ClinVar Miner

Submissions for variant NM_014159.7(SETD2):c.3167C>T (p.Ser1056Leu)

gnomAD frequency: 0.00001  dbSNP: rs776300341
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV004536693 SCV004120953 uncertain significance SETD2-related disorder 2023-08-19 criteria provided, single submitter clinical testing The SETD2 c.3167C>T variant is predicted to result in the amino acid substitution p.Ser1056Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0065% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-47162959-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Labcorp Genetics (formerly Invitae), Labcorp RCV003592036 SCV004290519 uncertain significance Luscan-Lumish syndrome 2023-04-10 criteria provided, single submitter clinical testing 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. 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 expected to disrupt SETD2 protein function. This variant has not been reported in the literature in individuals affected with SETD2-related conditions. This variant is present in population databases (rs776300341, gnomAD 0.006%). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 1056 of the SETD2 protein (p.Ser1056Leu).
Ambry Genetics RCV004364460 SCV004947450 uncertain significance Inborn genetic diseases 2024-01-08 criteria provided, single submitter clinical testing The c.3167C>T (p.S1056L) alteration is located in exon 3 (coding exon 3) of the SETD2 gene. This alteration results from a C to T substitution at nucleotide position 3167, causing the serine (S) at amino acid position 1056 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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