ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.270G>T (p.Gln90His)

gnomAD frequency: 0.00005  dbSNP: rs199960045
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000656993 SCV000227213 uncertain significance not provided 2015-05-14 criteria provided, single submitter clinical testing
GeneDx RCV000656993 SCV000565686 likely benign not provided 2019-12-12 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000765689 SCV000897031 uncertain significance Pitt-Hopkins-like syndrome 2; Chromosome 2p16.3 deletion syndrome 2018-10-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001035816 SCV001199154 uncertain significance Pitt-Hopkins-like syndrome 2 2024-09-24 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 90 of the NRXN1 protein (p.Gln90His). This variant is present in population databases (rs199960045, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with NRXN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 195130). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV002252019 SCV002522775 uncertain significance See cases 2021-08-13 criteria provided, single submitter clinical testing ACMG classification criteria: BP4
Ambry Genetics RCV002426841 SCV002741394 uncertain significance Inborn genetic diseases 2024-11-14 criteria provided, single submitter clinical testing The c.270G>T (p.Q90H) alteration is located in exon 2 (coding exon 1) of the NRXN1 gene. This alteration results from a G to T substitution at nucleotide position 270, causing the glutamine (Q) at amino acid position 90 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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