ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.11C>T (p.Ala4Val)

gnomAD frequency: 0.00001  dbSNP: rs1198368082
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000814987 SCV000955427 uncertain significance Pitt-Hopkins-like syndrome 2 2018-11-14 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with NRXN1-related disease. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change replaces alanine with valine at codon 4 of the NRXN1 protein (p.Ala4Val). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and valine.

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