ClinVar Genomic variation as it relates to human health

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM3,PP4. This variant was detected in homozygous state.

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 441 of the PRODH protein (p.Leu441Pro). This variant is present in population databases (rs2904551, gnomAD 0.6%), and has an allele count higher than expected for a pathogenic variant. This variant has been reported in individuals affected with type I hyperprolinemia and has been reported to be associated with neurological manifestations when present in the homozygous state. It is also reported to present at a higher frequency in affected individuals than unaffected controls in a small cohort from the French population (PMID: 12217952, 20524212). ClinVar contains an entry for this variant (Variation ID: 4008). 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 PRODH protein function. Experimental studies have shown that this missense change affects PRODH function (PMID: 15662599). 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.

PRODH: PP3, PS3:Supporting, PS4:Supporting

The L441P variant in the PRODH gene has been reported previously in association with hyperprolinemia type I (Jacquet et al., 2002). The NHLBI ESP Exome Sequencing Project reports L441P was observed in 58/8600 alleles from individuals of European-American background, with no homozygous individuals reported. The L441P variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. Functional studies show that the L441P variant leads to reduced stability of proline oxidase and significant reduction in its activity (Bender et al., 2005). The L441P variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

In silico prediction tools and conservation analysis predicted that this variant was probably damaging to the protein structure/function (REVEL: 0.732>=0.6, 3CNET: 0.975>=0.75). A missense variant is a common mechanism associated with Hyperprolinemia, type I. Amino acid change identical to known pathogenic variant has been previously reported with established evidence (ClinVar ID: VCV000004008, PMID:12217952). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

The c.1322T>C (p.L441P) alteration is located in exon 12 (coding exon 11) of the PRODH gene. This alteration results from a T to C substitution at nucleotide position 1322, causing the leucine (L) at amino acid position 441 to be replaced by a proline (P). Based on data from the Genome Aggregation Database (gnomAD) database, the PRODH c.1322T>C alteration was observed in 0.52% (1454/281208) of total alleles studied, with a frequency of 0.65% (231/35338) in the Latino subpopulation. This alteration has been reported in the homozygous state as well as in trans with other alterations in patients with hyperprolinemia who also had neurological symptoms (Jacquet, 2002; Afenjar, 2007; Guilmatre, 2010). This alteration was significantly associated with hyperprolinemia in a case-control study (Jacquet, 2005). This amino acid position is highly conserved in available vertebrate species. Functional studies demonstrate that this alteration results in a severe reduction of proline oxidase (POX) activity and reduced stability (Zhang, 2004; Bender, 2005). The in silico prediction for the p.L441P alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.

Variant summary: PRODH c.1322T>C (p.Leu441Pro) results in a non-conservative amino acid change in the encoded protein sequence. Three of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0052 in 249888 control chromosomes in the gnomAD database, including 12 homozygotes. c.1322T>C has been reported in the literature in individuals affected with Proline Dehydrogenase Deficiency, hyperprolinemia and autistic feature (example, Jacquet_2002, Minardi_2020, Raux_2007). These report(s) do not provide unequivocal conclusions about association of the variant with Proline Dehydrogenase Deficiency. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in less than 10% of enzymatic activity WT in vitro and inability to increase intracellular ROS levels (Nagano_2017). The following publications have been ascertained in the context of this evaluation (PMID: 12217952, 32725632, 28264926, 17135275). ClinVar contains an entry for this variant (Variation ID: 4008). Based on the evidence outlined above, the variant was classified as uncertain significance.

The PRODH p.Leu441Pro variant was identified in 4 of 934 proband chromosomes (frequency: 0.0043) from individuals or families with schizophrenia (Jacquet_2002_PMID:12217952; Jacquet_2005_PMID:1549470). This variant was also identified as a homozygous variant in two unrelated children with severe type I hyperprolinemia with neurological manifestations (Jacquet_2002_PMID:12217952). In transient transfection assays, this variant was found to severely (>70%) reduce POX activity (Bender_2005_PMID:15662599). The variant was identified in dbSNP (ID: rs2904551), LOVD 3.0 (classified as a VUS and pathogenic) and ClinVar (classified as likely pathogenic by GeneDx, Center for Pediatric Genomic Medicine Children's Mercy Hospital and Clinics and CeGaT Praxis fuer Humangenetik Tuebingen, and as uncertain significance by Invitae for Proline dehydrogenase deficiency). The variant was identified in control databases in 1454 of 281208 chromosomes (13 homozygous) at a frequency of 0.005171 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Latino in 231 of 35338 chromosomes (freq: 0.006537), Other in 46 of 7194 chromosomes (freq: 0.006394), East Asian in 117 of 19810 chromosomes (freq: 0.005906), Ashkenazi Jewish in 57 of 10298 chromosomes (freq: 0.005535), European (non-Finnish) in 639 of 128296 chromosomes (freq: 0.004981), African in 118 of 24764 chromosomes (freq: 0.004765), South Asian in 136 of 30462 chromosomes (freq: 0.004465), and European (Finnish) in 110 of 25046 chromosomes (freq: 0.004392). The p.Leu441 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein. The variant occurs outside of the splicing consensus sequence and 2 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.