Human Prion Point Mutations
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Known point variations in human prion gene coding region

  Last updated 16 Nov 00 webmaster.  Please submit missing mutations.
Compound and homozygous prion mutations Predicting missing CJD mutations: predictions from CpG effect. Nomenclature and ascertainment issues: recommendations Bovine and ovine alleles and mutations at CJD-causative sites from CpG effect. Deletions in prion octapeptide repeat region. Insertions in prion octapeptide repeat region. Prion gallery: 3D blow-ups of point mutation environments. Curated sequence database for prion genes from 80+ species. Doppel alleles and CpG: ancient tandem prion paralogue. Microsatellites in prion-doppel region useful in kindred tracking. OMIM, HGMD:treatments of prion mutations. NT_001001: largest finished contig at GenBank containing prion-doppel Prion and doppel at LocusLink SNPs in prion-doppel region: single nucleotide polymorphic markers Human genome browser: prion flanking genes (use chr20:4844409-5855419, prion is D0015)
Color key:causative*
stop causative*neutral*silent* based on consensus opinion
.222612total: 42 known point mutations, 24 causative
Initial DNA Final DNA Initial AA Final AA Codon Reference
cagCCTcat CCC Pro Pro P68P Windl (1999) Hum Gen 105:244.
aagCCGagt1 CTG Pro Leu P102L Hsiao (1989) Nature 338:342.
aagCCAaaa CTA Pro Leu P105L Kitamoto (1993) BBRC 191:709.
aagCCAaaa ACA Pro Thr P105T personal communication13
gcaGCAagc GTA Ala Val A117V Doh-Ura (1989) BBRC 163:974.
gcaGCAagc6 GCG Ala Ala A117A Hsiao (1989) Nature 338:342
gggGGCctt10 GGG Gly Gly G124G [Prusiner (1997) Science 278:245]
tacATGctg GTG Met Val M129V3 Doh-Ura (1989) BBRC 163:974.
cccATCata ATG Ile Met I138M15 Laplanche (2000) pers. comm.
ttcGGCcag1 AGC Gly Ser G142S16 Laplanche (2000) pers. comm.
gacTATgag TAG Tyr stop Y145s11 Ghetti (1996) PNAS 93:744
aacCAAgtg TAA Gln stop Q160s12 Finckh U (2000) Am J Hum Genet 66:110
caaGTGtac GTA? Val Val V161V [Prusiner (1997) Science 278:245]
agcAACcag AGC Asn Ser N171S5 Samaia (1997) Nature 390:241
cagAACaac AAT Asn Asn N173N Laplanche (2000) pers. comm.
gtgCACgac1y CAT His His H177H Ripoll (1993) Neurology 43:1934
cacGACtgc1y AAC Asp Asn D178N Goldfarb (1991) Lancet 337:425
tgcGTCaat1 ATC Val Ile V180I Kitamoto (1993) BBRTC 191:709
atcACAatc GCA Thr Ala T183A19 Nitrini (1997) Ann Neurol 42:138
cagCACacg CGC His Arg H187R Cervenakova (1999) Am J Med Genet 88(6):653
cacACGgtc1x AGG Thr Arg T188R Windl (1999) Hum Gen 105.244
cacACGgtc1x AAG Thr Lys T188K Finckh U (2000) Am J Hum Genet 66:110
cacACGgtc1x GAG Thr Ala T188A Collins S (2000) Arch. Neurol 57:1058
cacACGgtc1 ACA Thr Thr T188T Laplanche (2000) pers. comm.
gggGAGaac AAG Glu Lys E196K Peoc'h (2000) Human Mutation #323
aacTTCacc TCC Phe Ser F198S Hsiao (1992) Nature Genet.1:68
accGAGacc1 AAG Glu Lys E200K Goldgaber (1989) Exp. Neurol.106:204.
accGACgtt1 AAC Asp Asn D202N8 Piccardo (1998) J N Exp Neur 57:979
accGACgtt1y GAT Asp Asp D202D Laplanche (2000) pers. comm.
gacGTTaag1y ATT Val Ile V203I14 Peoc'h (2000) Human Mutation #323
gagCGCgtg1 CAG Arg His R208H Mastrianni (1996) Neurol.47:1305
gagCGCgtg1 CGT Arg Arg R208R Laplanche (2000) pers. comm.
gtgGTTgag ATT Val Ile V210I Pocchiari (1993) Ann. Neurol.34:802.7
gttGAGcag CAG Glu Gln E211Q Peoc'h (2000) Human Mutation #323
gagCAGatg CGG Gln Pro Q212P Piccardo (1998) J N Exp Neur 57:979
gagCAGatg CAA Gln Gln Q212Q Windl (1999) Hum Gen 105.244.
accCAGtac CGG Gln Arg Q217R Hsiao (1992) Nature Genet. 1:68.
tacGAGagg1 AAG Glu Lys E219K2 Barbanti (1996) Neurobiology 47:734
cagAGAgga AGG Arg Arg R228R Windl 1999 Hum Gen 105.244.
ggaTCGagc1 TCA Ser Ser S230S4 Windl (1999) Hum Gen 105.244.
agcATGgtc AGG Met Arg M232R4 Kitamoto (1993) BBRC 191:709.
tctCCAcct TCA Pro Ser P238S4 Windl (1999) Hum Gen 105.244

