ClinVar Miner

Submissions for variant NM_001079866.2(BCS1L):c.889+1G>T

gnomAD frequency: 0.00001  dbSNP: rs1057516346
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000411192 SCV000485504 likely pathogenic GRACILE syndrome 2015-12-27 criteria provided, single submitter clinical testing
GeneDx RCV000522697 SCV000619524 pathogenic not provided 2017-08-14 criteria provided, single submitter clinical testing The c.889+1 G>T splice site variant in the BCS1L gene destroys the canonical splice donor site in intron 7. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Additionally, the c.889+1 G>T variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Although this variant has not been previously reported to our knowledge, it is expected to be a pathogenic variant.
Invitae RCV000522697 SCV002117415 likely pathogenic not provided 2023-08-24 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with BCS1L-related conditions. ClinVar contains an entry for this variant (Variation ID: 370247). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant is present in population databases (no rsID available, gnomAD 0.002%). This sequence change affects a donor splice site in intron 7 of the BCS1L gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BCS1L are known to be pathogenic (PMID: 12215968, 17314340, 19162478, 19508421, 22277166, 25895478).
Fulgent Genetics, Fulgent Genetics RCV002502421 SCV002811481 likely pathogenic Pili torti-deafness syndrome; GRACILE syndrome; Mitochondrial complex III deficiency nuclear type 1 2021-12-25 criteria provided, single submitter clinical testing
Baylor Genetics RCV003475942 SCV004210810 likely pathogenic Pili torti-deafness syndrome 2023-05-23 criteria provided, single submitter clinical testing

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