ClinVar Miner

Submissions for variant NM_000337.5(SGCD):c.394G>A (p.Val132Ile) (rs367819390)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000154571 SCV000204244 likely benign not specified 2014-03-24 criteria provided, single submitter clinical testing Val132Ile in exon 6 of SGCD: This variant is not expected to have clinical signi ficance due to a lack of conservation across species, including mammals. Of note , multiple mammals have an isoleucine (Ile) at this position despite high nearby amino acid conservation. In addition, computational prediction tools do not sug gest a high likelihood of impact to the protein. This variant has also been iden tified in 1/3616 African American chromosomes by the NHLBI Exome Sequencing Proj ect (http://evs.gs.washington.edu/EVS/).
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000724393 SCV000231516 uncertain significance not provided 2014-11-23 criteria provided, single submitter clinical testing
GeneDx RCV000724393 SCV000236380 uncertain significance not provided 2016-04-18 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SGCD gene. The V132I variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. This variant has been reported in multiple unrelated individuals who were tested for cardiomyopathy at GeneDx, one of whom also had a pathogenic variant in a different gene associated with inherited predisposition to cardiomyopathy. The V132I variant has been reported in ClinVar as a likely benign variant and a variant of uncertain significance by two outside laboratories (ClinVar: SCV000204244.2, SCV000231516.1; Landrum et al., 2016). This variant was not observed with any significant frequency in approximately 5,900 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project. The V132I variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Furthermore, this substitution occurs at a position where amino acids with similar properties to Valine are tolerated across species and where Isoleucine is the native amino acid at this position in multiple species. Finally, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign.
Invitae RCV000559296 SCV000638172 uncertain significance Limb-girdle muscular dystrophy, type 2F 2018-11-19 criteria provided, single submitter clinical testing This sequence change replaces valine with isoleucine at codon 132 of the SGCD protein (p.Val132Ile). The valine residue is moderately conserved and there is a small physicochemical difference between valine and isoleucine. This variant is present in population databases (rs367819390, ExAC 0.05%). This variant has been observed in an individual affected with dilated cardiomyopathy (PMID: 27532257). ClinVar contains an entry for this variant (Variation ID: 177914). 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 isoleucine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. 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.
Counsyl RCV000671469 SCV000796445 uncertain significance Dilated cardiomyopathy 1L; Limb-girdle muscular dystrophy, type 2F 2017-12-14 criteria provided, single submitter clinical testing

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