ClinVar Miner

Submissions for variant NM_014251.3(SLC25A13):c.1799dup (p.Tyr600Ter)

gnomAD frequency: 0.00001  dbSNP: rs80338726
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000006375 SCV001163571 pathogenic Neonatal intrahepatic cholestasis due to citrin deficiency criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001060497 SCV001225190 pathogenic Citrin deficiency 2024-07-02 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr600*) in the SLC25A13 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 76 amino acid(s) of the SLC25A13 protein. This variant is present in population databases (rs80338726, gnomAD 0.02%). This premature translational stop signal has been observed in individuals with citrin deficiency (PMID: 11153906, 11343052). This variant is also known as Mutation VI, 1800ins1. ClinVar contains an entry for this variant (Variation ID: 6006). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant disrupts the C-terminus of the SLC25A13 protein. Other variant(s) that disrupt this region (p.Arg605*, p.Glu601*) have been observed in individuals with SLC25A13-related conditions (PMID: 11153906, 11793471). This suggests that this may be a clinically significant region of the protein. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003472984 SCV004201635 pathogenic Citrullinemia, type II, adult-onset 2024-03-12 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005031399 SCV005671911 likely pathogenic Neonatal intrahepatic cholestasis due to citrin deficiency; Citrullinemia, type II, adult-onset 2024-06-14 criteria provided, single submitter clinical testing
OMIM RCV000006374 SCV000026556 pathogenic Citrullinemia type II 2001-05-01 no assertion criteria provided literature only
GeneReviews RCV000006374 SCV000041256 not provided Citrullinemia type II no assertion provided literature only
Natera, Inc. RCV001831516 SCV002079361 pathogenic Citrullinemia 2020-09-16 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004742218 SCV005362959 pathogenic SLC25A13-related disorder 2024-07-10 no assertion criteria provided clinical testing The SLC25A13 c.1799dupA variant is predicted to result in premature protein termination (p.Tyr600*). This variant was reported along with a second SLC25A13 variant in at least two individuals with citrullinaemia, type II (described as [VI] 1800ins1 in Yasuda et al 2000. PubMed ID: 11153906; described as mutation VI in Tazawa et al. 2001. PubMed ID: 11343052). Citrin protein was found to be absent in a liver sample from the patient described by Yasuda et al. (see Figure 4, Yasuda et al 2000. PubMed ID: 11153906). This variant is reported in 0.017% of alleles in individuals of Latino descent in gnomAD. Nonsense variants in SLC25A13 are expected to be pathogenic. Taken together, this variant is interpreted as pathogenic.
OMIM RCV005234781 SCV005880359 pathogenic CITRIN DEFICIENCY, NEONATAL ONSET 2001-05-01 no assertion criteria provided literature only

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