Alternative titles; symbols
HGNC Approved Gene Symbol: PPIL1
Cytogenetic location: 6p21.2 Genomic coordinates (GRCh38): 6:36,854,829-36,874,803 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 6p21.2 | Pontocerebellar hypoplasia, type 14 | 619301 | Autosomal recessive | 3 |
The PPIL1 gene encodes a component of the major spliceosome complex (MSC), which mediates pre-mRNA splicing essential for gene expression and regulation. PPIL1 is a cyclophilin peptidyl-prolyl isomerase, a group of enzymes initially identified as targets of immunosuppressants, but later found to promote conformational changes of protein substrates by catalyzing cis-trans isomerization of Xaa-proline peptide bonds (summary by Chai et al., 2021).
Cyclophilin (see 123840), first identified as a protein with high binding affinity for the immunosuppressive agent cyclosporin A, is one of the most effective therapeutic agents for prevention of graft rejection after organ transplantation.
Ozaki et al. (1996) isolated a human cDNA clone encoding a protein homologous to cyclophilins and showed that it is conserved in species ranging from human to prokaryotes. This cDNA contained an open reading frame of 498 nucleotides encoding a polypeptide of 166 amino acids. The predicted amino acid sequence had 41.6% homology to the human cyclophilins. Northern blot analysis indicated ubiquitous expression in adult human tissues, with the most abundant expression in heart and skeletal muscle.
Chai et al. (2021) found ubiquitous expression of Ppil1 in the developing mouse cortex, indicating a role in brain development.
Ozaki et al. (1996) localized the PPIL1 gene to 2p23.3-p23.1 by FISH. However, Mann et al. (1998) assigned the PPIL1 gene to 6p21.1 by FISH and radiation hybrid mapping.
Chai et al. (2021) noted that PPIL1 joins the MSC together with its interacting partner SKIIP (603055), which is required for activation of the spliceosome. These authors found that PPIL1 catalyzes the isomerization of PRP17 (CDC40; 605585) at gly94-pro95. The proteins form an enzyme-substrate pair in the spliceosome, and both are required for RNA splicing and neuronal survival. However, additional studies suggested that the isomerization of PRP17 was not critical for splicing function. Rather, the 2 proteins maintained a scaffolding, suggesting an additional nonenzymatic function.
In 17 patients from 9 unrelated families with pontocerebellar hypoplasia type 14 (PCH14; 619301), Chai et al. (2021) identified homozygous or compound heterozygous mutations in the PPIL1 gene (see, e.g., 601301.0001-601301.0005). The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. Most of the mutations were missense variants at conserved residues on the enzymatic face of the protein; in vitro studies showed that the mutations assessed either resulted in decreased protein stability or disrupted the interaction with SKIIP (603055). There were a few frameshift, splice site, and nonsense mutations, predicted to result in a loss of function. However, no patient carried loss-of-function mutations on both alleles. Knockdown of the PPIL1 gene in human HAP1 cells resulted in a disruption of global alternative RNA splicing, as detected by RNA-seq and RT-PCR studies. The detrimental effect seemed to be most severe toward introns with high GC content. The differential splicing events affected genes involved in neurodevelopment, but not those involved in cancer, cardiac disease, or immune disease. Studies in mutant mouse models showed similar results (see ANIMAL MODEL). Chai et al. (2021) concluded that disruption of splicing integrity resulting from PPIL1 mutations underlies the neurodegenerative process observed in these patients.
Chai et al. (2021) found that complete knockout of the Ppil1 gene in mice was embryonic lethal. Mice homozygous for the human A99T mutation (601301.0001) died within 24 hours. They had small head size, reduced cerebral and cerebellar volume, and decreased cortical surface area and thickness. Although the cortex showed normal lamination, postmitotic neuronal numbers were severely reduced due to apoptosis. There was also evidence of DNA damage, suggesting genome instability. Upregulation of apoptosis was not observed in other organs, indicating a neuronal-specific effect. Ppil1 protein levels were severely decreased compared to controls. RNA-seq analysis of brain tissue from A99T homozygous mice detected significant differential splicing events affecting genes involved in protein translation, RNA processing, DNA damage response, axon development, and the cell cycle.
