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Prion Protein Mutation Database

Pro39Leu (Polymorphism)

Back to PrP Mutation Map

Allele count in gnomAD: 9

Cases in literature: 3 (Italy)

Penetrance: Pathogenicity not established

Clinical presentation:

Variant first reported by Bernardi et al1 in two unrelated Italian patients.

Both patients (patients 1 and 2) shared a frontal dementia dominated by a dysexecutive syndrome and severe behavioural disturbances. Neither patient developed the typical clinical signs associated with prion diseases such as myoclonus or cerebellar ataxia. Neuroimaging findings showed marked frontal and temporal atrophy with a peculiar involvement of mesial frontal regions and left temporal lobe. The topography of cortical atrophy was concordant with the behavioural and language disorders. Hyperintense alterations of cortical and subcortical structures in FLAIR and Diffusion-weighted MR imaging were not seen. The patients did not show the typical EEG of prion disease with periodic sharp wave complexes.

The Pro39Leu mutation was also found in another (third) Italian patient with frontotemporal dementia, when a screen of seven hundred and sixty-one patients diagnosed with frontotemporal dementia and 719 controls was undertaken, by another group2. His phenotype was also dominated by a dysexecutive syndrome.

Of note, other mutations in the PRNP gene have been reported to induce a clinical phenotype imitating frontotemporal dementia: Pro102Leu3, Glu196Lys4, His187Arg5 and Thr183Ala6, Gln217Arg7; as well as the nonsense mutation Gln227Stop8 (See Truncating Mutations).

Neurological examination:

Patient 1: Clinical presentation aged 60 (male). Frontal signs and non-fluent aphasia. Cognitive dysfunction with stereotyped ritualistic behaviours, inappropriateness, mirror sign (inability to recognise ones’ own reflection), dressing and constructive apraxia. He became echolalic and uncommunicative, speech was almost unintelligible. He is alive at time of reporting aged 67 years with a severe frontal dementia1.

Patient 2: Clinical presentation aged 75 years (male). Frontal syndrome, non-fluent aphasia and mild-to-moderate akinetic rigid Parkinsonism with camptocormia. In the following years, the patient worsened with extrapyramidal signs, severe gait disturbance and freezing, dysarthria and dysphagia. The patient died aged 78 years1.

Patient 3: Clinical presentation aged 66 years (male). Disorientated in space and partially in time. Spontaneous speech was reduced, monotonous, and with reduced vocabulary. He had difficulty sustaining attention and had an apathetic attitude. Cranial nerves were intact. Deep tendon reflexes were reduced symmetrically. Tone was mildly increased, especially in the lower limbs. He was unstable on standing with mild multi-directional oscillations. His gait was slow and cautious. There was no evidence of dysmetria. Jaw jerk, glabellar and palmo-mental reflexes were present. Myoclonus was absent. At one year from onset he developed a preference for sweet food. He was alive at time of reporting aged 672.

Clinical investigations:

Patient 11, CT head and MR brain showed diffuse cortical atrophy prominent in the mesial frontal, temporal, and posterior parietal regions, mainly in the left side. EEG and EMG studies were normal.

Patient 21, MR brain showed a pattern of cortical atrophy that was similar to patient 1, with marked involvement of mesial frontal, temporal and posterior parietal regions in the left side, besides some lacunar ischaemic subcortical lesions. Brain single-photon emission computed tomography confirmed these findings, revealing a hypoperfusion of fronto-temporal-parietal cortical areas with relative sparing of the occipital lobe, brainstem and cerebellum. EEG did not show any typical periodic complexes of prion diseases. The clinical course for both patients was not rapidly progressive given the duration of disease was over 18 months. These clinical findings do not satisfy the diagnostic criteria for inherited prion disease.

