ClinVar Miner

Submissions for variant NM_152703.5(SAMD9L):c.4082T>C (p.Val1361Ala)

gnomAD frequency: 0.00006  dbSNP: rs202162088
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001316369 SCV001506988 uncertain significance not provided 2024-01-18 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 1361 of the SAMD9L protein (p.Val1361Ala). This variant is present in population databases (rs202162088, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with SAMD9L-related conditions. ClinVar contains an entry for this variant (Variation ID: 1017243). 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 SAMD9L 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.
Fulgent Genetics, Fulgent Genetics RCV002476473 SCV002780844 uncertain significance Monosomy 7 myelodysplasia and leukemia syndrome 1; Ataxia-pancytopenia syndrome; Spinocerebellar ataxia 49 2021-11-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV002543693 SCV003728828 uncertain significance Inborn genetic diseases 2022-12-19 criteria provided, single submitter clinical testing The c.4082T>C (p.V1361A) alteration is located in exon 5 (coding exon 1) of the SAMD9L gene. This alteration results from a T to C substitution at nucleotide position 4082, causing the valine (V) at amino acid position 1361 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV001316369 SCV003933581 uncertain significance not provided 2023-08-07 criteria provided, single submitter clinical testing Identified in an individual with leukemia, but it is not clear whether the variant was only in tumor cells or was also present in the germline (Kiel et al., 2015); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 28719003, 26740555, 26415585)

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