ClinVar Miner

Submissions for variant NM_014254.3(RXYLT1):c.17A>G (p.Lys6Arg)

gnomAD frequency: 0.00011  dbSNP: rs145516652
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001034624 SCV000772542 uncertain significance not provided 2022-10-14 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 6 of the RXYLT1 protein (p.Lys6Arg). This variant is present in population databases (rs145516652, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with RXYLT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 540603). 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 arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.
Fulgent Genetics, Fulgent Genetics RCV000650695 SCV000896325 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 2018-10-31 criteria provided, single submitter clinical testing
GeneDx RCV001034624 SCV001814561 uncertain significance not provided 2020-06-16 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Mayo Clinic Laboratories, Mayo Clinic RCV001034624 SCV004226360 uncertain significance not provided 2023-05-12 criteria provided, single submitter clinical testing BP4
Ambry Genetics RCV004025813 SCV004945773 uncertain significance Inborn genetic diseases 2021-08-02 criteria provided, single submitter clinical testing The c.17A>G (p.K6R) alteration is located in exon 1 (coding exon 1) of the TMEM5 gene. This alteration results from a A to G substitution at nucleotide position 17, causing the lysine (K) at amino acid position 6 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GenomeConnect - Invitae Patient Insights Network RCV000650695 SCV004228842 not provided Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 06-14-2021 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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