ClinVar Miner

Submissions for variant NM_004252.5(NHERF1):c.657C>G (p.Ile219Met)

gnomAD frequency: 0.00047  dbSNP: rs147104235
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000680101 SCV000807542 uncertain significance Hypophosphatemic nephrolithiasis/osteoporosis 2 2017-09-01 criteria provided, single submitter clinical testing Possible pathogenicity based on finding it once in our laboratory maternally inherited in a 16-year-old female with osteoporosis, increaed bone resorption, epistaxis, headaches, muscle/jiont aches, scoliosis, joint laxity. However, it has also been found in controls and in 3 other such individuals in our laboroatory without such phenotypes.
Labcorp Genetics (formerly Invitae), Labcorp RCV001065657 SCV001230627 uncertain significance not provided 2025-01-01 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 219 of the SLC9A3R1 protein (p.Ile219Met). This variant is present in population databases (rs147104235, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with SLC9A3R1-related conditions. ClinVar contains an entry for this variant (Variation ID: 561111). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.
PreventionGenetics, part of Exact Sciences RCV003965432 SCV004785158 likely benign NHERF1-related disorder 2023-11-15 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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