ClinVar Miner

Submissions for variant NM_025152.3(NUBPL):c.413G>A (p.Gly138Asp)

gnomAD frequency: 0.00071  dbSNP: rs201412882
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001112837 SCV001270537 uncertain significance Mitochondrial complex I deficiency, nuclear type 1 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV001853185 SCV002161973 uncertain significance not provided 2024-11-05 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 138 of the NUBPL protein (p.Gly138Asp). This variant is present in population databases (rs201412882, 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 NUBPL-related conditions. ClinVar contains an entry for this variant (Variation ID: 214876). 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 NUBPL protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change does not substantially affect NUBPL function (PMID: 29982452). 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.
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV002252052 SCV002523442 uncertain significance See cases 2019-04-16 criteria provided, single submitter clinical testing ACMG classification criteria: PP3
Ambry Genetics RCV002517249 SCV003686232 uncertain significance Inborn genetic diseases 2023-11-01 criteria provided, single submitter clinical testing (Maclean, 2018) Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Breakthrough Genomics, Breakthrough Genomics RCV001853185 SCV005192292 uncertain significance not provided criteria provided, single submitter not provided

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