
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000442390 SCV000526885 likely benign not specified 2016-04-27 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV000808410 SCV000948519 uncertain significance Koolen-de Vries syndrome 2024-03-04 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 asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 207 of the KANSL1 protein (p.Asn207Asp). 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: 385571). 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 with a negative predictive value of 80%. 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.
Ambry Genetics RCV002525400 SCV003702716 uncertain significance Inborn genetic diseases 2021-08-17 criteria provided, single submitter clinical testing The c.619A>G (p.N207D) 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 619, causing the asparagine (N) at amino acid position 207 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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