ClinVar Miner

Submissions for variant NM_003491.4(NAA10):c.247C>T (p.Arg83Cys)

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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000190675 SCV000244115 pathogenic Inborn genetic diseases 2016-03-30 criteria provided, single submitter clinical testing
Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg RCV000225365 SCV000267573 pathogenic Ogden syndrome 2016-03-31 criteria provided, single submitter clinical testing
GeneDx RCV000255490 SCV000321921 pathogenic not provided 2022-05-12 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect with an approximately 60% reduction in catalytic activity of NAA10 for all tested oligopeptides in in vitro enzymatic assays (Saunier et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 21700266, 25099252, 28628100, 26522270, 32698785, 27094817, 28967461, 30138938, 29100083, 32973342, 34200686, 33504798, 31093388, 31127942, 28135719, 33258288, 31785789)
CeGaT Center for Human Genetics Tuebingen RCV000255490 SCV001334452 pathogenic not provided 2023-11-01 criteria provided, single submitter clinical testing NAA10: PM2, PM5, PM6, PS4:Moderate, PP2, PS3:Supporting
Invitae RCV000255490 SCV001373962 pathogenic not provided 2023-02-23 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 83 of the NAA10 protein (p.Arg83Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with N-terminal acetyltransferase deficiency (PMID: 27094817). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 208664). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects NAA10 function (PMID: 27094817). For these reasons, this variant has been classified as Pathogenic.
Diagnostic Laboratory, Strasbourg University Hospital RCV001257765 SCV001434577 pathogenic Intellectual disability 2020-04-20 criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000255490 SCV001447793 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000255490 SCV001473397 pathogenic not provided 2019-09-29 criteria provided, single submitter clinical testing
Baylor Genetics RCV000225365 SCV001520401 pathogenic Ogden syndrome 2019-10-12 criteria provided, single submitter clinical testing This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Revvity Omics, Revvity Omics RCV000255490 SCV002018189 pathogenic not provided 2024-01-11 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV000225365 SCV002102462 pathogenic Ogden syndrome 2022-02-24 criteria provided, single submitter clinical testing _x000D_ Criteria applied: PS2_VSTR, PS4_MOD, PM1, PM2_SUP, PM5_SUP, PP3
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV002252040 SCV002523044 pathogenic See cases 2022-02-24 criteria provided, single submitter clinical testing ACMG classification criteria: PS3, PS4, PM2, PM6
3billion RCV000225365 SCV003841470 pathogenic Ogden syndrome 2023-02-23 criteria provided, single submitter clinical testing The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. The variant has been confirmed to be de novo as shown in the table above Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 27094817, 27094817). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.58; 3Cnet: 0.90). Same nucleotide change resulting in same amino acid change (ClinVar ID: VCV000208664) and a different missense change at the same codon (p.Arg83His / ClinVar ID: VCV000691256) have been previously reported as pathogenic/likely pathogenic with strong evidence. The variant has been previously reported as de novo in a similarly affected individual (PMID: 27094817). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
Daryl Scott Lab, Baylor College of Medicine RCV003401042 SCV004102714 pathogenic NAA10-related disorder 2023-11-10 criteria provided, single submitter clinical testing
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes RCV000255490 SCV000778261 pathogenic not provided 2017-05-26 no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000255490 SCV001741612 pathogenic not provided no assertion criteria provided clinical testing
OMIM RCV000225365 SCV001748650 pathogenic Ogden syndrome 2022-09-08 no assertion criteria provided literature only
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000255490 SCV001958503 pathogenic not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000255490 SCV001974508 pathogenic not provided no assertion criteria provided clinical testing

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