ClinVar Miner

Submissions for variant NM_000444.6(PHEX):c.2028_2032del (p.Thr677fs)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Lifecell International Pvt. Ltd RCV003159275 SCV003852648 likely pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets criteria provided, single submitter clinical testing A Heterozygous Frameshift variant c.2025_2029delCATCA in Exon 20 of the PHEX gene that results in the amino acid substitution p.Thr677fs*38 was identified. The observed variant is novel in gnomAD exomes and genomes. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. For these reasons, this variant has been classified as Likely Pathogenic.

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