Total submissions: 19
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, |
RCV000225365 | SCV000267573 | pathogenic | Ogden syndrome | 2016-03-31 | criteria provided, single submitter | clinical testing | |
Gene |
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) |
Ce |
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, |
RCV001257765 | SCV001434577 | pathogenic | Intellectual disability | 2020-04-20 | criteria provided, single submitter | clinical testing | |
Institute of Medical Genetics and Applied Genomics, |
RCV000255490 | SCV001447793 | pathogenic | not provided | 2020-10-23 | criteria provided, single submitter | clinical testing | |
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, |
RCV000255490 | SCV002018189 | pathogenic | not provided | 2024-01-11 | criteria provided, single submitter | clinical testing | |
Institute of Human Genetics, |
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, |
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, |
RCV003401042 | SCV004102714 | pathogenic | NAA10-related disorder | 2023-11-10 | criteria provided, single submitter | clinical testing | |
Laboratory of Molecular Genetics |
RCV000255490 | SCV000778261 | pathogenic | not provided | 2017-05-26 | no assertion criteria provided | clinical testing | |
Diagnostic Laboratory, |
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, |
RCV000255490 | SCV001958503 | pathogenic | not provided | no assertion criteria provided | clinical testing | ||
Clinical Genetics DNA and cytogenetics Diagnostics Lab, |
RCV000255490 | SCV001974508 | pathogenic | not provided | no assertion criteria provided | clinical testing |