ClinVar Miner

Submissions for variant NM_020166.5(MCCC1):c.1682-3A>G

gnomAD frequency: 0.00001  dbSNP: rs760180709
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520630 SCV000617483 pathogenic not provided 2016-07-29 criteria provided, single submitter clinical testing The c.1682-3 A>G splice site variant in the MCCC1 gene has been previously reported in association with mild 3-methylcrotonyl-CoA carboxylase (3-MCC) deficiency in an individual who was heterozygous for c.1682-3 A>G and a frame shift variant in the MCCC1 gene (Dantas et al., 2005). Functional analysis of c.1682-3 A>G found that it results in abnormal splicing (Dantas et al., 2005). Therefore, we interpret c.1682-3 A>G to be a pathogenic variant.
Invitae RCV002525116 SCV003525389 uncertain significance 3-methylcrotonyl-CoA carboxylase 1 deficiency 2022-04-08 criteria provided, single submitter clinical testing This sequence change falls in intron 14 of the MCCC1 gene. It does not directly change the encoded amino acid sequence of the MCCC1 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs760180709, gnomAD 0.003%). This variant has been observed in individual(s) with 3 methylcrotonyl-CoA carboxylase deficiency (PMID: 16010683). ClinVar contains an entry for this variant (Variation ID: 449385). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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 available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Baylor Genetics RCV002525116 SCV004194294 likely pathogenic 3-methylcrotonyl-CoA carboxylase 1 deficiency 2023-01-24 criteria provided, single submitter clinical testing

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