ClinVar Miner

Submissions for variant NM_017654.4(SAMD9):c.83T>C (p.Ile28Thr)

gnomAD frequency: 0.00005  dbSNP: rs776674692
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001992189 SCV002284081 uncertain significance not provided 2024-11-18 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 28 of the SAMD9 protein (p.Ile28Thr). This variant is present in population databases (rs776674692, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with SAMD9-related conditions. ClinVar contains an entry for this variant (Variation ID: 1497031). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SAMD9 protein function with a negative predictive value of 95%. 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 RCV001992189 SCV003935589 uncertain significance not provided 2022-12-23 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
PreventionGenetics, part of Exact Sciences RCV004553618 SCV004115942 uncertain significance SAMD9-related disorder 2022-11-04 criteria provided, single submitter clinical testing The SAMD9 c.83T>C variant is predicted to result in the amino acid substitution p.Ile28Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0081% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-92735328-A-G) and is interpreted as uncertain significance in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/1497031/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Fulgent Genetics, Fulgent Genetics RCV005042663 SCV005669755 uncertain significance Normophosphatemic familial tumoral calcinosis; MIRAGE syndrome; Monosomy 7 myelodysplasia and leukemia syndrome 2 2024-06-16 criteria provided, single submitter clinical testing

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