ClinVar Miner

Submissions for variant NM_000340.2(SLC2A2):c.682C>T (p.Arg228Ter)

dbSNP: rs773581866
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV002246720 SCV002519770 pathogenic Type 2 diabetes mellitus 2022-05-04 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003094039 SCV003525677 pathogenic Fanconi-Bickel syndrome 2022-09-07 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 1686207). This premature translational stop signal has been observed in individual(s) with Fanconi-Bickel syndrome (PMID: 22145468). This variant is present in population databases (rs773581866, gnomAD 0.006%). This sequence change creates a premature translational stop signal (p.Arg228*) 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).
Neuberg Centre For Genomic Medicine, NCGM RCV003094039 SCV005329496 pathogenic Fanconi-Bickel syndrome 2023-05-20 criteria provided, single submitter clinical testing The observed stop gained c.682C>T(p.Arg228Ter) variant in SLC2A2 gene has been reported in compound heterozygous state in an individual affected with Fanconi-Bickel syndrome (Su Z, et. al., 2011). This variant is present with an allele frequency of 0.001% in gnomAD Exomes database. This variant has been reported to the ClinVar database as Pathogenic. Computational evidence (MutationTaster - disease causing) predict a damaging effect on protein structure and function for this variant. The nucleotide change c.682C>T in SLC2A2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic.

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