ClinVar Miner

Submissions for variant NM_032575.3(GLIS2):c.1388C>T (p.Thr463Met)

gnomAD frequency: 0.00001  dbSNP: rs373198635
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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 RCV000793767 SCV000933137 uncertain significance Nephronophthisis 2022-07-05 criteria provided, single submitter clinical testing 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 variant has not been reported in the literature in individuals affected with GLIS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 640688). 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: "Deleterious"; PolyPhen-2: "Not Available"; 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. This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 463 of the GLIS2 protein (p.Thr463Met).
Fulgent Genetics, Fulgent Genetics RCV002507366 SCV002812876 uncertain significance Nephronophthisis 7 2021-09-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV004917649 SCV005591705 uncertain significance not specified 2024-08-28 criteria provided, single submitter clinical testing The c.1388C>T (p.T463M) alteration is located in exon 6 (coding exon 6) of the GLIS2 gene. This alteration results from a C to T substitution at nucleotide position 1388, causing the threonine (T) at amino acid position 463 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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