ClinVar Miner

Submissions for variant NM_015346.4(ZFYVE26):c.3950C>T (p.Thr1317Met)

gnomAD frequency: 0.00031  dbSNP: rs143719747
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000517433 SCV000616316 uncertain significance not specified 2016-08-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001066247 SCV001231254 uncertain significance Spastic paraplegia 2022-06-20 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 1317 of the ZFYVE26 protein (p.Thr1317Met). This variant is present in population databases (rs143719747, gnomAD 0.09%). This variant has not been reported in the literature in individuals affected with ZFYVE26-related conditions. ClinVar contains an entry for this variant (Variation ID: 448890). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine 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.
GeneDx RCV001755775 SCV001997682 uncertain significance not provided 2020-01-06 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Mayo Clinic Laboratories, Mayo Clinic RCV001755775 SCV002541211 uncertain significance not provided 2021-07-27 criteria provided, single submitter clinical testing
Ambry Genetics RCV002527559 SCV003675751 uncertain significance Inborn genetic diseases 2021-08-02 criteria provided, single submitter clinical testing The c.3950C>T (p.T1317M) alteration is located in exon 21 (coding exon 20) of the ZFYVE26 gene. This alteration results from a C to T substitution at nucleotide position 3950, causing the threonine (T) at amino acid position 1317 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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