ClinVar Miner

Submissions for variant NM_015166.4(MLC1):c.177+1G>T

gnomAD frequency: 0.00001  dbSNP: rs1374593138
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000661967 SCV000784298 uncertain significance Megalencephalic leukoencephalopathy with subcortical cysts 2018-03-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001380082 SCV001578025 pathogenic not provided 2023-05-05 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 548493). Disruption of this splice site has been observed in individuals with megalencephalic leukoencephalopathy with subcortical cysts (PMID: 12939431, 27264811). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 2 of the MLC1 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 MLC1 are known to be pathogenic (PMID: 11254442, 16470554, 24824219).
Kariminejad - Najmabadi Pathology & Genetics Center RCV001814208 SCV001755188 pathogenic Abnormality of the nervous system 2021-07-10 criteria provided, single submitter clinical testing
Baylor Genetics RCV003472059 SCV004194970 pathogenic Megalencephalic leukoencephalopathy with subcortical cysts 1 2023-10-16 criteria provided, single submitter clinical testing

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