ClinVar Miner

Submissions for variant NM_020166.5(MCCC1):c.1225C>T (p.Arg409Ter)

gnomAD frequency: 0.00001  dbSNP: rs1484347924
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000579365 SCV000680698 pathogenic not provided 2017-09-05 criteria provided, single submitter clinical testing The R409X nonsense variant in the MCCC1 gene has been reported previously in association with 3-methylcrotonyl-CoA carboxylase (3-MCC) deficiency (Stadler et al., 2006). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R409X variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). In summary, we interpret R409X to be a pathogenic variant.
Invitae RCV000653486 SCV000775365 pathogenic 3-methylcrotonyl-CoA carboxylase 1 deficiency 2024-01-26 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg409*) in the MCCC1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MCCC1 are known to be pathogenic (PMID: 11181649, 15359379, 22642865). This variant is present in population databases (no rsID available, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with 3-Methylcrotonyl-CoA carboxylase deficiency (PMID: 16835865). ClinVar contains an entry for this variant (Variation ID: 488805). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000653486 SCV004194273 pathogenic 3-methylcrotonyl-CoA carboxylase 1 deficiency 2023-07-30 criteria provided, single submitter clinical testing
Natera, Inc. RCV000653486 SCV002079102 pathogenic 3-methylcrotonyl-CoA carboxylase 1 deficiency 2020-09-29 no assertion criteria provided clinical testing

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