ClinVar Miner

Submissions for variant NM_006363.6(SEC23B):c.689+1G>A

gnomAD frequency: 0.00003  dbSNP: rs398124226
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000081409 SCV000113340 pathogenic not provided 2012-09-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000689848 SCV000817517 pathogenic Congenital dyserythropoietic anemia, type II; Cowden syndrome 7 2024-09-22 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 6 of the SEC23B 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 SEC23B are known to be pathogenic (PMID: 19561605, 25044164). This variant is present in population databases (rs398124226, gnomAD 0.005%). Disruption of this splice site has been observed in individuals with congenital dyserythropoietic anemia type II (PMID: 19561605, 19621418). ClinVar contains an entry for this variant (Variation ID: 95389). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001195899 SCV001366323 pathogenic Congenital dyserythropoietic anemia, type II 2019-04-02 criteria provided, single submitter clinical testing This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PM2,PM3.
Revvity Omics, Revvity RCV000081409 SCV002020048 pathogenic not provided 2021-05-05 criteria provided, single submitter clinical testing
MGZ Medical Genetics Center RCV002288579 SCV002580338 pathogenic Cowden syndrome 7 2021-08-20 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000689848 SCV005656378 pathogenic Congenital dyserythropoietic anemia, type II; Cowden syndrome 7 2024-05-02 criteria provided, single submitter clinical testing

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