ClinVar Miner

Submissions for variant NM_001083116.3(PRF1):c.866C>T (p.Thr289Met)

gnomAD frequency: 0.00015  dbSNP: rs150628656
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000818085 SCV000958680 uncertain significance Familial hemophagocytic lymphohistiocytosis 2 2021-12-21 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 289 of the PRF1 protein (p.Thr289Met). This variant is present in population databases (rs150628656, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with PRF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 660806). 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: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002261228 SCV002542802 uncertain significance Autoinflammatory syndrome 2016-12-12 criteria provided, single submitter clinical testing
Ambry Genetics RCV003243338 SCV003938149 uncertain significance Inborn genetic diseases 2023-05-23 criteria provided, single submitter clinical testing The c.866C>T (p.T289M) alteration is located in exon 3 (coding exon 2) of the PRF1 gene. This alteration results from a C to T substitution at nucleotide position 866, causing the threonine (T) at amino acid position 289 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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