This table is also available as a simple comma delimited database suitable for import into Excel etc.


0. Intronic alleles are known at -21 (G to A)of 5' UTR and +4 (A to C) of 3' UTR. The polymorphism G21A (5.6%) is found 21 bp upstream from the start of exon 3: gttctcctcttcattttgcag agcagtcattATG. Palmer, Hum Mutat 1996;7(3):280-281, S82948.

1. Spontaneous deamidation of methylated C (CpG hotspot effect) leads to enhanced frequency; CpG mutations account for a disproportionate amount of all coding human point mutation.

1x. Of 17 CpG mutations in the table, 14 have canonical CpG transitional outcomes (C to T or G to A). At codon 188, four distinct changes are seen, only one is canonical. A hotspot is present but possibly local DNA secondary structure affects the mutational spectrum. The neutral change occurred in a patient with frontal dementia.

1y. At these codons, the CpG (and canonical outcomes) was split over consecutive codons.

2. Neutral polymorphism, common in Japan.

3. Much investigated common polymorphism that modulates disease susceptibility and onset. All nvCJD cases are met/met at codon 129

4. Cleaved off in mature prion in forming lipid PGI anchor.

5. Reported in a normal patient prior to schizophrenia family: Hum Mutat 1994;4(1):42-50

6. Silent mutation in third codon position, 5.4% EU population, PvuII restriction site negative.

7. Also seen in French patient by Ripoll L, Neurology 1993 Oct;43(10):1934-1938, by Furukawa H , J Neurol Sci 1996 Sep 15; 141(1-2):120-122, Shyu WC, J Neurol Sci 1996 Nov;143(1-2):176-80, and Zerr I Neurology. 2000 Sep 26;55(6):811-5 (15 families), making this one of the most common mutations with no explanation in sight.

10. The silent allele at codon 124 has an estimated incidence of 0.5%. Windl 1999 Hum Gen 105.244.

11. Y145stop causes cerebral arterial angiopathy form of CJD in a non-politically correct way (no alpha helix to beta sheet conversion).

12. Q160stop occurred in two brothers in cis with M129 but in trans with met or val (later onset). A second novel mutation was found at a known position, T188K, in a case lacking familial history. In another lineage, a 4 octapeptide repeat was not pathogenic.Details. Finckh et al. Am J Hum Genet 2000 Jan;66(1):110-117.

13. A family member supplied the webmaster with details on 17 Jan 00. The father (apparent founder) died of CJD at age 42, his DNA samples were lost. After onset at age 30 in a son, P105T was diagnosed, with M/V at 129. A still healthy daughter is P105T M/V. The case will likely be reported by Paul Brown of NIH.

14. Codon 203 is a buried methionine in canids; val in primates, most rodents, and early-branching artiodactyls; and isoleucine in most ruminants and cat, ie this position, while quite conservative within old taxonomic lineages, admits non-pathogenic isoleucine. The Italian kindred was small; the patient had no family history of neurologic disorders and very late onset (69); CpG sites are mutational hotspots. The mutation may however be weakly causative.

15. French male, 57, frontal dementia, not CJD. A non CpG transversion. Leucine is the mammal ancestral amino acid at position138 -- isoleucine is restricted to great apes, rodents are all methionine, marsupial valine, phenylalanine is a rare sheep allele. Thus all possibilities in the the first column of the genetic code occur suggesting that the I138M is neutral. [Birds and turtle have histidine or arginine here; doppel alignability does not begin until position 139 isoleucine.]

16. CpG seen in a North Africa man, 69, with multiple sclerosis and in a Mali woman, 25, with viral meningoencephalitis. These are conceivably a single ancient kindred given the geographic proximitiy and apparent rarity of this substitution. This change is neutral in the sense of no association with CJD, but the serine is not a conservative change for this glycine in terms of normal structure/function (recessively?). The context, HFG, is a highly conserved region -- no glycine substitutions are seen in any sequenced species, suggesting a very small side chain is required here for packing or turning. Even the 5 doppel sequences align and are conserved FG here. (Birds are all FD.) This substitution could be tested in vitro for Fyn signaling capabilities.

