ClinVar Miner

Submissions for variant NM_000155.2(GALT):c.-119_-116delGTCA (rs111033640)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000185922 SCV000238877 pathogenic not provided 2018-12-04 criteria provided, single submitter clinical testing When c.-119_116delGTCA promoter mutation (Duarte-2 variant) is present on the same GALT allele (in cis) as the N314D, the result is an impaired regulatory domain of the GALT enzyme and approximately 50% of normal galactose-1-phosphate uridyltransferase (GALT) activity (Bosch et al., 2005). Newborns who are compound heterozygotes for the Duarte-2 variant (D" mutation) and a mutation associated with classic galactosemia ("G" mutation) are considered to have Duarte-2 variant galactosemia or D/G galactosemia which may be identified by newborn screening programs and is associated with approximately 50% of control galactosyltransferase activity, on average (Elsas, 2001)."
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000185922 SCV000858734 other not provided 2018-07-23 criteria provided, single submitter clinical testing
Invitae RCV000022037 SCV000959727 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2019-01-09 criteria provided, single submitter clinical testing This sequence change deletes 4 nucleotides (-119_-116delGTCA) in the GALT promoter without disrupting the protein coding sequence. This variant is present in population databases (rs111033640, 1KG 5.0%). This variant is unique to the D2 allele and is a well-known cause of Duarte galactosemia with a partial reduction, typically 14%-25% of wild-type GALT enzyme activity (PMID: 25473725). ClinVar contains two entries for this variant (Variation ID: 140570, 25111). Experimental studies have shown that this variant causes diminished GALT promoter activity in vitro and reduced GALT mRNA level in patient cells (PMID: 11286503, 11479743, 19224951). For these reasons, this sequence change has been classified as Pathogenic.
Mendelics RCV000022037 SCV001137799 likely pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2019-05-28 criteria provided, single submitter clinical testing
OMIM RCV000003809 SCV000023974 pathogenic Classical galactosemia, homozygous Duarte-type 2009-05-01 no assertion criteria provided literature only
Research and Development, ARUP Laboratories RCV000022037 SCV000042712 benign Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2012-12-04 no assertion criteria provided clinical testing Converted during submission to Benign.
Integrated Genetics/Laboratory Corporation of America RCV000022037 SCV000052459 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2015-10-15 no assertion criteria provided clinical testing
GeneReviews RCV000022037 SCV000257439 benign Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2014-09-23 no assertion criteria provided literature only

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