ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.4610_4614delinsGCATC (p.Ile1537_Met1538delinsSerIle)

dbSNP: rs796053195
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189233 SCV000242865 uncertain significance not specified 2014-05-23 criteria provided, single submitter clinical testing c.4610_4614delinsGCATC: p.Ile1537_Met1538delinsSerIle (I1537_M1538delinsSI) in exon 26 of the SCN2A gene (NM_021007.2). The normal sequence with the bases that are deleted in braces followed by the inserted bases in brackets is: AGCA{TCATG}[GCATC]ATCC.A variant of unknown significance has been identified in the SCN2A gene. The c.4610_4614delTCATGinsGCATC variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The c.4610_4614delTCATGinsGCATC variant results in two missense changes, p.I1537S and p.M1538I. These two variants are present on the same chromosome (in cis).The I1537S missense change has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It 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 I1537S 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. This substitution alters a conserved position in transmembrane segment S1 in the fourth homologous domain. In silico analysis predicts this variant is probably damaging to the protein structure/function.The M1538I missense change has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It 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. This substitution alters a conserved position in transmembrane segment S1 in the fourth homologous domain. However, the M1538I variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Based on the currently available information, it is unclear whether the c.4610_4614delinsGCATC variant is a pathogenic mutation or a rare benign variant. The variant is found in INFANT-EPI panel(s).
GenomeConnect - Simons Searchlight RCV001265412 SCV001443538 likely pathogenic Complex neurodevelopmental disorder 2018-02-23 no assertion criteria provided provider interpretation Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2018-02-23 and interpreted as Likely Pathogenic. Variant was initially reported on 2014-05-27 by GTR ID of laboratory name 26957. The reporting laboratory might also submit to ClinVar.

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