ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.1196_1202del (p.Thr399fs) (rs761292021)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000671518 SCV000796502 likely pathogenic Alstrom syndrome 2017-12-27 criteria provided, single submitter clinical testing
Invitae RCV000671518 SCV001233884 pathogenic Alstrom syndrome 2020-10-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Thr400Lysfs*11) in the ALMS1 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 not been reported in the literature in individuals with ALMS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 555656). Loss-of-function variants in ALMS1 are known to be pathogenic (PMID: 17594715). For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001074661 SCV001240253 pathogenic Retinal dystrophy 2019-02-22 criteria provided, single submitter clinical testing
MAGI'S LAB - Medical Genetics Laboratory, MAGI GROUP RCV000671518 SCV001426409 pathogenic Alstrom syndrome 2020-08-04 criteria provided, single submitter clinical testing The p.(Thr399Lysfs*11) variant has been reported in two brothers with an atypical form of Alstrom syndrome (Lombardo 2020). It is a null variant in a gene where loss-of-funcion is a known mechanism of disease. It has been found at extremely low frequency in GnomAD. The variant has been detected in trans with a pathogenic variant, the p.(Glu3771Trpfs*18). In summary, the p.(Thr399Lysfs*11) variant meets the ACMG Guidelines (Richards 2015) criteria to be classified as pathogenic (PVS1, PM2, PM3 and PP5).
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001267997 SCV001446562 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV001267997 SCV001746655 pathogenic not provided 2021-03-01 criteria provided, single submitter clinical testing

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