17. E196E may also have been found: gggGAGaac to AAG However, the citation cannot be located by the individual recalling this. By using Blastn(nr) of wildtype DNA at GenBank and sorting through artefacts, R148R CGT to CGC (X83416, Hood lab) and K204R AAG to AGG within a 4x insertion entry (AF085477 , Cervenakova ) emerge. The latter is a typo and has now been corrected (pers. comm.)

18. Chimpanzees, the nearest neighbor of humans, have silent transition mutations A2A and L9L not corresponding to known polymorphism sites in humans; E168Q which would thus likely be neutral if it ever showed up in humans, the N171S which was reported in humans from Brazil, and a silent T183T where humans can have a fatal T183A. Therfore in this gene there has been no long term carry-forward of polymorphisms other than maybe N171S.

19. Another kindred of T183Awas reported by Finckh et al. in Ann N Y Acad Sci 2000;920:100-6.

Homozygous and compound mutations

Last updated: 12 Oct 00 webmaster
The issue here is in compound or homozygous prion gene mutations, whether disease onset is shorter with more extreme pathology, or the same as when a single chromosome is affected. Familial CJD is a rare autosomal dominant disorder, meaning that the homozygous condition is rarer as the square, except possibly for E200K where there is a potential for ethnic intermarriage.

The expectation from the standard prion fibril model is earlier onset of disease in homozygotes, attributable to protein dosage. In the heterozygote, the bad protein may or may not be able to effectively recruit normal prion protein from the other allele to the fibril. If it cannot (or if it can but caps or otherwise interferes with fibril extension), the delay in onset might be quite dramatic in the heterozygote.

The expected effect (earlier onset) has now been observed in EE200KK (5 of 70 cases homozygous; Ann Neurol 2000 Feb;47(2):257-60 Simon ES et al.) though onset is still midlife with unchanged symptoms of the same severity, suggesting that fibrils in heterozygotes are mixes of the respective monomers (or that 200K can seed a E200 fibril) as happens in V210I and some sporadic CJD. (It has not been possible so far to distinguish mixed fibrils from a mix of pure fibrils.) Note E200K has a slight tendency to earlier generational onset for unknown reasons.

Note in M129V F198S and M129V Q217R, only the abnormal allele accumulates in amyloid. The same holds in D178N but not in a case of extra repeats.

EE200KK apparently does not leave the cell lacking in normal prion function. As a toxic-gain-of-function disorder with no comprehensive assay for normal function, it has not yet been possible to experimentally determine whether mutations are neutral with respect to normal prion function and simply predispose to fibril formation. Unless a compensatory mechanism exists -- and doppel lacks the copper binding domain -- the implication is that E200K has near-normal prion function.

Note also compound mutations:

-- Muramoto found P102L cis to 219E with no amyloid cross-recruitment [Neurosci Lett 2000 288(3):179-182].
-- Laplanche found a E211Q mutation cis to silent 124 G allele [2000) Human Mutation #323].
-- Pocchiari found a del R2 trans to a V210I central Italian family [Ann Neurol. 1993 Dec;34(6):802-7].
-- Perry found a del R2 in an Alabama FAD, parent R2/R34 [Am J Med Genet. 1995 Feb 27;60(1):12-8].
-- Yamada found a del R2 in a Japanese family trans to P105L [Neurology. 1999 Jul 13;53(1):181-8].
-- Masullo found a homozygous del R2 in an Italian, adopted. [Ann N Y Acad Sci 1994 Jun 6;724:358-60]
-- Vnencak-Jones found a del R34 mid-Tennessee in cis with E200K [Am J Hum Genet. 1992 Apr;50(4):871-2].
-- Laplanche saw a del R34 in a Tunisian E200K family [Rev Neurol (Paris) 1991;147(12):825-7].
-- Bosque saw a del R34 in a Tennessee family with D178N [Neurology 1992 Oct;42(10):1864-70].
-- Cervenakova reported a del R34/R3g34 in an African-American family [T Subacute SE, Elsevier 1996 pp. 433-444].
-- Reder described a deletion in combination with D178N [Neurology 1995 Jun;45(6):1068-75].
-- Ghetti writes in a 1996 TSE book that 'no homozygous F198S has yet been seen in the Indiana kindred.
-- Hitoshi found a V180I M232R double mutation in trans in an 84 year old Japanese man [J Neurol Sci 1993 Dec 15;120(2):208-12].
-- Mastrianni reported a silent GCA-to-GCG at codon 117 on the opposite allele to A117V [Neurology 1995 Nov;45(11):2042-50]
-- Seno observed an E219K polymorphism on the same allele as E200K [Acta Neuropathol (Berl) 2000 Feb;99(2):125-30].

