Total submissions: 5
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Invitae | RCV000017472 | SCV001414737 | pathogenic | Fanconi-Bickel syndrome | 2019-10-03 | criteria provided, single submitter | clinical testing | For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SLC2A2 are known to be pathogenic (PMID: 11810292). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has been observed in individuals and families affected with Fanconi-Bickel syndrome (PMID: 9354798, 11810292). ClinVar contains an entry for this variant (Variation ID: 16092). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Arg365*) in the SLC2A2 gene. It is expected to result in an absent or disrupted protein product. |
| Laboratory of Cyto- |
RCV000017472 | SCV002102792 | pathogenic | Fanconi-Bickel syndrome | 2022-03-07 | criteria provided, single submitter | clinical testing | |
| Fulgent Genetics, |
RCV002490379 | SCV002794729 | pathogenic | Type 2 diabetes mellitus; Fanconi-Bickel syndrome | 2022-03-22 | criteria provided, single submitter | clinical testing | |
| Lifecell International Pvt. |
RCV000017472 | SCV003929436 | pathogenic | Fanconi-Bickel syndrome | criteria provided, single submitter | clinical testing | A Heterozygous Nonsense variant c.1093C>T in Exon 9 of the SLC2A2 gene that results in the amino acid substitution p.Arg365* was identified. The observed variant has a maximum allele frequency of 0.00001/0.00006% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. This variant has been reported as Pathogenic in the ClinVar database (Variant ID: 16092). This variant was reported among patients for Fanconi-Bickel syndrome (Santer R et al., 2002). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. | |
| OMIM | RCV000017472 | SCV000037744 | pathogenic | Fanconi-Bickel syndrome | 2002-01-01 | no assertion criteria provided | literature only |