ClinVar Miner

Submissions for variant NM_000390.4(CHM):c.715C>T (p.Arg239Ter) (rs776256380)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000302207 SCV000338914 pathogenic not provided 2016-01-08 criteria provided, single submitter clinical testing
GeneDx RCV000302207 SCV000890160 pathogenic not provided 2018-06-22 criteria provided, single submitter clinical testing The R239X nonsense variant has been reported previously in association with choroideremia (Francis et al., 2005; Jolly et al., 2015). The variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In summary, we consider this variant to be pathogenic.
Fulgent Genetics,Fulgent Genetics RCV000763635 SCV000894505 pathogenic Choroideremia 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000302207 SCV000964509 pathogenic not provided 2019-01-03 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg239*) in the CHM gene. It is expected to result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has been observed in several individuals affected with choroideremia (PMID: 23811034, 16087855, 26133251, 12827496, Invitae), and was observed to segregate with choroideremia in two families (PMID: 16087855, 26133251). ClinVar contains an entry for this variant (Variation ID: 285756). Loss-of-function variants in CHM are known to be pathogenic (PMID: 9067750, 23811034). For these reasons, this variant has been classified as Pathogenic.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000302207 SCV001248392 pathogenic not provided 2016-10-01 criteria provided, single submitter clinical testing
Sharon lab,Hadassah-Hebrew University Medical Center RCV000763635 SCV001160984 pathogenic Choroideremia 2019-06-23 no assertion criteria provided research

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