ClinVar Miner

Submissions for variant NM_014251.3(SLC25A13):c.1063C>T (p.Arg355Ter)

gnomAD frequency: 0.00003  dbSNP: rs758827458
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000523426 SCV000617513 pathogenic not provided 2021-04-02 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 25525159, 19036621, 31589614)
Illumina Laboratory Services, Illumina RCV000779547 SCV000916216 uncertain significance Citrullinemia type II 2018-10-17 criteria provided, single submitter clinical testing The SLC25A13 c.1063C>T (p.Arg355Ter) variant is a stop-gained variant predicted to result in premature termination of the protein. The p.Arg355Ter variant has been reported in one study in which it was found in a presumed compound heterozygous state with a second null variant in two individuals with citrin deficiency, both of whom also carried additional variants in cis (Dimmock et al. 2009). The p.Arg355Ter variant was shown to be absent from over 300 control chromosomes, but is reported at a frequency of 0.000024 in the European (non-Finnish) population of the Genome Aggregation Database. Based on the limited evidence and the potential impact of stop-gained variants, the p.Arg355Ter variant is classified as a variant of unknown significance but suspicious for pathogenicity for citrin deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV000806593 SCV000946598 pathogenic Citrin deficiency 2023-12-12 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg355*) in the SLC25A13 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC25A13 are known to be pathogenic (PMID: 10369257, 14680984, 27405544). This variant is present in population databases (rs758827458, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with citrin deficiency (PMID: 19036621). ClinVar contains an entry for this variant (Variation ID: 449394). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003476219 SCV004201643 pathogenic Citrullinemia, type II, adult-onset 2023-02-27 criteria provided, single submitter clinical testing
Natera, Inc. RCV001834681 SCV002079379 pathogenic Citrullinemia 2020-08-14 no assertion criteria provided clinical testing

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