ClinVar Miner

Submissions for variant NM_015120.4(ALMS1):c.5145T>G (p.Tyr1715Ter) (rs772136379)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000494458 SCV000582569 pathogenic not provided 2017-04-13 criteria provided, single submitter clinical testing The Y1715X variant in the ALMS1 gene has been reported in one patient with Alstrom syndrome who harbored a second nonsense variant in the ALMS1 gene in trans (Piñeiro-Gallego et al., 2012). Additionally, this variant has been classified as a likely pathogenic variant by another clinical laboratory in ClinVar (SCV000223919.1; Landrum et al., 2016). This variant is predicted to cause loss of normal protein function either by protein truncation or nonsense-mediated mRNA decay. Other nonsense variants in the ALMS1 gene have been reported in Human Gene Mutation Database in association with Alstrom syndrome (Stenson et al., 2014). Furthermore, the Y1715X variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server)
Invitae RCV000192391 SCV001234870 pathogenic Alstrom syndrome 2019-06-05 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr1715*) in the ALMS1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs772136379, ExAC 0.003%). This variant has been observed in several individuals affected with ALMS1-related conditions (PMID: 22876109, 28432734, 25846608). ClinVar contains an entry for this variant (Variation ID: 212728). Loss-of-function variants in ALMS1 are known to be pathogenic (PMID: 17594715). For these reasons, this variant has been classified as Pathogenic.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000494458 SCV001247529 pathogenic not provided 2016-12-01 criteria provided, single submitter clinical testing
Knight Diagnostic Laboratories, Oregon Health and Sciences University RCV000192391 SCV000223919 likely pathogenic Alstrom syndrome 2014-08-12 no assertion criteria provided clinical testing
Counsyl RCV000192391 SCV000793022 pathogenic Alstrom syndrome 2017-07-25 no assertion criteria provided clinical testing
Laboratory of Genetics in Ophthalmology,Institut Imagine RCV001255897 SCV001432500 pathogenic Retinal dystrophy, early-onset severe no assertion criteria provided research

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