ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.6157C>T (p.Arg2053Ter)

dbSNP: rs587783450
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000145682 SCV000192786 pathogenic CHARGE association 2013-02-08 criteria provided, single submitter clinical testing
GeneDx RCV000389698 SCV000329271 pathogenic not provided 2015-12-30 criteria provided, single submitter clinical testing The R2053X nonsense variant in the CHD7 gene has been reported previously in association with CHARGE syndrome (Lalani et al., 2006; Sanlaville et al., 2006; Husu et al., 2013). Approximately 45% of CHD7 pathogenic variants are nonsense changes predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay (Janssen et al., 2012; Zentner et al, 2010). Additionally, the R2053X variant was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Therefore, the presence of the R2053X pathogenic variant is consistent with a diagnosis of CHARGE syndrome
Fulgent Genetics, Fulgent Genetics RCV000763601 SCV000894446 pathogenic CHARGE association; Hypogonadotropic hypogonadism 5 with or without anosmia 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000145682 SCV000947897 pathogenic CHARGE association 2023-11-25 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg2053*) in the CHD7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CHD7 are known to be pathogenic (PMID: 22461308, 25077900). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with CHARGE syndrome (PMID: 16400610, 22033296, 22462537, 25077900). ClinVar contains an entry for this variant (Variation ID: 158307). For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV000389698 SCV001249587 pathogenic not provided 2019-07-01 criteria provided, single submitter clinical testing

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