ClinVar Miner

Submissions for variant NM_031885.5(BBS2):c.563del (p.Ile188fs)

gnomAD frequency: 0.00001  dbSNP: rs1367927635
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667813 SCV000792318 likely pathogenic Bardet-Biedl syndrome 2 2017-06-14 criteria provided, single submitter clinical testing
Invitae RCV001224369 SCV001396559 pathogenic Bardet-Biedl syndrome 2023-11-17 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ile188Thrfs*13) in the BBS2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BBS2 are known to be pathogenic (PMID: 11285252, 20177705, 24608809, 26518167). This variant is present in population databases (no rsID available, gnomAD 0.02%). This premature translational stop signal has been observed in individuals with Bardet-Biedl syndrome and retinitis pigmentosa (PMID: 24608809, 31960602). ClinVar contains an entry for this variant (Variation ID: 552531). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001224369 SCV001774528 pathogenic Bardet-Biedl syndrome 2021-07-11 criteria provided, single submitter clinical testing Variant summary: BBS2 c.563delT (p.Ile188ThrfsX13) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 8e-06 in 251312 control chromosomes. c.563delT has been reported in the literature in individuals affected with Bardet-Biedl Syndrome (example, Xing_2014, Dan_2020, Meng_2021). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Fulgent Genetics, Fulgent Genetics RCV002477490 SCV002784318 pathogenic Bardet-Biedl syndrome 2; Retinitis pigmentosa 74 2021-08-17 criteria provided, single submitter clinical testing
Baylor Genetics RCV000667813 SCV004213985 pathogenic Bardet-Biedl syndrome 2 2023-10-21 criteria provided, single submitter clinical testing
Natera, Inc. RCV000667813 SCV002089301 pathogenic Bardet-Biedl syndrome 2 2020-02-01 no assertion criteria provided clinical testing
Department of Pediatrics, National Cheng-Kung University Hospital RCV000667813 SCV004042839 pathogenic Bardet-Biedl syndrome 2 no assertion criteria provided clinical testing

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