ClinVar Miner

Submissions for variant NM_001283009.2(RTEL1):c.1648C>T (p.Arg550Cys)

gnomAD frequency: 0.00001  dbSNP: rs369419645
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000478358 SCV000571807 likely pathogenic not provided 2023-04-17 criteria provided, single submitter clinical testing Observed in large population cohorts (gnomAD; internal data); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29361909, 30995915)
Labcorp Genetics (formerly Invitae), Labcorp RCV000688506 SCV000816122 uncertain significance Dyskeratosis congenita, autosomal recessive 5; Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 2022-07-19 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 550 of the RTEL1 protein (p.Arg550Cys). This variant is present in population databases (rs369419645, gnomAD 0.01%). This missense change has been observed in individual(s) with pulmonary fibrosis (PMID: 30995915). This variant is also known as p.Arg574Cys. ClinVar contains an entry for this variant (Variation ID: 422356). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest 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.
3billion RCV000984211 SCV002058712 uncertain significance Dyskeratosis congenita, autosomal recessive 5 2022-01-03 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000028, PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.713, PP3_P). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.
Sema4, Sema4 RCV002255417 SCV002535297 uncertain significance Dyskeratosis congenita 2022-03-05 criteria provided, single submitter curation
Counsyl RCV000984211 SCV001132278 uncertain significance Dyskeratosis congenita, autosomal recessive 5 2019-01-09 no assertion criteria provided clinical testing

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