ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.600C>T (p.Gly200=) (rs201481698)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000598907 SCV000709873 uncertain significance not provided 2018-02-22 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the NRXN1 gene. The c.600 C>T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.600 C>T variant is observed in 28/17456 (0.2%) alleles from individuals of East Asian background, including 1 homozygous individual (Lek et al., 2016). Several in silico splice prediction models predict that c.600 C>T may create a new cryptic splice donor site in exon 2. However, in the absence of RNA/functional studies, the actual effect of c.600 C>T on splicing is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768037 SCV000898864 uncertain significance Pitt-Hopkins-like syndrome 2; Schizophrenia 17 2018-09-27 criteria provided, single submitter clinical testing NRXN1 NM_001135659.2 exon 2 p.Gly200= (c.600C>T): This variant has not been reported in the literature but is present in 0.1% (28/17456) of East Asian alleles, including 1 homozygote in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/2-51254812-G-A). This variant is present in ClinVar (Variation ID:503668). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is a silent variant and does not change the amino acid, reducing the probability that this variant is disease causing. However, computational tools designed to predict splicing suggest a potential effect from this variant. Further studies are needed to understand its impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Invitae RCV001080918 SCV001011300 benign Pitt-Hopkins-like syndrome 2 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001080918 SCV001299260 uncertain significance Pitt-Hopkins-like syndrome 2 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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