ClinVar Miner

Submissions for variant NM_006363.6(SEC23B):c.569G>A (p.Arg190Gln)

gnomAD frequency: 0.00028  dbSNP: rs201160833
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000178916 SCV000231096 uncertain significance not provided 2014-06-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001071842 SCV001237170 likely benign Congenital dyserythropoietic anemia, type II; Cowden syndrome 7 2025-01-30 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001141445 SCV001301789 uncertain significance Congenital dyserythropoietic anemia, type II 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV000178916 SCV004039959 uncertain significance not provided 2023-03-27 criteria provided, single submitter clinical testing Identified in the heterozygous state in a patient with anemia, jaundice, abnormal blood cell morphology, and transfusion dependence (Moreno-Carralero et al., 2018); Identified with another SEC23B variant, phase unknown, in a fetus with increased nuchal transparency in the published literature (Gabriel et al., 2022); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29901818, 34958143)
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000178916 SCV004564444 uncertain significance not provided 2023-03-02 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004737283 SCV005348396 uncertain significance SEC23B-related disorder 2024-08-08 no assertion criteria provided clinical testing The SEC23B c.569G>A variant is predicted to result in the amino acid substitution p.Arg190Gln. This variant was reported as a single variant in an individual with dyserythropoietic congenital anemia (Table 3, Moreno-Carralero et al. 2018. PubMed ID: 29901818) and together with second variant in SEC23B in fetus with increased nuchal transparency (Table S1,Gabriel et al. 2021. PubMed ID: 34958143). This variant is reported in 0.071% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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