Table 1.
Examples of type I phosphovariants
| Gene name (Swiss-Prot ID) | Variation sitea (Swiss-Prot variant ID) | Phosphory lation site | Local peptide sequenceb | Effectc | Reference(s) for variationd | Reference(s) for phosphorylation sitee |
|---|---|---|---|---|---|---|
| Panel a: Type I(−) phosphovariants | ||||||
| Phosphovariants causing Mendelian inherited disease | ||||||
| EDNRB (P24530) | S305N (VAR_003472) | S305 | CEMLRKK S GMQIALN | Hirschsprung disease type 2 | 8852659 | 14636059 |
| FANCA (O15360) | S858R (VAR_017498) | S858 | QSRDTLC S CLSPGLI | Fanconi anemia | 10094191 11091222 | 17924679 |
| KCNJ1 (P48048) | S219R (VAR_019726) | S219 | RVANLRK S LLIGSHI | Bartter syndrome type 2 | 8841184 | 8621594 |
| L1CAM (P32004) | S1194L (VAR_003947) | S1194 | AFGSSQP S LNGDIKP | Hydrocephalus due to stenosis of the aqueduct of Sylvius mental retardation, aphasia, shuffling gait and adducted thumbs syndrome | 8556302 7881431 | 17081983 |
| MAPT (P10636) | S622N (VAR_010350) | S622 | KHVPGGG S VQIVYKP | Frontotemporal dementia and parkinsonism linked chromosome 17 | 10208578 | 7706316 |
| MAPT (P10636) | S637F (VAR_019665) | S637 | VDLSKVT S KCGSLGN | Pick disease | 11891833 | 11104762 9199504 |
| MAPT (P10636) | S669L (VAR_019667) | S669 | DFKDRVQ S KIGSLDN | Fatal respiratory hypoventilation | 14595660 | 11104762 |
| MITF (O75030) | S405P (VAR_010302) | S405 | QARAHGL S LIPSTGL | Waardenburg syndrome type IIa | 8589691 | 10587587 |
| NFKBIA (P25963) | S32I (VAR_034871) | S32 | LLDDRHD S GLDSMKD | Autosomal dominant anhidrotic ectodermal dysplasia with immunodeficiency | 14523047 | 10882136 9721103 8601309 16319058 10723127 9214631 |
| PER2 (O15055) | S662G (VAR_029080) | S662 | ALPGKAE S VASLTSQ | Familial advanced sleep-phase syndrome | 11232563 | 11232563 |
| PTPN11 (Q06124) | Y62D (VAR_015605) | Y62 | KIQNTGD Y YDLYGGE | Patients with Noonan syndrome 1 manifesting juvenile myelomonocytic leukemia | 11992261 12325025 12960218 12717436 | 15951569 15592455 |
| RAF1 (P04049) | S259F (VAR_037809) | S259 | SQRQRST S TPNVHMV | Noonan syndrome type 5 | 17603483 | 8349614 11997508 11971957 10576742 |
| RAF1 (P04049) | T491R (VAR_037819) | T491 | IGDFGLA T VKSRWSG | Noonan syndrome type 5 | 17603483 | 11447113 |
| RAF1 (P04049) | T491I (VAR_037818) | T491 | IGDFGLA T VKSRWSG | Noonan syndrome type 5 | 17603483 | 11447113 |
| RPS6KA3 (P51812) | S227A (VAR_006195) | S227 | DHEKKAY S FCGTVEY | Coffin–Lowry syndrome | 8955270 | 17192257 |
| STAT3 (P40763) | Y657C (VAR_037381) | Y657 | FAEIIMG Y KIMDATN | Hyperimmunoglobulin E recurrent infection syndrome autosomal dominant | 17881745 | 15037656 |
| TGFBR2 (P37173) | Y336N (VAR_022352) | Y336 | AKGNLQE Y LTRHVIS | Loeys–Dietz aortic aneurysm syndrome | 15731757 | 9169454 |
| TNNI3 (P19429) | S166F (VAR_029454) | S166 | LGARAKE S LDLRAHL | Hypertrophic cardiomyopathy | 12974739 | 11121119 |
