ClinVar Miner

Submissions for variant NM_001378457.1(DMXL2):c.2096T>C (p.Ile699Thr)

gnomAD frequency: 0.00040  dbSNP: rs117017152
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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 RCV002022965 SCV002305178 uncertain significance not provided 2025-02-03 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 699 of the DMXL2 protein (p.Ile699Thr). This variant is present in population databases (rs117017152, gnomAD 0.1%), 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 DMXL2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1512307). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Benign". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV002548207 SCV003740457 likely benign Inborn genetic diseases 2021-09-16 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Mayo Clinic Laboratories, Mayo Clinic RCV002022965 SCV004227417 uncertain significance not provided 2022-07-28 criteria provided, single submitter clinical testing BP4
CeGaT Center for Human Genetics Tuebingen RCV002022965 SCV005330746 likely benign not provided 2024-08-01 criteria provided, single submitter clinical testing DMXL2: BP4, BS1

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