Tranchant in Rev Neurol (Paris) 1991;147(4):274-8 found a "double mutation of codon 117 leading to loss of the restriction site PvuII and to the replacement of an alanine by a valine" in a family of Alsatian origin including 10 healthy family members, a litle confusing since GCA to GTA is the usual A117V, GCA to GCG the usual silent PvuII loss. Perhaps what is meant is simply A117V in the background of the PvuII polymorphism, ie the family is heterozygous for ala/val at codon 117 and compound trans for the silent change. This is the only mutation affecting center of the conserved palindromic and amyloid core.

Gabizon observed earlier in Am J Hum Genet 1993 Oct;53(4):828-35 that 'The identification of three Libyan Jews homozygous for the Lys200Arg mutation suggests frequent intrafamilial marriages, a custom documented by genealogical investigations." These cases were apparently subsumed in the 5 homozygotes of the 2000 Simon study.

Hsiao observed in N Engl J Med 1991 Apr 18;324(16):1091-7 that "one patient was homozygous for the lysine mutation [E200K], and her clinical course did not differ from that of the patients heterozygous for the mutation.... The similarity of the clinical courses of the patient homozygous for this mutation and the patients heterozygous for it argues that familial Creutzfeldt-Jakob disease is a true dominant disorder. ' This case probably is probably included in the 1993 Gabizon study.

Predictions from the CpG effect

24 Jan 98 webmaster; updated 05 Nov 00

 G+C content
 G+C blur r=3
 CpG all
 CpG observed
 CpG CJD sites
 domain structure
 non-CpG observed
 non-CpG CJD
 all CJD sites
 domain structure
 arg lys/glu asp

Recall that:

"The fifth base in human DNA, 5-methylcytosine, is inherently mutagenic. This has led to marked changes in the distribution of the CpG methyl acceptor site and an 80% depletion in its frequency of occurrence in vertebrate DNA. The coding regions of many genes contain CpGs which are methylated in sperm and serve as hot spots for mutation in human genetic diseases. Fully 30-40% of all human germline point mutations are thought to be methylation-induced even though the CpG dinucleotide is under-represented and efficient cellular repair systems exist." [Bioessays 1992 Jan;14(1):33-36]

Looking at the existing set of 42 point mutations and overall distribution of 23 CpG dinucleotides in the human prion gene, it emerges that about half the potential codons have been affected (mainly post-P102, reflecting non-uniformity in causative mutation distribution and resulting ascertainment bias). A CpG mutation has two canonical outcomes, TpG or CpA, after deamination (G to A outnumbers C to T in this gene by10:4). This gives 46 possibilities of which 14 have been observed as mutations so far. Four CpG sites with multiple kindreds, E200K, T188, D178, and P102, tend to dominate overall familial point-CJD. (The repeat region is a hotspot of a different kind, for replication slippage; no particular repeat insertion is favored in familial repeat-CJD; single repeat deletions are more orderly.)

Note that the observed sites have a pronounced tendency to be distally clustered. This could be attributed to ascertainment bias, to proximal sites failing to give rise to CJD (supported by lack of non-CpG, non-repeat mutations in the post-signal region), or to non-uniform susceptibility of DNA to the CpG effect across the gene (eg T188 appears hyper-susceptible). Note 0/14 sites early in the gene are observed whereas 13/20 late sites have been reported. Non-CJD outcomes for CpG are generally detected in control cases, so one measure of sequencing intensity is that of 15 potential CpG sites involving, a respectable 4 have been reported in the distal region. Under-reporting of silent and neutral mutations has been productively addressed by polling cooperating laboratories. However this cannot fix an older ascertainment focus beginning with codon 102 driven by restriction enzymes and older sequencing technology.

After considering all these issues, the likliest scenario is that point mutations (including CpG) prior to the earliest known CJD mutation at codon 102 do occur with reasonable frequency but that the limited spectrum of amino acid substitution achievable from canonical CpG hotspot changes does not give rise to CJD, meaning control chromosomes distal restriction fragments are mainly sequenced, lowering liklihood of observation of proximal silent and neutral mutation. This includes R25H, R37Q, R48L, and G54S, the first two covalently modified, the last codon in the first repeat (a type of change seen in wildtype rodents). The first three changes may adversely affect normal function without causing CJD, notably R37Q. There is no screen for loss of prion function, which would likely be an altogether different disease and very much rarer if autosomal recessive.