| TSC1 (Q92574) | T417I (VAR_009403) | T417 | SLPQATV T PPRKEER | Tuberous sclerosis complex, could be a polymorphism | 10570911 10607950 | 14551205 |
| Phosphovariants found in cancer | ||||||
| CDH1 (P12830) | S838G (VAR_001322) | S838 | LVFDYEG S GSEAASL | Ovarian cancer | 8075649 | 10671552 |
| CTNNB1 (P35222) | S23R (VAR_017612) | S23 | PDRKAAV S HWQQQSY | Hepatocellular carcinoma, no effect | 10435629 12027456 | 12027456 |
| CTNNB1 (P35222) | S33F (VAR_017617) | S33 | QQQSYLD S GIHSGAT | Pilomatrixoma, medulloblastoma and hepatocellular carcinoma | 10666372 10435629 10192393 | 12000790 12114015 11818547 |
| CTNNB1 (P35222) | S33L (VAR_017618) | S33 | QQQSYLD S GIHSGAT | Hepatocellular carcinoma | 10435629 | 12000790 12114015 11818547 |
| CTNNB1 (P35222) | S37A (VAR_017624) | S37 | YLDSGIH S GATTTAP | Medulloblastoma, hepatocellular carcinoma | 12027456 10435629 10666372 | 12000790 12114015 11818547 |
| CTNNB1 (P35222) | S37C (VAR_017625) | S37 | YLDSGIH S GATTTAP | Pilomatrixoma, hepatoblastoma | 9927029 10192393 | 12000790 12114015 11818547 |
| CTNNB1 (P35222) | S37F (VAR_017626) | S37 | YLDSGIH S GATTTAP | Pilomatrixoma | 10192393 | 12000790 12114015 11818547 |
| CTNNB1 (P35222) | T41A (VAR_017629) | T41 | GIHSGAT T TAPSLSG | Hepatoblastoma and hepatocellular carcinoma, also in a desmoid tumor | 12051714 10398436 9927029 12027456 10655994 10435629 | 12051714 12114015 11818547 12000790 |
| CTNNB1 (P35222) | T41I (VAR_017630) | T41 | GIHSGAT T TAPSLSG | Pilomatrixoma and hepatocellular carcinoma | 10192393 10435629 | 12051714 12114015 11818547 12000790 |
| CTNNB1 (P35222) | S45F (VAR_017631) | S45 | GIHSGAT T TAPSLSG | Hepatocellular carcinoma | 10435629 | 12051714 12000790 11955436 |
| CTNNB1 (P35222) | S45P (VAR_017632) | S45 | GATTTAP S LSGKGNP | Hepatocellular carcinoma | 10435629 | 12051714 12000790 11955436 |
| FAM10A4 (Q8IZP2) | S71L (VAR_023644) | S71 | DLKADEP S SEESDLE | B-cell leukemia, multiple myeloma, and prostate cancer | 12079276 | 17081983 |
| MET (P08581) | Y1230C (VAR_006292) | Y1230 | FGLARDM Y DKEYYSV | Hereditary papillary renal carcinoma | 9140397 | 12475979 |
| MET (P08581) | Y1230H (VAR_006293) | Y1230 | FGLARDM Y DKEYYSV | Hereditary papillary renal carcinoma | 9140397 | 12475979 |
| NME1 (P15531) | S120G (VAR_004625) | S120 | GRNIIHG S DSVESAE | Neuroblastoma | 8047138 | 8810265 |
| RB1 (P06400) | S567L (VAR_005579) | S567 | SLAWLSD S PLFDLIK | Retinoblastoma | 10671068 2594029 | 10207050 |
| TP53 (P04637) | T155A (VAR_005901) | T155 | DSTPPPG T RVRAMAI | Esophageal cancer | 1868473 | 12628923 |
| Phosphovariants related with polymorphism | ||||||
| BARD1 (Q99728) | S186G (VAR_038371) | S186 | SYEFVSP S PPADVSE | Polymorphism (rs16852741) | 15855157 | |
| C10orf11 (Q9H2I8) | S153F (VAR_033686) | S153 | SSEDVAS S PERHYTP | Polymorphism (rs35349706) | 16964243 | |