Patient 32, underwent neuropsychological testing which showed an MMSE of 17/30, multiple EEGs did not reveal periodism, EMG revealed a mild chronic sensorimotor axonal polyneuropathy and MR brain showed bilateral frontal lobe atrophy with confluent lesions in the white matter and no alteration in DWI MR imaging. Of note, neuroimaging showed that atrophy was mainly frontal without the temporal or left parietal atrophy noted in patients 1 and 2. This is consistent with the absence of language problems in this patient. Lumbar puncture showed a weak positivity for protein 14.3.3. CSF amyloid- level was 1031 pg/mL (reference range: 550 pg/mL) and total tau was 540 pg/mL (refence range: 375 pg/mL). Paired autoantibodies in plasma and CSF were all negative. Brain MR showed neither cortical ribboning nor basal ganglia hyperintensities on DWI. Multiple lesions in the white matter, interpreted as vascular lesions, were observed, together with bilateral frontal lobe atrophy. FDG-PET showed hypometabolism in the prefrontal cortex and insula bilaterally and in the right caudate. EEG showed no periodic complexes. A repeat lumbar puncture showed the absence of protein 14.3.3, Amyloid- levels were 714 pg/mL and total tau was 152 pg/mL, phosphorylated tau level was 28 pg/mL (reference range: 52 pg/mL). No oligoclonal bands were present in the CSF. In addition, autoantibodies were absent. The results of these investigations together with examination findings, again do not support the diagnosis of prion disease.

Genetic analysis:

Patients 1 and 21: c. 116C>T (CCG to CTG). A heterozygous transition in the second base of codon 39. The absence of this substitution was assessed in 200 cognitively healthy controls. Genotype at codon 129: Patient 1 was Met/Met homozygous and patient 2 was Met/Val heterozygous (it is not known which is the in cis allele in patient 2). Mutations in dementia causative genes PSEN1, PSEN2, MAPT, GRN and C9orf72 were excluded.

Patient 32: Pro39Leu mutation with Met/Met homozygosity at codon 129. Genetic testing was negative for MAPT, GRN and C9orf72 gene mutations.

Neuropathological studies:

None undertaken.

Structure-based protein function annotation:

Proline 39 lies in the N-terminal domain between the fist polybasic charged cluster (CC1) and the octapeptide repeat region, and is perfectly conserved amongst mammalian sequences9,10. Biophysical evidence converges on the finding that that the partially structured N-terminus and the globular C-terminal domain directly interact in a functionally important manner11,12. This cis interaction is mediated by both Cu2+ 12-15 and Zn2+ 16 binding to the octapeptide repeat domain, as well as electrostatic interactions between the polybasic N-terminus clusters CC1 and CC2 and a negatively charged pocket on the globular C-terminal domain contributed predominantly by α-helices 2 and 312,14,16-19 (see Architecture of PrP).

Binding of divalent ions Cu2+ and Zn2+ drives an intra-molecular contact between the N- and C-terminal domains; a number of mutations linked to familial prion disease reside in regions of contact. NMR experiments demonstrate that mutations D178N and E200K systematically weaken the cis N-C interaction, likely through reduction of negative surface on the docking surface of the C-terminus, possibly contributing to the disease phenotype12,16. The weakened cis interaction observed in mutants P102L and V210I cannot be explained by charge disruption; it is possible that loss of proline alters conformational dynamics required to mediate effective docking of the N-terminus onto the C-terminal pocket16. Interestingly, the Q219K polymorphism, associated with resistance to sporadic CJD in the Japanese population20, was seen induce a moderate strengthening of the N-C interaction16. Therefore, it may be possible that increased stability of the PrPC quaternary N-C interaction creates a barrier to misfolding and is, in turn, protective against prion disease.

Proline is the only amino acid whose sidechain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring; therefore, proline is an imino acid, as in its isolated form, it contains an NH2+ rather than an NH3+ group, this leaves the backbone at this point with no amide hydrogen so that no hydrogen bonding is possible21. Additionally, the Pro five-membered ring imposes rigid constraints on N-C rotation, and thus imparts conformational rigidity22. It has previously been proposed that an extended poly(L-proline) II (PPII) helix structure can form in the octapeptide repeat region of PrP23 of a type involved in regulatory, multiple weak interactions when present in other proteins24-25. PPII helix is the predominant secondary structure in proteins with a high degree of conformational flexibility26 and this structure is noted to impart a rheomorphic (flowing) character27.