Non-uniform susceptibility to mutation across the gene, due to some physical structure limiting accessibility to mutation, cannot be dismissed out of hand. Secondary structure software predicts all sorts of hairpins; the repeat region sees frequent replication slippage of strand alignment; proximal regional sequencing problems are commonly encountered.

Be this as it may, it is easy to predict here on 13 Oct 00 what the next novel reported mutations will be: R208C and V209M are the single most probable (even though the latter may not be causative for CJD) because they are distal, canonical hotspots, and codon 208 has been quite active. After that, G to A changes at R148H, R151H, and R156H are prime candidates, though again these appear more conservative and are in a region (helix 1) without non-CpG causative changes. Among distal C to T non-silentchanges, T188M, R208C, and S230L can confidently be expected to show up soon.

Another curious situation is that valine at codon 129 makes for a CpG site in conjunction with codon 128. Valine occurs at a 10% allele frequency. The canonical CpG outcomes for TAC GTG are TAT GTG (tyr-val, ie silent) and TAC ATG (tyr-met, ie undetectably back to wildtype). Methionine is clearly ancestral here. What happened here is a simple A to G transition resulted in a valine codon and a new CpG site as well (creation and disappearance rates of CpG are at near-equilibrium in mammals). Thus, while valine at codon 129 may represent a single very old kindred; methionine here may be a mix of ancestral primate and kindreds reflecting CpG outcomes from valine. Nearby markers tightly associated with the valine kindred might be able to resolve this latter class.

Note also the silent A117 polymorphism, in which a CpG has been created in 0.5% of the population (through drift). (Other mutations, such as T183A, H187R, Q212P, and Q217R create new CpG sites, but these have not become abundant.) This is at risk of secondary T to C change to A117V, a known CJD mutation. Indeed, it might be worth revisiting flanking markers in these kindreds.

Note that CpG rate enhancement very much influences the structural interpretation of amino acid substitutions. That is, leucine at 102, asparagine at 178, or lysine at 200 are not necessarily among the worst of the 19 amino acid substitutions that could occur (about 0.5% of "point mutations" change 2 adjacent nucleotides), nor necessarily even the worst that could occur via a single nucleotide change: 102S, 102T, 102A, 102Q, 102R; D178H, D178Y, D178G, D178A, D178V; E200Q, E200x, E200G, E200A E200V. Instead, P102L, D178N and E200K are merely the favored substitutions under CpG, which is the favored mutational event.

In contrast, where there is no known rate enhancement mechanism, observed non-CpG causative mutations may be more informative about structural changes predisposing to amyloid. The remaining mutations are weighted 19:6 transitions:transversions, a typical ratio in phylogeny. Thus one wonders, why these and not all the others, especially with multiple kindreds such as P105L.

The screening effort has improved in recent years but still is not been commensurate with the plausible dimensions of nvCJD. A single lab in Sweden could look at 220,000 individual samples in another disease. In one year. It is high time to systematically screen the promoter regions and 3'UTR in nvCJD amd sporadic CJD. The upstream exons and intron junctions are conveniently small and sequencing runs are cheap. Why begin a species sequence with the CDS when for another 30 bases one obtains the at-risk exon junction? If the 3'UTR is unimportant, why are have three subregions been conserved for 100 million years? Sequencing entire intron 2 is however unwarranted.

We can't even begin to recognize promoter polymorphisms in CJD without baseline data. The much-touted technique of seeking conserved non-coding regions by cross-species alignment yields mixed results in the prion gene. Meanwhile, in Alzheimer, very high-risk APOE -491A /epsilon 4 double mutants [Nat.Gen. 18:69 98 give mild up-regulation coupled with a susceptibility allele. A similar scenario makes sense for observed early onset of nvCJD: over-production via up-regulation in a higher exposure group with met/met susceptiblity.

It is not possible to have an intelligent discussion of "sporadic" CJD until all these familial cases are excluded.

American families report over and over that they are not referred anyone for sequencing the gene from their CJD family member; often samples are not retained. In the past, some labs took a quick swing at the distal region because of the restriction endonucleases they had on the shelf. Then they wrote a paper about how P102L, D178N, E200K, and V210I are the most common mutations. Which they may well be, but this doesn't follow from such data.

Nomenclatural and ascertainment issues in CJD genetics

13 Oct 00 webmaster
-- Recommended reporting Neutral and silent alleles are under-reported (insufficient to merit publication; perceived lack of significance). Numerous researchers have cooperated in recent years to get these on the record; others refuse to cooperate or publish their findings.

