ClinVar Miner

Submissions for variant NM_020533.3(MCOLN1):c.31+1G>A

gnomAD frequency: 0.00003  dbSNP: rs1057516246
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410923 SCV000485352 likely pathogenic Mucolipidosis type IV 2015-11-24 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000410923 SCV001577495 likely pathogenic Mucolipidosis type IV 2024-01-31 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 1 of the MCOLN1 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 MCOLN1 are known to be pathogenic (PMID: 11030752, 11317355, 37972748). This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with MCOLN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 370118). 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.
Natera, Inc. RCV000410923 SCV002091360 likely pathogenic Mucolipidosis type IV 2019-11-13 no assertion criteria provided clinical testing

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