ClinVar Miner

Submissions for variant NM_002968.2(SALL1):c.3938G>A (p.Arg1313His) (rs529030284)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489514 SCV000577473 uncertain significance not provided 2017-03-28 criteria provided, single submitter clinical testing The R1313H variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R1313H variant is observed in 3/8634 (0.035%) alleles from individuals of East Asian background, in the ExAC dataset (Lek et al., 2016). The R1313H variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is conserved across species, yet in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. In summary, based on the currently available information, it is unclear whether this variant is pathogenic or a rare benign variant.
Invitae RCV001212454 SCV001384037 uncertain significance Townes syndrome 2020-02-24 criteria provided, single submitter clinical testing This sequence change replaces arginine with histidine at codon 1313 of the SALL1 protein (p.Arg1313His). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and histidine. This variant is present in population databases (rs529030284, ExAC 0.03%). This variant has not been reported in the literature in individuals with SALL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 426902). 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 tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.

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