-- The upstream dozen bases of exon 3 should be determined up through the splice junction, given the potential for splice-skipping to doppel. Dut to late onset, generational records are usually lacking; it should not be assumed that a case of CJD lacking mutations in the coding region is non-familial.

-- The number of distinct kindreds for each mutational type has not been carefully investigated; however, E200K and some others definitely reflect independent founder events.

-- Ascertainment effort has not always been evenly distributed along the gene; some researchers simply screened codons 102, 129, 178, and 200 for known mutations rather than sequencing the whole coding exon. A unknown proportion of sporadic CJD may actually be attributable to missed coding mutations. The proportion of familial coding CJD is more realistically set at 15%.

-- No systematic examination of upstream untranslated exons or splice sites has ever been undertaken in CJD. A unknown proportion of sporadic CJD may actually be caused by prion gene mutations outside the coding region that give rise to protein overproduction.

-- The mutational map cannot be saturated in view of the number of new sites reported in 1999 from Europe alone (despite a decade of prior sequencing).

--The full allotype must be determined in familial CJD, in particular the cis and trans status of polymorphism codons 129 and 219 and compounding mutations, but often this was not. The doppel allele is determined as well in modern research.

-- Recommended notation (complex example): V129M D178N E219K delR2/insR12232a2a4 to indicate one chromosome carries V, D, and E at the indicated codons as well as a repeat deletion of type R2, whereas the other chromosome has N (the mutation at 178), M and K in cis at the polymorphic positions, and two extra modified repeats (non-causative) yielding R12232a2a4. Cis/trans issues are critical to kindred tracking, age of onset, variation in presentation, amyloid composition and recruitment (like-like principle), and to infectivity.

-- Modern familial CJD surveys also determine the status of the 5 doppel alleles and certain microsatellites; an additional novel cis-trans issue arises from intergenic splicing. Doppel provides close-in polymorphisms for kindred tracking in prion diseases.

-- Comparative primate genomics unequivocably establish 5-repeat-GCA117-M129M-E217E as the human wildtype ancestral gene; these are assumed if not specified. GenBank regretably carries a 4-repeat sequence (2% polymorphism) as its human genome standard (X83416 HeLa).

-- The combinatorics of 42 point mutations, 6 deletions, and 28 insertions give rise to an astronomical number of possible haplotypes, which then must be squared to get genotypes. These genotypes cannot be inferred from traditional diagnostic phenotypes (GSS, FFI, CJD, etc); indeed, neurological diagnostics cannot even distinguish sporadic from familial.

-- Recommended nomenclature The underlying reason for hair-splitting in prion disease nomenclature was political: to make a rare monogenic disease appear as a whole family of diseases to grant agencies. The correct disease family (25+ genes) to which prion disease belongs is congophilic cross-beta amyloidoses, as explicitly recognized by GG Glenner in two prominent 1980 review articles. Insulin amyloidosis was the first established infectious protein-only disorder (crossing the species barrier as well: pig to human); others are still under study.

-- Fatal familial insomnia (FFI) is generally defined as D178N _129M, ie, there needs to be a methionine at codon 129 on the same allele as the asparagine mutation, otherwise FFI is unspecified. Gerstmann-Straussler-Scheinker (GSS) is an ill-conceived assemblage of genetically different diseases that includes P102L, P105L, A117V, Y145-, F198S, Q217R, and certain repeat insertions; useage should probably be restricted to the genotype of the original case, P102L M129M E217E.

-- In fact, it would be better to simply call everything prion disease, while specifying the genotype. Creutzfeldt denied in a 1953 interview that his 1920's cases involved CJD (consistent with modern review); Jakob's original case was familial GSS (ie, JCD makes no more sense than CJD). The origin of kuru is unknown; subsequent rounds were non-familial.

-- Prion disease in animals has an equally unfortunate nomenclature: scrapie (sheep and goats), chronic wasting disease (CWD, cervids), bovine spongiform encephalopathy (BSE), transmissible mink encephalopathy (TME). When transmitted to humans, BSE is called new variant CJD (nvCJD). Scrapie and CWD transmit to humans according to in vitro proxy conversion, but they cannot be resolved yet from sporadic CJD and no names have been chosen yet.

-- As a practical matter, CJD and prion will always be the principle search terms at Medline -- no one can change the titles and abstracts of 6500 papers spanning 8 decades of older literature. The recommended search term at Medline is (((((((prion[All Fields]) OR scrapie[All Fields]) OR bse[All Fields]) OR spongiform[All Fields]) OR Creutzfeldt[All Fields]) OR gss[All Fields]) OR ffi[All Fields])).

