ClinVar Miner

Submissions for variant NM_001099922.3(ALG13):c.320A>G (p.Asn107Ser) (rs398122394)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Arab Genomic Studies,Sheikh Hamdan Award for Medical Sciences RCV000056321 SCV000693888 pathogenic Epileptic encephalopathy, early infantile, 36 2017-07-15 criteria provided, single submitter clinical testing
Courtagen Diagnostics Laboratory,Courtagen Life Sciences RCV000056321 SCV000236520 pathogenic Epileptic encephalopathy, early infantile, 36 2015-02-27 criteria provided, single submitter clinical testing
GeneDx RCV000289979 SCV000329059 pathogenic not provided 2017-07-13 criteria provided, single submitter clinical testing The N107S pathogenic variant in the ALG13 gene has been reported previously as a de novo change in several females with early onset severe epilepsy and intellectual disability who underwent exome sequencing (deLigt et al., 2012; Allen et al., 2013; Smith-Packard et al., 2015; Kobayashi et al., 2016). The N107S variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The N107S variant is a conservative amino acid substitution and occurs at a position where amino acids with similar properties to Asparagine are tolerated across species. Therefore, the presence of N107S is consistent with a diagnosis of CDG-ALG13
Invitae RCV000056321 SCV000541277 pathogenic Epileptic encephalopathy, early infantile, 36 2018-11-26 criteria provided, single submitter clinical testing This sequence change replaces asparagine with serine at codon 3 of the ALG13 protein (p.Asn3Ser). The asparagine residue is weakly conserved and there is a small physicochemical difference between asparagine and serine. This variant is not present in population databases (rs398122394, ExAC no frequency). This variant has been reported in individuals affected with infantile spasms, Lennox-Gastaut syndrome, West syndrome and severe intellectual disability (PMID: 23934111, 26482601, 24896178, 25732998, 26138355, 24781210). In many of these individuals this variant was reported to be de novo. It is also known as c.320A>G, p.N107S and g.110928268 in the literature. 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). For these reasons, this variant has been classified as Pathogenic.
Laboratory of Molecular Genetics (Pr. Bezieau's lab),CHU de Nantes RCV000289979 SCV000920487 pathogenic not provided 2018-05-30 criteria provided, single submitter clinical testing
OMIM RCV000056321 SCV000087490 pathogenic Epileptic encephalopathy, early infantile, 36 2013-09-12 no assertion criteria provided literature only
Undiagnosed Diseases Network,NIH RCV000056321 SCV000746641 pathogenic Epileptic encephalopathy, early infantile, 36 2017-01-26 criteria provided, single submitter clinical testing

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