ClinVar Miner

Submissions for variant NM_002299.4(LCT):c.89C>T (p.Ser30Phe)

gnomAD frequency: 0.00003  dbSNP: rs368308800
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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 RCV001135457 SCV001295238 uncertain significance Congenital lactase deficiency 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Invitae RCV001856728 SCV002225749 uncertain significance not provided 2022-03-11 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 30 of the LCT protein (p.Ser30Phe). This variant is present in population databases (rs368308800, gnomAD 0.008%). 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: 894535). 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: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). 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 RCV002556887 SCV003720852 uncertain significance Inborn genetic diseases 2022-01-26 criteria provided, single submitter clinical testing The c.89C>T (p.S30F) alteration is located in exon 1 (coding exon 1) of the LCT gene. This alteration results from a C to T substitution at nucleotide position 89, causing the serine (S) at amino acid position 30 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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