ClinVar Miner

Submissions for variant NM_138477.4(CDAN1):c.3128A>T (p.Asp1043Val)

gnomAD frequency: 0.00003  dbSNP: rs80338698
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000020957 SCV000915672 uncertain significance Congenital dyserythropoietic anemia, type I 2018-12-10 criteria provided, single submitter clinical testing The CDAN1 c.3128A>T (p.Asp1043Val) missense variant is reported to be one of the most common pathogenic congenital dyserythropoietic anemia (CDA) variants in the European population, accounting for approximately 5% (4/75) of the disease-causing alleles (Tamary and Dgany 2009). Only one study was identified in the literature, in which the p.Asp1043Val variant was identified in a compound heterozygous state with a stop-gained variant in one patient with CDA (Dgany et al. 2002). The p.Asp1043Val variant was absent from 180 controls and is reported at a frequency of 0.00003019 in the European (non-Finnish) population of the Genome Aggregation Database. Based on the evidence, the p.Asp1043Val variant is classified as a variant of unknown significance but suspicious for pathogenicity for congenital dyserythropoietic anemia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Mayo Clinic Laboratories, Mayo Clinic RCV002260970 SCV002541250 uncertain significance not provided 2021-06-29 criteria provided, single submitter clinical testing
Invitae RCV002260970 SCV003442834 uncertain significance not provided 2022-03-13 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 21750). This missense change has been observed in individual(s) with congenital dyserythropoietic anemia (PMID: 12434312, 32518175). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs80338698, gnomAD 0.003%). This sequence change replaces aspartic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 1043 of the CDAN1 protein (p.Asp1043Val).

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