ClinVar Miner

Submissions for variant NM_014141.6(CNTNAP2):c.479G>A (p.Arg160His) (rs138738227)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000723722 SCV000113536 uncertain significance not provided 2017-01-10 criteria provided, single submitter clinical testing
GeneDx RCV000723722 SCV000240836 uncertain significance not provided 2018-12-10 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the CNTNAP2 gene. The R160H variant hasnot been published as a pathogenic variant, nor has it been reported as a benign variant to ourknowledge. The R160H variant is observed in 43/66,734 (0.06%) alleles from individuals of Europeanbackground in large population cohorts (Lek et al., 2016). The R160H variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant.or a rare benign variant.
Illumina Clinical Services Laboratory,Illumina RCV000293667 SCV000467211 uncertain significance Pitt-Hopkins-like syndrome 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000351078 SCV000467212 uncertain significance Pitt-Hopkins-like syndrome 2016-06-14 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000187254 SCV000594176 uncertain significance not specified 2017-03-15 criteria provided, single submitter clinical testing
Invitae RCV000293667 SCV000645120 uncertain significance Pitt-Hopkins-like syndrome 1 2018-10-01 criteria provided, single submitter clinical testing This sequence change replaces arginine with histidine at codon 160 of the CNTNAP2 protein (p.Arg160His). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and histidine. This variant is present in population databases (rs138738227, ExAC 0.06%). This variant has not been reported in the literature in individuals with CNTNAP2-related disease. ClinVar contains an entry for this variant (Variation ID: 95574). 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"). 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.
Ambry Genetics RCV000716639 SCV000847481 uncertain significance History of neurodevelopmental disorder 2017-10-13 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient evidence

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