Total submissions: 3
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Natera, |
RCV002031053 | SCV007522861 | likely pathogenic | 3-methylcrotonyl-CoA carboxylase 2 deficiency | 2025-03-26 | criteria provided, single submitter | clinical testing | The c.691A>T variant in MCCC2 is a missense variant predicted to cause substitution of isoleucine to phenylalanine at amino acid 231. This variant is rare in the general population with a frequency below the threshold expected for the associated phenotype(s). This variant has been observed in one or more individuals affected with the associated recessive disease, as either homozygous or compound heterozygous with a second variant (PMID: 29767664, 26589311). This variant has been identified in one or more affected individuals with a phenotype highly consistent with the associated gene (PMID: 29767664). Computational prediction algorithms indicate this variant is likely to affect gene or protein function. Given the available evidence, this variant is classified as Likely Pathogenic. |
| Baylor Genetics | RCV002031053 | SCV004194320 | likely pathogenic | 3-methylcrotonyl-CoA carboxylase 2 deficiency | 2024-01-29 | criteria provided, single submitter | clinical testing | |
| Labcorp Genetics |
RCV002031053 | SCV002313893 | likely pathogenic | 3-methylcrotonyl-CoA carboxylase 2 deficiency | 2024-03-12 | criteria provided, single submitter | clinical testing | This sequence change replaces isoleucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 231 of the MCCC2 protein (p.Ile231Phe). This variant is present in population databases (rs531567604, gnomAD 0.003%). This missense change has been observed in individual(s) with 3-Methylcrotonylglycinuria (PMID: 26589311, 29767664). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1521022). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MCCC2 protein function with a negative predictive value of 80%. 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. |