ClinVar Miner

Submissions for variant NM_000340.2(SLC2A2):c.775+1G>A

gnomAD frequency: 0.00001  dbSNP: rs756874949
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000594596 SCV000708938 pathogenic not provided 2017-05-31 criteria provided, single submitter clinical testing
Invitae RCV001060330 SCV001225010 likely pathogenic Fanconi-Bickel syndrome 2023-05-23 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. ClinVar contains an entry for this variant (Variation ID: 502268). Disruption of this splice site has been observed in individual(s) with Fanconi-Bickel syndrome (PMID: 11810292). This variant is present in population databases (rs756874949, gnomAD 0.004%). This sequence change affects a donor splice site in intron 6 of the SLC2A2 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 SLC2A2 are known to be pathogenic (PMID: 11810292).
Fulgent Genetics, Fulgent Genetics RCV002483654 SCV002777878 pathogenic Type 2 diabetes mellitus; Fanconi-Bickel syndrome 2022-05-05 criteria provided, single submitter clinical testing
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV001060330 SCV003915824 pathogenic Fanconi-Bickel syndrome 2023-04-14 criteria provided, single submitter clinical testing A homozygous 5’ splice site variant in intron 6 of the SLC2A2 gene that affects the invariant GT donor splice site downstream of exon 6 (c.775+1G>A) was detected. The observed variant has been previously reported in the patients affected with Fanconi-Bickel syndrome [PMID: 31589614]. The variant has not been reported in the 1000 genomes databases and has a minor allele frequency of 0.001%, 0.0008% and 0.0004% n the gnomAD (v3.1), gnomdAD (v2.1) and topmed databases respectively. The in-silico predictions of the variant is damaging by MutationTaster2. The reference base is conserved across species. In summary, the variant meets our criteria to be classified as pathogenic.

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