ClinVar Miner

Submissions for variant NM_014251.3(SLC25A13):c.852_855del (p.Met285fs) (rs80338720)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center RCV000239614 SCV000267504 pathogenic Citrullinemia type II 2016-03-18 criteria provided, single submitter reference population
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000724667 SCV000331844 pathogenic not provided 2017-09-29 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000239614 SCV000470730 pathogenic Citrullinemia type II 2017-04-27 criteria provided, single submitter clinical testing The SLC25A13 c.852_855delTATG (p.Met285ProfsTer2) variant, also referred to in the literature as c.851_854del and c.851del4, is a frameshift variant that leads to premature truncation of the protein, and is one of the most common pathogenic variants in Japanese persons with citrin deficiency. Across a selection of available literature, the p.Met285ProfsTer2 variant has been identified in a homozygous state in 30 patients, in a compound heterozygous state in 27 patients, and in a heterozygous state in two patients in whom a second variant was not identified (Kobayashi et al. 1999; Ohura et al. 2001; Tamamori et al. 2002; Song et al. 2011). The p.Met285ProfsTer2 variant was absent from 127 controls and is reported at a frequency of 0.01515 in the Kinh in Ho Chi Minh City, Vietnam population of the 1000 Genomes Project. Based on the collective evidence and the potential impact of frameshift variants, the p.Met285ProfsTer2 variant is classified as pathogenic for citrin deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV000344746 SCV000646232 pathogenic Citrin deficiency 2020-10-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Met285Profs*2) in the SLC25A13 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs569808959, ExAC 0.4%). This variant has been reported as the most common cause of citrin deficiency in China and the second most common in Japan, although it has been reported in other populations (PMID: 10369257, 27577219, 12512993, 23022256, 23067347, 26852511, 27347070, 27405544, 27577219, 27578510). This variant is also known as c.851del4 in the literature. ClinVar contains an entry for this variant (Variation ID: 225472). Loss-of-function variants in SLC25A13 are known to be pathogenic (PMID: 27405544, 14680984, 10369257). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000006368 SCV001163576 pathogenic Neonatal intrahepatic cholestasis caused by citrin deficiency criteria provided, single submitter clinical testing
OMIM RCV000239614 SCV000026549 pathogenic Citrullinemia type II 2002-11-01 no assertion criteria provided literature only
OMIM RCV000006368 SCV000026550 pathogenic Neonatal intrahepatic cholestasis caused by citrin deficiency 2002-11-01 no assertion criteria provided literature only
GeneReviews RCV000239614 SCV000041264 pathologic Citrullinemia type II 2012-01-05 no assertion criteria provided curation Converted during submission to Pathogenic.
SingHealth Duke-NUS Institute of Precision Medicine RCV000006368 SCV000853101 pathogenic Neonatal intrahepatic cholestasis caused by citrin deficiency 2017-06-07 no assertion criteria provided curation
Natera, Inc. RCV001272102 SCV001453749 pathogenic Late-onset citrullinemia 2020-09-16 no assertion criteria provided clinical testing

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