ClinVar Miner

Submissions for variant NM_016335.5(PRODH):c.1357C>T (p.Arg453Cys) (rs3970559)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute for Genomic Medicine (IGM) Clinical Laboratory,Nationwide Children's Hospital RCV000454992 SCV000864289 likely benign not specified 2017-04-18 criteria provided, single submitter clinical testing BS1, BP6; This alteration has an allele frequency that is greater than expected for the associated disease, and was reported as a benign/likely benign alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory).
Invitae RCV000004214 SCV000631842 uncertain significance Proline dehydrogenase deficiency 2018-12-23 criteria provided, single submitter clinical testing This sequence change replaces arginine with cysteine at codon 453 of the PRODH protein (p.Arg453Cys). The arginine residue is highly conserved and there is a large physicochemical difference between arginine and cysteine. This variant is present in population databases (rs3970559, ExAC 3%). This variant has previously been reported as a susceptibility allele for hyperprolinemia (PMID: 15494707, 22090377, 24842239). However, this assertion was based on a small study size and other causes of clinical symptoms were not ruled out. ClinVar contains an entry for this variant (Variation ID: 4006). Experimental studies have shown that this missense change reduces POX1 activity (PMID: 15662599). In summary, this variant is a missense change that has been described as a risk factor for hyperprolinemia and has been shown to affect protein function. However, it is very common in the population. For these reasons, it has been classified as a Variant of Uncertain Significance.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000454992 SCV000540120 benign not specified 2016-03-29 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 3% in African population, >1% in most other populations. In addition, no clearly associated clinical manifestations
OMIM RCV000004214 SCV000024380 pathogenic Proline dehydrogenase deficiency 2005-03-01 no assertion criteria provided literature only
OMIM RCV000004215 SCV000024381 risk factor Schizophrenia 4 2005-03-01 no assertion criteria provided literature only

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