ClinVar Miner

Submissions for variant NM_018368.4(LMBRD1):c.416C>T (p.Thr139Met)

gnomAD frequency: 0.00005  dbSNP: rs767657325
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001950269 SCV002221764 uncertain significance Methylmalonic aciduria and homocystinuria type cblF 2022-07-06 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 139 of the LMBRD1 protein (p.Thr139Met). This variant is present in population databases (rs767657325, gnomAD 0.08%). This variant has not been reported in the literature in individuals affected with LMBRD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1439848). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 RCV002563378 SCV003575907 uncertain significance Inborn genetic diseases 2021-01-27 criteria provided, single submitter clinical testing The c.416C>T (p.T139M) alteration is located in exon 5 (coding exon 5) of the LMBRD1 gene. This alteration results from a C to T substitution at nucleotide position 416, causing the threonine (T) at amino acid position 139 to be replaced by a methionine (M). The p.T139M alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Breakthrough Genomics, Breakthrough Genomics RCV004694021 SCV005189099 uncertain significance not provided criteria provided, single submitter not provided

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