ClinVar Miner

Submissions for variant NM_014251.3(SLC25A13):c.1311+1G>A

gnomAD frequency: 0.00001  dbSNP: rs80338723
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 7
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000796573 SCV000936092 pathogenic Citrin deficiency 2023-11-20 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 13 of the SLC25A13 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SLC25A13 are known to be pathogenic (PMID: 10369257, 14680984, 27405544). This variant is present in population databases (rs80338723, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with citrin deficiency (PMID: 10369257, 29659898). This variant is also known as IVS13+1G>A. ClinVar contains an entry for this variant (Variation ID: 6005). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003472983 SCV004203615 pathogenic Citrullinemia, type II, adult-onset 2024-03-20 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV003488327 SCV004238360 pathogenic not provided 2023-03-09 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV004786241 SCV005401048 pathogenic Neonatal intrahepatic cholestasis due to citrin deficiency criteria provided, single submitter clinical testing The observed invariant splice donor c.1311+1G>A variant in SLC25A13 gene has been reported previously reported in multiple individuals affected with citrin deficiency (Kobayashi et al., 1999; Kobayashi et al., 2003 Hirayama et al., 2018). The c.1311+1G>A variant is present with allele frequency of 0.0004% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Pathogenic. Loss of function variants in SLC25A13 gene have been previously reported to be disease causing (Lin et al., 2016). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000006373 SCV000026555 pathogenic Citrullinemia type II 1999-06-01 no assertion criteria provided literature only
GeneReviews RCV000006373 SCV000041251 not provided Citrullinemia type II no assertion provided literature only
Natera, Inc. RCV001277071 SCV001463806 pathogenic Late-onset citrullinemia 2020-09-16 no assertion criteria provided clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.