ClinVar Miner

Submissions for variant NM_030962.4(SBF2):c.2669G>A (p.Arg890Gln)

gnomAD frequency: 0.00001  dbSNP: rs755699993
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000372252 SCV000375058 uncertain significance Charcot-Marie-Tooth disease type 4B2 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001344489 SCV001538547 uncertain significance Charcot-Marie-Tooth disease type 4 2020-06-04 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals with SBF2-related conditions. ClinVar contains an entry for this variant (Variation ID: 306593). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant is present in population databases (rs755699993, ExAC 0.002%). This sequence change replaces arginine with glutamine at codon 890 of the SBF2 protein (p.Arg890Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine.
Ambry Genetics RCV004021528 SCV004945702 uncertain significance Inborn genetic diseases 2023-12-11 criteria provided, single submitter clinical testing The c.2669G>A (p.R890Q) alteration is located in exon 22 (coding exon 22) of the SBF2 gene. This alteration results from a G to A substitution at nucleotide position 2669, causing the arginine (R) at amino acid position 890 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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