The PPII structure is an extended left-handed helix with three-fold rotational symmetry; the average dihedral angles of residues and being -77 and 145, respectively22. The initial suggestion of a PPII helix in the N-terminus23 had been largely overlooked, as NMR studies on full-length recombinant PrP found no evidence of for such a structure28, additionally, this peptide is rich in tryptophan, which can contribute substantially to CD spectra in the far UV29-30. However, lack of main-chain hydrogen bonding in PPII helices makes NMR determination of this type of structure difficult, especially if it is in equilibrium with random coil or other types of secondary structure, and retrospective analysis of crystallographic and NMR PrPC structures does in fact find PPII helices forming most of the N-terminus31. CD spectroscopy of synthetic peptides comprising residues 48-9323 and 57-9130, 58-9132, and 60-9133 containing the four octapeptide repeats have given spectra with features diagnostic of a PPII conformation; a strong minimum at 195 nm and weaker maximum at 220 nm34, which is lost upon addition of copper ions to this metal binding motif30,32-33. The presence of an N-terminus PPII helix, interspersed with -turns, has recently been confirmed by both Raman optical activity35 and the finding that the specific sequence Ser-Pro44-Gly-Gly can form a PPII structure in aqueous buffers, act as a substrate for prolyl 4-hydroxylation in CHO cells and in brain cells of mice infected with prions, strongly suggest that the polypeptide forms an extended PPII structure in vivo36. Hydroxylation to 4-hydroxyproline by polyl 4-hydroxylase occurs within the consensus sequence X-Pro-Gly37 and requires, principally, a PPII conformation38, as well as a partial -turn, to extend the -X-Pro-Gly- motif into the catalytic site for hydroxylation39.

Therefore, the PPII structure and factors influencing its dynamic flexibility, may be critical for a role of PrP in normal cellular functioning and signalling36. Although, the role of this region in the prion disease process has been somewhat overlooked, primarily, because transgenic mice that are devoid of much of the N-terminal region still support prion replication40, indicating that the N-terminal region is not required a priori for the PrPC-PrPSc conversion process. The presence of a large amount of PPII structure in the N-terminal region, is consistent with the flexibility and conformational adaptability required for its ability to bind metal ions, modulate properties of full-length protein via interactions with the structured C-terminal region, as well as facilitating molecular interactions with myriad ligands within the intra- or extra-cellular environment41.

With respect to Pro39Leu, it is our conclusion42 (and others’43) that this variant constitutes a polymorphic variant, that is common in controls and rare in cases, which has coincidentally co-segregated in the three patients with frontotemporal dementia detailed above. However, if this residue participates in a PPII structure, its substitution may subtly modify dynamical properties of the N-terminus that permit ligand binding and correct orientation of the N-C interaction, although in this case, not to an extent that facilitates its misfunction. Such a mechanism, however, may underlie the pathogenic loss-of-proline mutants: Pro84Ser, Pro102Leu, Pro105Leu/Ser/Thr.

In silico Pathogenicity predictions:

Pon-P2 (independent)44:

  • Probability of pathogenicity: 0.539
  • Standard error: 0.058
  • Prediction: Unknown

Revel (ensemble)45:

  • Score: 0.883
  • Prediction: Pathogenic

A stringent REVEL score threshold of 0.75 is applied, above which the variant is classified as pathogenic.


