ClinVar Miner

Submissions for variant NM_014251.3(SLC25A13):c.1763G>A (p.Arg588Gln)

gnomAD frequency: 0.00001  dbSNP: rs121908532
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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) RCV000728351 SCV000855909 uncertain significance not provided 2017-07-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV001267011 SCV001445192 likely pathogenic Inborn genetic diseases 2018-02-19 criteria provided, single submitter clinical testing
Genesolutions, Medical Genetics Institutes, Ho Chi Minh City, Vietnam RCV002508184 SCV002546535 pathogenic Neonatal intrahepatic cholestasis due to citrin deficiency 2022-06-30 criteria provided, single submitter clinical testing
Invitae RCV003581555 SCV004277027 likely pathogenic Citrin deficiency 2023-04-06 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 6007). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Arg588 amino acid residue in SLC25A13. Other variant(s) that disrupt this residue have been observed in individuals with SLC25A13-related conditions (PMID: 27829683), which suggests that this may be a clinically significant amino acid residue. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Experimental studies have shown that this missense change affects SLC25A13 function (PMID: 18367750). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SLC25A13 protein function. This missense change has been observed in individual(s) with citrin deficiency (PMID: 18392553, 36599957). 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 (rs121908532, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 588 of the SLC25A13 protein (p.Arg588Gln).
OMIM RCV000006376 SCV000026558 pathogenic Citrullinemia type II 2008-03-27 no assertion criteria provided literature only
Natera, Inc. RCV001831517 SCV002079362 likely pathogenic Citrullinemia 2021-04-01 no assertion criteria provided clinical testing

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