ClinVar Miner

Submissions for variant NM_000760.4(CSF3R):c.1624T>C (p.Trp542Arg)

gnomAD frequency: 0.00001  dbSNP: rs763748002
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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 RCV001070336 SCV001235559 uncertain significance Autosomal recessive severe congenital neutropenia due to CSF3R deficiency 2024-11-11 criteria provided, single submitter clinical testing This sequence change replaces tryptophan, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 542 of the CSF3R protein (p.Trp542Arg). This variant is present in population databases (rs763748002, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with CSF3R-related conditions. ClinVar contains an entry for this variant (Variation ID: 863380). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CSF3R 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.
Genetic Services Laboratory, University of Chicago RCV001819795 SCV002072373 uncertain significance not specified 2019-04-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV004977995 SCV005562423 uncertain significance Inborn genetic diseases 2024-07-09 criteria provided, single submitter clinical testing The c.1624T>C (p.W542R) alteration is located in exon 13 (coding exon 11) of the CSF3R gene. This alteration results from a T to C substitution at nucleotide position 1624, causing the tryptophan (W) at amino acid position 542 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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