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  2. Oldoni E, Fumagalli GG, Serpente M et al. PRNP P39L Variant is a Rare Cause of Frontotemporal Dementia in Italian Population. Journal of Alzheimers Disease 2016; 50(2): 353-357. (PMID: 26757195)
  3. Giovagnoli AR, Di Fede G, Aresi A et al. Atypical frontotemporal dementia as a new clinical phenotype of Gerstmann-Straussler-Scheinker disease with the PrP-P102L mutation. Description of a previously unreported Italian Family. Neurological Sciences 2008; 29(6): 405-410. (PMID: 19030774)
  4. Clerici F, Elia A, Girotti F et al. Atypical presentation of Creutzfeldt-Jakob disease: the first Italian case associated with E196K mutation in the PRNP gene. Journal of the Neurological Sciences 2008; 275(1-2): 145-147. (PMID: 18706660)
  5. Hall DA, Leehey MA, Filley CM et al. PRNP H187R mutation associated with neuropsychiatric disorders in childhood and dementia. Neurology 2005; 64(7): 1304-1306. (PMID: 15824374)
  6. Nitrini R, Teixeira da Silva LS, Rosemberg S et al. Prion disease resembling frontotemporal dementia and parkinsonism linked to chromosome 17. Arquivos de Neuropsiquitria 2001; 59(2-A): 161-164. (PMID: 11400017)
  7. Woulfe J, Kertesz A, Frohn I et al. Gerstmann-Staräussler-Scheinker disease with the Q217R mutation mimicking frontotemporal dementia. Acta Neuropathologica 2005; 110: 317-319. (PMID: 16025285)
  8. Jansen C, Parchi P, Capellari S et al. Prion protein amyloidosis with divergent phenotype associated with two novel nonsense mutations in PRNP. Acta Neuropathologica 2010; 119(2): 189-197. (PMID: 19911184)
  9. Wopfner F, Weidenhöfer G, Schneider R et al. Analysis of 27 mammalian and 9 avian PrPs reveals high conservation of flexible regions of the prion protein. Journal of Molecular Biology 1999; 289(5): 1163-1178. (PMID: 10373359)
  10. van Rheede T, Smolenaars MMW, Madsen O, de Jong WW. Molecular Evolution of the Mammalian Prion Protein. Molecular Biology and Evolution 2003; 20(1): 111-121. (PMID: 12519913)
  11. Evans EGB and Millhauser GL. Copper- and Zinc-Promoted Interdomain Structure in the Prion Protein: A mechanism for Autoinhibition of the Neurotoxic N-terminus. Progress in Molecular Biology and Translational Science 2017; 150: 35-56. (PMID: 28838668)
  12. McDonald AJ, Leon DR, Markham KA et al. Altered Domain Structure of the Prion Protein Caused by Cu2+ Binding and Functionally relevant Mutations: Analysis by Cross-Linking, MS/MS and NMR. Structure 2019; 27(6): 907-922.e5. (PMID: 30956132)
  13. Wu B, McDonald AJ, Markham K et al. The N-terminus of the prion protein is a toxic effector regulated by the C-terminus. eLife 2017; 6: e23473. (PMID: 28527237)
  14. Evans EGB, Pushie MJ, Markham KA et al. Interaction between Prion Protein’s Copper-Bound Octarepeat Domain and a Charged C-Terminal Pocket Suggests a Mechanism for N-Terminal Regulation. Structure 2016; 24(7): 1057-1067. (PMID: 27265848)
  15. Thakur AK, Srivastava AK, Srinivas V et al. Copper alters aggregation beahviour of prion protein and induces novel interactions between its N- and C-terminal regions. Journal of Biological Chemistry 2011; 286(44): 38533-38545. (PMID: 21900252)
  16. Spevacek AR, Evans EGB, Miller JL et al. Zinc Drives a Tertiary Fold in the Prion Protein with Familial Disease mutation Sites at the Interface. Structure 2013; 21(2): 236-246. (PMID: 23290724)
  17. Martínez J, Sánchez R, Castellanos M et al. PrP charge structure encodes interdomain interactions. Scientific Reports 2015; 5: 13623. (PMID: 26323476)
  18. Markham KA, Roseman GP, Linsley RB et al. Molecular Features of the Zn2+ Binding Site in the Prion Protein Probed by 113Cd NMR. Biophysical Journal 2019; 116(4): 610-620. (PMID: 30678993)
  19. Roseman GP, Wu B, Wadolkowski MA et al. Intrinsic toxicity of the cellular prion protein is regulated by its conserved central region. FASEB Journal 2020; 34(6): 8734-8748. (PMID: 32385908) 
  20. Shibuya S, Higuchi J, Shin RW et al. Codon 219 Lys allele of PRNP is not found in sporadic Creutzfeldt-Jakob disease. Annals of Neurology 1998; 43(6): 826-828. (PMID: 9629853)
  21. Betts MJ and Russell RB. Amino acid properties and consequences of substitutions. In Bioinformatics for Geneticists. Barnes MR, Gray IC eds. Wiley 2003.
