ClinVar Miner

Submissions for variant NM_015466.4(PTPN23):c.2680C>T (p.His894Tyr)

gnomAD frequency: 0.00003  dbSNP: rs967738491
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001873214 SCV002113872 uncertain significance not provided 2022-10-17 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 894 of the PTPN23 protein (p.His894Tyr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of PTPN23-related conditions (PMID: 31395947). ClinVar contains an entry for this variant (Variation ID: 636313). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0". The tyrosine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center RCV003320745 SCV004024556 uncertain significance Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity 2023-08-15 criteria provided, single submitter clinical testing
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes RCV003389062 SCV004101212 uncertain significance Neurodevelopmental disorder 2023-01-20 criteria provided, single submitter clinical testing
3billion RCV003320745 SCV005328837 likely benign Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity 2024-09-20 criteria provided, single submitter clinical testing The homozygous variant was found in patients diagnosed with another variant in a different gene, with no symptoms related to the gene containing the homozygous variant.
Regeneron Genetics Center, Regeneron RCV000853200 SCV000927107 likely pathogenic Global developmental delay; Brain atrophy 2019-02-15 no assertion criteria provided research Identified in cohort of patients with neurodevelopmental disorder accompanied by structural brain abnormalities

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