ClinVar Miner

Submissions for variant NM_000337.5(SGCD):c.191T>C (p.Ile64Thr) (rs376780156)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000183902 SCV000236385 uncertain significance not provided 2019-01-03 criteria provided, single submitter clinical testing The I64T variant of uncertain significance in the SGCD gene has not been published as pathogenic or been reported as benign to our knowledge. This variant is observed in 8/121,872 alleles from individuals of European (non-Finnish) ancestry and 4/30,950 alleles from individuals of Latino ancestry in large population cohorts (Lek et al., 2016). The I64T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, in-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000183902 SCV000704340 uncertain significance not provided 2016-12-19 criteria provided, single submitter clinical testing
Invitae RCV000705812 SCV000834828 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2F 2019-09-13 criteria provided, single submitter clinical testing This sequence change replaces isoleucine with threonine at codon 64 of the SGCD protein (p.Ile64Thr). The isoleucine residue is moderately conserved and there is a moderate physicochemical difference between isoleucine and threonine. This variant is present in population databases (rs376780156, ExAC 0.009%). This variant has not been reported in the literature in individuals with SGCD-related disease. ClinVar contains an entry for this variant (Variation ID: 202088). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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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