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  23. Smith CJ, Drake AF, Banfield BA et al. Confirmational properties of the prion octa-repeat and hydrophobic sequences. FEBS Letters 1997; 405(3): 378-384. (PMID: 9108322)
  24. Siligardi G and Drake AF. The importance of extended conformations and, in particular, the PPII conformation for the molecular recognition of peptides. Biopolymers 1995; 37(4): 281-292. (PMID: 7540055)
  25. Wright PE and Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology 1999; 293(2): 321-331. (PMID: 10550212)
  26. Bernardi L and Bruni AC. Mutations in Prion Protein Gene: Pathogenic Mechanisms in C-Terminal vs. N-Terminal Domain, a Review. International Journal of Molecular Sciences 2019; 20(14): 3606. (PMID: 31340582)
  27. Syme CD, Blanch EW, Holt C et al. A Raman optical activity study of rheomorphism in caseins, synucleins and tau. European Journal of Biochemistry 2002; 269(1): 148-156. (PMID: 11784308)
  28. Donne DG, Viles JH, Growth D et al. Structure of the recombinant full-length hamster prion protein PrP (29-231): the N terminus is highly flexible. Proceedings of the National Academy of Sciences USA; 1997: 94(25): 13452-13457. (PMID: 9391046)
  29. Freskgård PO, Mårtensson LG, Jonasson P et al. Assignment of the contribution of the tryptophan residues to the circular dichroism spectrum of human carbonic anhydrase II. Biochemistry 1994; 33(47): 14281-14288. (PMID: 7947839)
  30. Whittal RM, Ball HL, Cohen FE et al. Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry. Protein Science 2000; 9(2): 332-343. (PMID: 10716185)
  31. Adzhubei AA, Sternberg MJE, Makarov AA. Polyproline-II Helix in proteins: Structure and Function. Journal of Molecular Biology 2013; 425(12): 2100-2132. (PMID: 23507311)
  32. Viles JH, Cohen FE, Prusiner SB et al. Copper binding to the prion protein: structural implication of four identical cooperative binding sites. Proceedings of the National Academy of Sciences USA 1999; 96(5): 2042-2047. (PMID: 10051591)
  33. Hornshaw MP, McDermott JR, Candy JM, Lakey JH. Copper bidning to the N-terminal tandem repeat region of mammalian and avian prion protein: structural studies using synthetic peptides. Biochemical and Biophysical Research Communications 1995; 214(3): 993-939. (PMID: 7575574)
  34. Woody RW. Circular dichroism spectrum of peptides in the poly(Pro)II conformation. Journal of the American Chemical Society 2009; 131(23): 8234-8245. (PMID: 19462996)
  35. Blanch EW, Gill AC, Rhie AGO et al. Raman optical activity demonstrates poly(L-proline) II helix in the N-terminal region of the ovine prion protein: implications for function and misfunction. Journal of Molecular Biology 2004; 343(2): 467-476. (PMID: 15451674)
  36. Gill AC, Ritchie MA, Hunt LG et al. Post-translational hydroxylation at the N-terminus of the prion protein reveals presence of PPII structure in vivo. EMBO Journal 2000; 19(20): 5324-5331. (PMID: 11032800)
  37. Kivirikko KI and Pihlajaniemi T. Collagen hydroxylases and the protein disulfide isomerase subunit of prolyl 4-hydroxylases. Advances in Enzymology and Related Areas of Molecular Biology 1998; 72: 325-398. (PMID: 9559057)
  38. Myllyharju J and Kivirikko KI. Identification of a novel proline-rich peptide-binding domain in prolyl 4-hydroxylase. EMBO Journal 1999; 18(2): 306-312. (PMID: 9889187)
  39. Atreya PL and Ananthanarayanan VS. Interaction of prolyl 4-hydroxylase with synthetic peptide substrates. A conformational model for collagen proline hydroxylation. Journal of Biological Chemistry 1991; 266(5): 2852-2858. (PMID: 1847136)
  40. Fischer M, Rülicke T, Raeber A et al. Prion protein (PrP) with amino-proximal deletions restoring susceptibility of PrP knockout mice to scrapie. EMBO Journal 1996; 15: 1255-1264. (PMID: 8635458)
  41. Mahabadi HM and Taghibiglou C. Cellular Prion Protein (PrPc): Putative Interacting Partners and Consequences of the Interaction. International Journal of Molecular Sciences 2020; 21(19): 7058. (PMID: 32992764)
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  45. Ioannidis NM, Rothstein JH, Pejaver V et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. American Journal of Human Genetics 2016; 99(4): 877-885. (PMID: 27666373)