Science Week caries this account:

"In 1921 and 1923, Alfons Maria Jakob (1884-1931) published 4 papers on an apparently newly dentified neurological disease, and in one of these papers, Jakob refers to a previous paper in 1920 by Hans Gerhard Creutzfeld (1885-1964), in which, according to Jakob, Creutzfeld entifies a similar disease. Since the Creutzfeld paper appeared first, this new disease entity came to be called Creutzfeld-Jakob disease.

In a letter to Nature (7 May 98 393:11), F. Katscher points out that analysis of the case reported by Creutzfeld indicates his case does not belong to the transmissible spongiform encephalopathy group, that Creutzfeld himself stated this sometime between 1945 and 1964, and that Creutzfeld-Jakob disease should really be called Jakob disease, but since that would suggest a new disease, a compromise solution is to rearrange the order of the names to Jakob-Creutzfeld disease.

But here is more: Jakob's original slide preparations still exist, and of the 5 cases originally presented by Jakob in his first 4 papers, Katscher points out that present analysis indicates that only 2 of these cases are what we currently understand as Creutzfeld-Jakob disease."

-- CJD is used both generically and for whatever remains after FFI and GSS are removed. nvCJD is non-familial and occurred so far only in M129M; kuru is also non-familial and mainly M129M. Octapeptide repeat insertion disease (sometimes called OPRI) is best specified by providing the repeat sequence, eq, R122323g234.

-- Sporadic CJD is a heterogeneous collection whose origins not currently understood; Classical CJD (in place of sporadic) is a newly-coined comfort term introduced to bolster confidence in blood transmission, reassurances with little scientific basis. About 85% of all CJD is sporadic (cannot be attributed to prion gene coding region mutation nor currently acknowledged infection risk factors). It is not known whether CJD arises from gene dosage (over-production due to promoter mutations or trisomy) or spontaneously (from intrinsic stochastic protein oligomerization).

-- iatrogenic CJD has its conventional meaning. The main sources so far are cadaver pituitary growth hormone and dura mater transplants. No cases of transmission by vaccine (eg, Semples rabies vaccine prepared in scrapie sheep brain, or measles vaccine prepared in fetal BSE calf serum) have been reported in human; two serious accidents are documented in veterinary vaccines.

CpG mutations in bovines yielding known CJD alleles

04 Nov 00 webmaster (a similar analysis could be done in sheep
Recalling that the CpG effect occurs across vertebrates, these might be expected to cause hotspots for mutations in cows. There has always been a concern about a steady background of one per million incidence of TSE in any mammal (Gibbs Principle). While the the bovine prion gene has its share of CpG occurences, the effect of hotspot changes at these is in general unpredictable.

However, a certain subset of these gives rise to legitimate concern: those CpG changes in bovine DNA giving rise to an amino acid substitution that, had they occured in human DNA in the homologous position, would cause CJD. It turns out that bovine and human sequences are similar enough that two known human CJD hotspot mutations are applicable to bovines: E200K and R208H.

Because prion genes are very slowly evolving, only miniscule differences are found in comparing human and bovine sequence threaded to known mouse and hamster nmr structures: this supports but does not prove that the consequences of the same mutations are similar. The most immediate concern for 'familial' BSE arises from octapeptide insertional repeats and E200K.

The table below shows normal bovine in the first row with blue highlighting for residues where homologous changes in humans is associated with CJD. The second row shows in red the effect of C to T changes from the CpG effect, the third row the effect of G to A. Where blue and red align, I predict the change is causative for BSE. (Other sites are not ruled out by any means, simply not supported.) E200K is a very high frequency allele in familial CJD.

Note that in regards to human P102L, the pity here was the CpG site was newly created in hominoids (CpG are in depleted equilibrium in placental mammals), being the CCC codon in all species prior to divergence with orangutan. For a similar reason, mule deer are at special risk, unlike humans, for A117V, just as pronghorn are at T188R.

At D178N and D202N, cattle again are spared -- the problem is the silent CAC codon at H177, mainly affecting primates and rodents, similar to V180I, and the ACT T201.

By using the curated prion sequence database, it is a simple matter to list all species at risk for hotspot amino acid changes that cause CJD in humans at the comparable site. In species such as pigs, sheep, and cows where 100's of millions of animals are kept, it is inevitable that such mutations arise on a yearly basis.

Different forms of the bovine PrP gene

Goldmann W; Hunter N; Martin T; Dawson M; Hope J 
AFRC Institute for Animal Health, Edinburgh, U.K. 
J Gen Virol 72 ( Pt 1): 201-4 (1991)
... We report here the sequence of different forms of the bovine PrP gene which contain either five or six copies of a short, G-C-rich element which encodes the octapeptide Pro-His-Gly-Gly-Gly-Trp-Gly-Gln or its longer variants Pro-Gln/His-Gly-Gly-Gly-Gly-Trp-Gly-Gln. Out of 12 cattle, we found eight animals homozygous for genes with six copies of the Gly-rich peptide (6:6), while four were heterozygous (6:5). Two confirmed cases of BSE occurred in (6:6) homozygous animals.

