ClinVar Miner

Submissions for variant NM_020166.5(MCCC1):c.1679dup (p.Asn560fs)

dbSNP: rs1394547323
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000653492 SCV000775372 pathogenic 3-methylcrotonyl-CoA carboxylase 1 deficiency 2023-10-14 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Asn560Lysfs*10) 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 not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with 3-methylcrotonyl-CoA carboxylase deficiency (PMID: 24078573, 25382614; Invitae). This variant is also known as c.1680insA. ClinVar contains an entry for this variant (Variation ID: 542948). For these reasons, this variant has been classified as Pathogenic.
Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital RCV000653492 SCV001739454 pathogenic 3-methylcrotonyl-CoA carboxylase 1 deficiency 2020-02-28 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003424257 SCV004118662 pathogenic MCCC1-related condition 2023-01-17 criteria provided, single submitter clinical testing The MCCC1 c.1679dupA variant is predicted to result in a frameshift and premature protein termination (p.Asn560Lysfs*10). This variant was reported to be causative for 3-methylcrotonyl-CoA carboxylase deficiency (Wu et al. 2019. PubMed ID: 31901042; Liu et al. 2021. PubMed ID: 34539730). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Frameshift variants in MCCC1 are expected to be pathogenic. This variant is interpreted as pathogenic.
Baylor Genetics RCV000653492 SCV004191954 pathogenic 3-methylcrotonyl-CoA carboxylase 1 deficiency 2023-10-04 criteria provided, single submitter clinical testing
Natera, Inc. RCV000653492 SCV002079088 pathogenic 3-methylcrotonyl-CoA carboxylase 1 deficiency 2021-09-09 no assertion criteria provided clinical testing

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