ClinVar Miner

Submissions for variant NM_000340.2(SLC2A2):c.901C>T (p.Arg301Ter)

gnomAD frequency: 0.00004  dbSNP: rs121909743
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000017473 SCV000915036 pathogenic Fanconi-Bickel syndrome 2018-09-19 criteria provided, single submitter clinical testing The SLC2A2 c.901C>T (p.Arg301Ter) variant is a stop-gained variant that is predicted to result in a premature termination of the protein. The p.Arg301Ter variant has been reported in at least four studies in which it is found in a total of 17 individuals with Fanconi-Bickel syndrome, including in 16 in a homozygous state and in one in a compound heterozygous state with a nonsense variant (Santer et al. 2002; Su et al. 2011; Fridman et al. 2014; Dweikat et al. 2016). The variant was also found in a heterozygous state in two unaffected individuals (Su et al. 2011). Control data are unavailable for this variant, which is reported at a frequency of 0.000102 in the Ashkenazi Jewish population of the Genome Aggregation Database but this is based on one allele in a region of good sequence coverage so the variant is presumed to be rare. Due to the potential impact of stop-gained variants and the evidence from the literature, the p.Arg301Ter variant is classified as pathogenic for Fanconi-Bickel syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Institute of Human Genetics, University of Leipzig Medical Center RCV000017473 SCV001428626 pathogenic Fanconi-Bickel syndrome 2017-05-12 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000017473 SCV002020702 pathogenic Fanconi-Bickel syndrome 2023-04-13 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002496390 SCV002816839 pathogenic Type 2 diabetes mellitus; Fanconi-Bickel syndrome 2024-02-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000017473 SCV003525377 pathogenic Fanconi-Bickel syndrome 2022-04-09 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 16093). This premature translational stop signal has been observed in individual(s) with Fanconi-Bickel syndrome (PMID: 9354798, 24718840, 27487919). This variant is present in population databases (rs121909743, gnomAD 0.01%). This sequence change creates a premature translational stop signal (p.Arg301*) in the SLC2A2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC2A2 are known to be pathogenic (PMID: 11810292).
OMIM RCV000017473 SCV000037745 pathogenic Fanconi-Bickel syndrome 2002-01-01 no assertion criteria provided literature only

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