[GET-dev] Re: anecdotally interesting, was: Also of interest

[Kimberly Robasky]

I went through the whole list, and the only other variant that shows
up in our genomes also has high frequency (>20%), associated with
increased prostate cancer risk.  My guess is that this one may be
real, given the statistic I recently heard at B&W that prostate cancer
is found in 40% of all male autopsies:

ELAC2 S217L
http://evidence.personalgenomes.org/?q=ELAC2+S217L




On Fri, May 21, 2010 at 11:27 AM, Kimberly Robasky <krobasky at gmail.com> wrote:
> ADD1,00460,Gly-Trp:
>
> breaks an experimentally-validated phosphorylation site
> is described in OMIM as:Hypertension, salt-sensitive essential,
> susceptibility to
>
> The following PGPs have this high-frequency (25%), mostly innocuous variant:
>
> Seong-Jin Kim
> hom T @ chr4:2876505
> snp-2
> hom T @ chr4:2876505
> NA07022
> het T @ chr4:2876505
> Stanley Lapidus (alternate)
> het T @ chr4:2876505
> NA12878
> het T @ chr4:2876505
> NA18517
> het T @ chr4:2876505
> NA18555
> het T @ chr4:2876505
> NA18956
> hom T @ chr4:2876505
> D#kgao
> het T @ chr4:2876505
>
> On Fri, May 21, 2010 at 11:17 AM, Kimberly Robasky <krobasky at gmail.com> wrote:
>> Here's a comprehensive list of 124 OMIM variants that break known,
>> experimentally validated phosphorylation sites, with variants falling
>> in highest scoring scan-x motifs listed first:
>>
>> RAF1,00257,Ser-Leu
>> BUB1B,00550,Arg-Gln
>> DSP,02834,Arg-His
>> ADD1,00460,Gly-Trp
>> ELAC2,00217,Ser-Leu
>> UPF3B,00160,Tyr-Asp
>> GJA1,00362,Arg-Gln
>> FLCN,00079,Ser-Trp
>> ABL1,00253,Tyr-His
>> LMNA,00399,Arg-Cys
>> SLC4A1,00040,Glu-Lys
>> PRKAR1A,00074,Arg-Cys
>> KCNQ1,00583,Arg-Cys
>> CTNNB1,00041,Thr-Ala
>> CTNNB1,00037,Ser-Phe
>> CTNNB1,00041,Thr-Ile
>> CTNNB1,00045,Ser-Phe
>> CTNNB1,00037,Ser-Cys
>> CTNNB1,00045,Ser-Pro
>> CDH1,00838,Ser-Gly
>> SMN1,00030,Asp-Asn
>> CDKL5,00175,Arg-Ser
>> CD44,00046,Arg-Gly
>> PTPN11,00063,Tyr-Cys
>> PTPN11,00061,Asp-Gly
>> PTPN11,00062,Tyr-Asp
>> WT1,00396,Asp-Gly
>> WT1,00396,Asp-Asn
>> KCNJ11,00023,Glu-Lys
>> PTEN,00170,Ser-Arg
>> CREBBP,01378,Arg-Pro
>> L1CAM,01194,Ser-Leu
>> LMNA,00298,Arg-Cys
>> CDK4,00024,Arg-Cys
>> CDK4,00024,Arg-His
>> RPS6KA3,00227,Ser-Ala
>> HSPB1,00136,Arg-Trp
>> RAF1,00261,Pro-Ser
>> SCN4A,01313,Thr-Met
>> ATG16L1,00300,Thr-Ala
>> APC,01395,Ser-Cys
>> NFKBIA,00032,Ser-Ile
>> KIT,00820,Asp-Gly
>> ZAP70,00518,Ser-Arg
>> RUNX2,00200,Thr-Ala
>> RUNX2,00191,Ser-Asn
>> CTNNB1,00032,Asp-Tyr
>> CTNNB1,00032,Asp-Gly
>> CTNNB1,00033,Ser-Tyr
>> CTNNB1,00033,Ser-Phe
>> FLT3,00835,Asp-Asn
>> FLT3,00835,Asp-Glu
>> FLT3,00835,Asp-Val
>> FLT3,00835,Asp-His
>> FLT3,00835,Asp-Tyr
>> RAF1,00491,Thr-Arg
>> GLI3,00625,Arg-Trp
>> TGFBR2,00427,Pro-Leu
>> TPM1,00054,Glu-Lys
>> NME1,00120,Ser-Gly
>> MYC,00059,Pro-Ala
>> CPS1,00544,Thr-Met
>> PTPN11,00279,Tyr-Cys
>> ANTXR2,00381,Tyr-Cys
>> TFAP2A,00255,Arg-Gly
>> DSP,00299,Ser-Arg
>> PER2,00662,Ser-Gly
>> PDGFRA,00846,Asp-Tyr
>> KRT12,00135,Arg-Ile
>> KRT12,00135,Arg-Gly
>> KRT12,00135,Arg-Thr
>> CHEK2,00428,Ser-Phe
>> SMN1,00044,Asp-Val
>> WNK4,01185,Arg-Cys
>> APRT,00065,Asp-Val
>> RPS6KA3,00383,Arg-Trp
>> HCN4,00553,Asp-Asn
>> RB1,00567,Ser-Leu
>> TRPM7,01482,Thr-Ile
>> SHROOM4,01089,Ser-Leu
>> TPP1,00206,Arg-Cys
>> LMNA,00453,Arg-Trp
>> AVPR2,00113,Arg-Trp
>> MC1R,00160,Arg-Trp
>> MC1R,00151,Arg-Cys
>> MC1R,00157,Thr-Ile
>> MRE11A,00481,Thr-Lys
>> SSTR5,00240,Arg-Trp
>> RPE65,00091,Arg-Trp
>> BEST1,00141,Arg-His
>> CYP17A1,00329,Tyr-Asp
>> TIRAP,00180,Ser-Leu
>> MEF2A,00283,Gly-Asp
>> CASQ2,00307,Asp-His
>> HSPB1,00135,Ser-Phe
>> NCF1,00042,Arg-Gln
>> CRYAA,00049,Arg-Cys
>> PGAM2,00089,Glu-Ala
>> SLC4A1,00056,Lys-Glu
>> ABL1,00315,Thr-Ile
>> STK11,00194,Asp-Tyr
>> TEK,00897,Tyr-Ser
>> KRT14,00125,Arg-His
>> KRT14,00125,Arg-Cys
>> KCNQ2,00214,Arg-Trp
>> TGFBR2,00336,Tyr-Asn
>> EDNRB,00305,Ser-Asn
>> KRT17,00094,Arg-His
>> KRT17,00094,Arg-Cys
>> KRT17,00094,Arg-Pro
>> FGFR2,00341,Thr-Pro
>> FGFR2,00347,Ser-Cys
>> FGFR2,00340,Tyr-His
>> ACTB,00183,Arg-Trp
>> LBR,00119,Pro-Leu
>> BMP15,00235,Tyr-Cys
>> KRT17,00098,Tyr-Asp
>> GATA1,00218,Asp-Tyr
>> GATA1,00216,Arg-Gln
>> GATA1,00218,Asp-Gly
>> ACTG1,00089,Thr-Ile
>> TGFBR1,00200,Thr-Ile
>> FGFR2,00354,Ser-Cys
>> FGFR2,00351,Ser-Cys
>>
>