ClinVar Miner

Submissions for variant NM_000155.4(GALT):c.1060-1G>A (rs367543268)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000725094 SCV000333965 pathogenic not provided 2015-08-24 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000022275 SCV001360424 likely pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2019-11-07 criteria provided, single submitter clinical testing Variant summary: GALT c.1060-1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 3' acceptor site and creates an alternate adjacent 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 251440 control chromosomes. To our knowledge, no occurrence of c.1060-1G>A in individuals affected with Galactosemia and no experimental evidence demonstrating its impact on protein function have been reported in the literature. However, at-least one laboratory that has submitted a pathogenic classification of this variant to ClinVar before 2014 reports this variant as "detected in a male patient with Duarte 2 haplotype and enzyme activity of 4.8 micromol/hour/gHB". They go on to state, "This mutation is expected to affect normal splicing of exon 11." Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (n=1)/likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Research and Development, ARUP Laboratories RCV000022275 SCV000042960 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2012-12-04 no assertion criteria provided clinical testing Converted during submission to Pathogenic.
Counsyl RCV000022275 SCV000794610 likely pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2019-07-12 no assertion criteria provided clinical testing

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