In 3 patients from 2 unrelated consanguineous families of Egyptian origin (families 1 and 2) with pontocerebellar hypoplasia type 14 (PCH14; 619301), Chai et al. (2021) identified a homozygous c.295G-A transition (c.295G-A, NM_016059.1) in the PPIL1 gene, resulting in an ala99-to-thr (A99T) substitution at a conserved residue on the enzymatic face of the protein. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. It was found at a low frequency (1.4 x 10(-5)) in the gnomAD database. Patient fibroblasts and HEK293 cells transfected with the mutation showed decreased PPIL1 protein levels compared to controls. Mice homozygous for the human A99T mutation died within 24 hours. They had small head size, reduced cerebral and cerebellar volume, and decreased cortical surface area and thickness. Although the cortex showed normal lamination, postmitotic neuronal numbers were severely reduced due to apoptosis. There was also evidence of DNA damage, suggesting genome instability. Upregulation of apoptosis was not observed in other organs, indicating a neuronal-specific effect. RNA-seq analysis of brain tissue from A99T homozygous mice detected significant differential splicing events affecting genes involved in protein translation, RNA processing, DNA damage response, axon development, and the cell cycle.
In 2 sibs, born of consanguineous Pakistani parents (family 3), with pontocerebellar hypoplasia type 14 (PCH14; 619301), Chai et al. (2021) identified a homozygous c.319A-G transition (c.319A-G, NM_016059.1) in the PPIL1 gene, resulting in a thr107-to-ala (T107A) substitution at a conserved residue on the enzymatic face of the protein. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in the gnomAD database. HEK293 cells transfected with the mutation showed normal PPIL1 protein levels, but decreased thermal stability and increased propensity for aggregation. The T107A variant showed decreased interaction with SKIIP (603055).
In a sister and brother, born of unrelated European American parents (family 8), with pontocerebellar hypoplasia type 14 (PCH14; 619301), Chai et al. (2021) identified compound heterozygous mutations in the PPIL1 gene: a c.379A-G transition (c.379A-G, NM_016059.1), resulting in a thr127-to-ala (T127A) substitution, and an intronic c.280+1G-A transition (601301.0004), predicted to result in a splicing abnormality. The T127A mutation occurred at a highly conserved residue on the enzymatic face of the protein. HEK293 cells transfected with the T127A mutation showed decreased PPIL1 protein levels compared to controls. Two affected sibs from another European American family (family 9) were compound heterozygous for T127A and a c.133C-T transition, resulting in an arg45-to-ter (R45X; 601301.0005) substitution. The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. T127A was present at a low frequency in the gnomAD database (6.7 x 10(-5)), whereas R45X was not present in gnomAD. Functional studies of the variants were not performed.
For discussion of the intronic c.280+1G-A transition (c.280+1G-A, NM_016059.1) in the PPIL1 gene, predicted to result in a splicing abnormality, that was found in compound heterozygous state in 2 sibs with pontocerebellar hypoplasia type 14 (PCH14; 619301) by Chai et al. (2021), see 601301.0003.
For discussion of the c.133C-T transition (c.133C-T, NM_016059.1) in the PPIL1 gene, resulting in an arg45-to-ter (R45X) substitution, that was found in compound heterozygous state in 2 sibs with pontocerebellar hypoplasia type 14 (PCH14; 619301) by Chai et al. (2021), see 601301.0003.
Chai, G., Webb, A., Li, C., Antaki, D., Lee, S., Breuss, M. W., Lang, N., Stanley, V., Anzenberg, P., Yang, X., Marshall, T., Gaffney, P., and 25 others. Mutations in spliceosomal genes PPIL1 and PRP17 cause neurodegenerative pontocerebellar hypoplasia with microcephaly. Neuron 109: 241-256.e9, 2021. [PubMed: 33220177] [Full Text: https://doi.org/10.1016/j.neuron.2020.10.035]
Mann, S. S., Pettenati, M. J., von Kap-herr, C., Hart, T. C. Reassignment of peptidyl prolyl isomerase-like 1 gene (PPIL1) to human chromosome region 6p21.1 by radiation hybrid mapping and fluorescence in situ hybridization. Cytogenet. Cell Genet. 83: 228-229, 1998. [PubMed: 10072585] [Full Text: https://doi.org/10.1159/000015186]
Ozaki, K., Fujiwara, T., Kawai, A., Shimizu, F., Takami, S., Okuno, S., Takeda, S., Shimada, Y., Nagata, M., Watanabe, T., Takaichi, A., Takahashi, E., Nakamura, Y., Shin, S. Cloning, expression and chromosomal mapping of a novel cyclophilin-related gene (PPIL1) from human fetal brain. Cytogenet. Cell Genet. 72: 242-245, 1996. [PubMed: 8978786] [Full Text: https://doi.org/10.1159/000134199]