Frequencies of bovine PrP gene variants

Hunter N; Goldmann W; Smith G; Hope J 
Institute for Animal Health, Neuropathogenesis Unit, Edinburgh. 
Vet Rec 135: 400-3 (1994)
...Polymorphisms and mutations of the PrP gene have been associated with the incidence of experimental and natural scrapie in other animals and this study of the bovine PrP gene was undertaken to discover whether there was a similar association with PrP genotype in cattle with BSE. There are two known polymorphisms of the coding region of the bovine PrP gene, a silent HindII restriction site polymorphism and a difference in the number of an octapeptide repeated sequence (either five or six copies). An analysis of 370 cattle in Scotland revealed no difference between the frequencies of these PrP genotypes in healthy cattle and cattle with BSE.


Sheep scrapie: likely a byproduct of inbreeding

15 Nov 00 webmaster
There are probably a dozen known point variations in the prion gene for sheep. Frequencies and combinations depends on breed and flock. The susceptibility to scrapie is influenced in a complex way by which alleles are present in donor and recipient; this was quantitated for many permutations in vitro in the 1999 dissertation of Alex Bossers. Sheep and human amino acid sequences are easily aligned in the region of variant sheep alleles.

Sheep, being strongly selected for qualities such as wool, evidently fixed various alleles in the prion gene as an unwitting byproduct of intensive inbreeding. Scrapie may have originated from the genetic engineering of the 1730's as familial TSE rather than as sporadic.

Wildtype ovine prion sequence is unambiguous and correctly given at GenBank entry AJ000739. By Blastp of this sequence, viewed as "anchor-queried with identities", the 10 alleles with entries are quickly recovered, along with the wildtype sheep/human differences.

One ses already that the CpG hotspot R208Q allele (R211Q in sheep numbering) is highly problematic, given that R208H causes CJD. Wildtype sheep have 11 CpG sites, of which only two are manifested as sheep "alleles" namely R154H and R211Q (the latter also being found in goat). The other 8 alleles of sheep are otherwise highly conserved sites in mammals and in fact variations never seen in other species experiencing natural selection.

These alleles do not necessarily cause scrapie in and of themselves, though some of them might and others certainly affect susceptibility. Most are not neutral and indeed likely result in impairment of normal prion function. Sheep are not at risk for P102L or D178N hotspot mutation, but are for E200K and R208H, which would still be a risk even after breeding programs to eliminate high risk alleles for scrapie (which unsurprisingly do not include wildtype).

100 ............M..............................S...........H.... 159 human numbering
103 ......................................F..................... 162
103 .................................V.......................... 162
103 ...................................................H........ 162
103 ..................................T......................... 162
103 .........T.................................................. 162
103 ........................................R................... 162

160.......M.E...............I..................V.M.............E 219 human numbering
163 ................................................Q........... 222
163 ........R................................................... 222
163 ........H................................................... 222
163 .............K.............................................. 222

Amino acid polymorphisms of prions in Japanese sheep

T. Ikeda, M. Horiuchi, N. Ishiguro, Y. Muramatsu, G. D. Kai-Uwe & M. Shinagawa
J Gen Virol 76: 2577-2581 (1995)
We investigated the relationships between amino acid polymorphisms of the prion protein (PrP), restriction fragment length polymorphisms (RFLP) of the PrP gene and the incidence of natural scrapie in Japan. Six variant alleles of the PrP gene were found in healthy sheep. Based on the substitutions at codons 112, 136, 154 and 171, these allelic variants were designated, by amino acid at these codons, PrPMARQ, PrPTARQ, PrPMVRQ, PrPMAHQ, PrPMARR and PrPMARH. Each RFLP haplotype (e1h2, e1h2 or e3h1) consisted bo multiple alleles including PrPMARQ. Three of these variant alleles were found in scrapie-affected Suffolk sheep. PrPMARQ was associated with high disease incidence, PrPTARQ and PrPMARR were associated with low disease incidence. We found that one scrapie-affected Suffolk was homozygous for PrPMARR and four PrPSc-positive Suffolks carried PrPMVRQ. Both of two scrapie-affected Corriedales and two out of three scrapie-affected cross-breeds between Suffolk and Corriedale carried PrPMARH, suggesting that this allele associates with high incidence of scrapie in Corriedale and its cross-breeds.

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