ClinVar Miner

Submissions for variant NM_002834.5(PTPN11):c.15-4del

dbSNP: rs1223869705
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV000761126 SCV000891042 uncertain significance Noonan syndrome 2020-09-22 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001517426 SCV001725915 benign RASopathy 2023-08-17 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003994107 SCV004813949 uncertain significance not specified 2024-02-08 criteria provided, single submitter clinical testing Variant summary: PTPN11 c.15-4delT alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Consensus agreement among computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 8e-06 in 251230 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.15-4delT in individuals affected with Noonan Syndrome/Leopard Syndrome or other PTPN11-related disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 620622). Based on the evidence outlined above, the variant was classified as uncertain significance.

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