ClinVar Miner

Submissions for variant NM_001040167.2(LFNG):c.559C>T (p.Arg187Cys)

gnomAD frequency: 0.00008  dbSNP: rs764283232
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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 RCV001374237 SCV001571035 uncertain significance Spondylocostal dysostosis 3, autosomal recessive 2020-08-29 criteria provided, single submitter clinical testing 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. 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: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with LFNG-related conditions. This variant is present in population databases (rs764283232, ExAC 0.02%). This sequence change replaces arginine with cysteine at codon 187 of the LFNG protein (p.Arg187Cys). The arginine residue is weakly conserved and there is a large physicochemical difference between arginine and cysteine.
GeneDx RCV001773739 SCV001993164 uncertain significance not provided 2021-01-08 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV003169928 SCV003879180 uncertain significance Inborn genetic diseases 2023-01-20 criteria provided, single submitter clinical testing The c.559C>T (p.R187C) alteration is located in exon 3 (coding exon 3) of the LFNG gene. This alteration results from a C to T substitution at nucleotide position 559, causing the arginine (R) at amino acid position 187 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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