ClinVar Miner

Submissions for variant NM_001080517.3(SETD5):c.2902A>G (p.Thr968Ala)

gnomAD frequency: 0.00002  dbSNP: rs905963301
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001570253 SCV001794515 uncertain significance not provided 2019-08-23 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); 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
Labcorp Genetics (formerly Invitae), Labcorp RCV001570253 SCV002979203 uncertain significance not provided 2024-01-17 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 968 of the SETD5 protein (p.Thr968Ala). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SETD5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1204013). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SETD5 protein function with a negative predictive value of 80%. 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.
Ambry Genetics RCV004656630 SCV005162218 uncertain significance Inborn genetic diseases 2024-06-13 criteria provided, single submitter clinical testing The c.2902A>G (p.T968A) alteration is located in exon 19 (coding exon 17) of the SETD5 gene. This alteration results from a A to G substitution at nucleotide position 2902, causing the threonine (T) at amino acid position 968 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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