ClinVar Genomic variation as it relates to human health

Variant summary: The CPT2 c.149C>A (p.Pro50His) variant involves the alteration of a conserved nucleotide and 4/4 in silico tools (SNPsandGO not captured due to low reliability index) predict a damaging outcome. This variant was found in 2/11728 control chromosomes at a frequency of 0.0001705, which does not exceed the estimated maximal expected allele frequency of a pathogenic CPT2 variant (0.0015811). Multiple publications cite the variant in compound heterozygote affected individuals, which were found to have low CPT II activity. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

• The p.Pro50His variant in the CPT2 gene has been previously reported in the homozygous or compound heterozygous state in many individuals affected with CPT II deficiency, and is recognized as one of the most common disease-causing variants identified in individuals with the myopathic presentation of disease (Taggart et al., 1999; Wieser et al., 2003; Ørngreen et al., 2005; Isackson et al., 2006). • The p.Pro50His variant is typically associated with the later-onset myopathic form of disease, but has been reported in association with the severe infantile form when compound heterozygous with a truncating variant (Vladutiu et al., 2002). • Heterozygous carriers of the p.Pro50His variant have been rarely reported to be clinically affected with adult- onset myopathy (Isackson et al., 2006). • • • These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Pro50His variant as pathogenic for autosomal recessive CPT II deficiency based on the information above. [ACMG evidence codes used: PM3_Very Strong; PM2; PS3_Supporting; PP3]This variant has been identified in 17/10,486 European (Finnish) chromosomes (32/164,218 chromosomesoverall) by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant hasbeen seen in the general population, its frequency is low enough to be consistent with a recessive carrierfrequency.Functional studies of the p.Pro50His variant are supportive of a deleterious effect to the protein and haveshown decreased stability of the mutant CPT II protein (Verderio et al., 1995)

The p.Pro50His variant in CPT2 has been reported in the homozygous state in least 2 individuals and in the compound heterozygous state in at least 5 individuals with CPTII deficiency, at least 2 of whom were found to have low CPT II activity and segregated with disease in 1 affected relative. Most of these individuals had the myopathic form with juvenile to adult onset, however one individual who had a loss of function variant on the other copy of the CPT2 gene had infantile onset (Verderio 1995 PMID: 7711730, Taggart 1999 PMID: 10090476, Vladutiu 2002 PMID: 12410208, Wieser 2003 PMID: 12707442, Orngreen 2005 PMID: 15622536, Isackson 2006 PMID: 16996287, Corti 2008 PMID: 17936304). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 8954) and has been identified in 0.1% (15/10614) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). In vitro functional studies provide some evidence that this variant significantly affects the CPT II catalytic activity (Verderio 1995 PMID: 7711730) and computational prediction tools and conservation analyses are consistent with pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive CPTII deficiency though it should we noted that this variant typically causes the milder myopathic form; however, when found with a loss of function variant, it can cause more severe disease. ACMG/AMP Criteria applied: PM3_VeryStrong, PP3, PS3_Supporting, PP4.

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

Common CPT2 pathogenic variant found in approximately 6.5% of mutant alleles in patients with the adult myopathic form of carnitine palmitoyltransferase II (CPT2) deficiency (Bonnefont et al., 2004); Published functional studies in found P50H is associated with significantly reduced carnitine palmitoyltransferase II enzyme activity compared to wild type (Wataya et al. 1998); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 10090476, 12707442, 15363638, 22975760, 7711730, 31589614, 12410208, 15622536, 20301431, 31541997, 12673791, 17936304, 16996287, 33673806, 9600456)

This sequence change replaces proline, which is neutral and non-polar, with histidine, which is basic and polar, at codon 50 of the CPT2 protein (p.Pro50His). This variant is present in population databases (rs28936375, gnomAD 0.2%). This missense change has been observed in individual(s) with CPT2 deficiency (PMID: 7711730, 10090476, 12410208, 12707442, 16996287, 17936304). 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: 8954). 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 expected to disrupt CPT2 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects CPT2 function (PMID: 7711730). For these reasons, this variant has been classified as Pathogenic.

This sequence change in CPT2 is predicted to replace proline with histidine at codon 50, p.(Pro50His). The proline residue is highly conserved (65/65 vertebrates, UCSC), and is located in the carnitine o-acyltransferase domain. There is a moderate physicochemical difference between proline and histidine. The highest population minor allele frequency in the population database gnomAD v2.1 is 0.16% (17/10,486 alleles) in the Finnish population. However, the highest continental population minor allele frequency is 0.02% (11/64,794 alleles) in the European (non-Finnish) population, which is consistent with recessive disease. This variant is one of the most common pathogenic variants associated with the myopathic form of CPTII deficiency identified in Europeans (PMID: 20301431). It has been detected in multiple individuals CPTII deficiency diagnosed on muscle biopsy in the homozygous state or compound heterozygous for the variant and a pathogenic or likely pathogenic variant (PMID: 7711730, 12673791, 12707442, 16996287). In vitro enzyme assays demonstrated the variant has reduced enzyme function at different temperatures indicating that this variant impacts protein function (PMID: 34063237). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (6/6 algorithms). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PS3_Supporting, PM2_Supporting, PP3, PP4.