ClinVar Miner

Submissions for variant NM_000209.4(PDX1):c.719C>G (p.Pro240Arg)

gnomAD frequency: 0.00003  dbSNP: rs753881947
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000516994 SCV000614429 uncertain significance not specified 2016-09-30 criteria provided, single submitter clinical testing
Personalized Diabetes Medicine Program, University of Maryland School of Medicine RCV001174446 SCV001337585 uncertain significance Monogenic diabetes 2018-03-07 criteria provided, single submitter research ACMG criteria: PP3 (3 predictors), BP4 (8 predictors), PM2 (absent in database), NOTE: Athena calls VUS=VUS
Fulgent Genetics, Fulgent Genetics RCV002481677 SCV002780358 uncertain significance Maturity-onset diabetes of the young type 4; Pancreatic agenesis 1; Type 2 diabetes mellitus 2021-11-03 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004553135 SCV004107496 uncertain significance PDX1-related disorder 2023-08-03 criteria provided, single submitter clinical testing The PDX1 c.719C>G variant is predicted to result in the amino acid substitution p.Pro240Arg. This variant was reported in an individual with type 1 diabetes (Supplemental Table 7, Yu et al 2019. PubMed ID: 31264968). This variant is reported in 0.0063% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/13-28498705-C-G). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Labcorp Genetics (formerly Invitae), Labcorp RCV003727759 SCV004537107 uncertain significance not provided 2023-08-07 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. 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 tolerated. ClinVar contains an entry for this variant (Variation ID: 447926). This missense change has been observed in individual(s) with type 1 diabetes (PMID: 31264968). This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 240 of the PDX1 protein (p.Pro240Arg).

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