ClinVar Miner

Submissions for variant NM_002299.4(LCT):c.3286G>A (p.Ala1096Thr)

gnomAD frequency: 0.00066  dbSNP: rs146467199
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000279445 SCV000416497 uncertain significance Congenital lactase deficiency 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000350754 SCV000416498 uncertain significance Lactose intolerance 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV001859967 SCV002307292 uncertain significance not provided 2022-10-26 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1096 of the LCT protein (p.Ala1096Thr). This variant is present in population databases (rs146467199, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with LCT-related conditions. ClinVar contains an entry for this variant (Variation ID: 331189). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt LCT protein function. 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.
Ambry Genetics RCV002521291 SCV003580377 uncertain significance Inborn genetic diseases 2022-08-02 criteria provided, single submitter clinical testing The c.3286G>A (p.A1096T) alteration is located in exon 8 (coding exon 8) of the LCT gene. This alteration results from a G to A substitution at nucleotide position 3286, causing the alanine (A) at amino acid position 1096 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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