ClinVar Miner

Submissions for variant NM_006946.4(SPTBN2):c.4374G>T (p.Glu1458Asp)

gnomAD frequency: 0.00021  dbSNP: rs142378119
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000992854 SCV001145420 likely benign not provided 2018-09-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000992854 SCV002371034 likely benign not provided 2024-10-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV002549813 SCV003709537 uncertain significance Inborn genetic diseases 2022-04-22 criteria provided, single submitter clinical testing The c.4374G>T (p.E1458D) alteration is located in exon 21 (coding exon 20) of the SPTBN2 gene. This alteration results from a G to T substitution at nucleotide position 4374, causing the glutamic acid (E) at amino acid position 1458 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV000992854 SCV004167669 uncertain significance not provided 2023-04-18 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004526057 SCV005040495 uncertain significance not specified 2024-03-28 criteria provided, single submitter clinical testing Variant summary: SPTBN2 c.4374G>T (p.Glu1458Asp) results in a conservative amino acid change located in the Spectrin repeat (IPR002017) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00018 in 251358 control chromosomes. This frequency does not allow for any conclusion about variant significance. To our knowledge, no occurrence of c.4374G>T in individuals affected with Spinocerebellar Ataxia 5 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 805353). Based on the evidence outlined above, the variant was classified as uncertain significance.

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