| CTNND1 (O60716) | Y217C (VAR_020929) | Y217 | PDGYSRH Y EDGYPGG | Polymorphism (rs11570194) | 15592455 16212419 | |
| CTPS (P17812) | S571I (VAR_027055) | S571 | RDTYSDR S GSSSPDS | Polymorphism (rs17856308) | 15489334 | 16097034 17081983 |
| HIF1A (Q16665) | T796A (VAR_015854) | T796 | ESGLPQL T SYDCEVN | Polymorphism (rs1802821) | 17382325 | |
| INSR (P06213) | Y1361C (VAR_015933) | Y1361 | SYEEHIP Y THMNGGK | Polymorphism (rs13306449) | 7657032 | 11401470 |
| KRT36 (O76013) | T315M (VAR_020306) | T315 | EIIELRR T VNALEIE | Polymorphism (rs2301354) | 17081983 | |
| MYH15 (Q9Y2K3) | T1125A (VAR_030238) | T1125 | KTVKELQ T QIKDLKE | Polymorphism (rs3900940) | 17081983 | |
| PDLIM5 (Q96HC4) | S136F (VAR_023779) | S136 | PRPFGSV S SPKVTSI | Polymorphism (rs2452600) | 17287340 | |
| PNN (Q9H307) | S671G (VAR_023368) | S671 | HKSSKGG S SRDTKGS | Polymorphism (rs13021) | 10095061 | 17287340 |
| SUB1 (P53999) | S11G (VAR_032870) | S11 | SKELVSS S SSGSDSD | Polymorphism (rs17850527) | 15489334 | 17081983 16689930 |
| SRRM2 (Q9UQ35) | S883C (VAR_027260) | S883 | SPDPELK S RTPSRHS | Polymorphism (rs17136053) | 17287340 | |
| TP53 (P04637) | S366A (VAR_022317) | S366 | PGGSRAH S SHLKSKK | Polymorphism | 9183006 | |
| Panel b: Type I(+) phosphovariants | ||||||
| DDX27 (Q96GQ7) | G766S | S766 | ALKQYRA G PSFEERK | Unknown | 16565220 | 16565220 |
aLocations and amino acid changes of the variations in the proteins.
bPeptide sequences with 15-mer amino acids. The amino acids in the eighth position are phosphorylated residues.
cThe meanings or consequences of the variations. We referred to the feature tables of Swiss-Prot for these effects. If the polymorphisms are enrolled in dbSNP, the IDs of dbSNP are written in the parentheses.
dPubmed ID for the references of the variations
ePubmed ID for the references of the phosphorylation sites
Protein names which are abbreviated by their gene names: epithelial cadherin (precursor), CDH1; catenin β-1, CTNNB1; probable ATP-dependent RNA helicase DDX27, DDX27; endothelin B receptor (precursor), EDNRB; protein FAM10A4, FAM10A4; Fanconi anemia group A protein, FANCA; ATP-sensitive inward rectifier potassium channel 1, KCNJ1; keratin, type I cuticular Ha6, KRT36; Neural cell adhesion molecule L1, L1CAM; microtubule-associated protein tau, MAPT; hepatocyte growth factor receptor (precursor), MET; microphthalmia-associated transcription factor, MITF; NF-κ-B inhibitor α, NFKBIA; nucleoside diphosphate kinase A, NME1; period circadian protein homolog 2, PER2; tyrosine-protein phosphatase nonreceptor type 11, PTPN11; RAF proto-oncogene serine/threonine-protein kinase, RAF1; retinoblastoma-associated protein, RB1; ribosomal protein S6 kinase alpha-3, RPS6KA3; signal transducer and activator of transcription 3, STAT3; TGF-beta receptor type-2 (precursor), TGFBR2; cardiac troponin I, TNNI3; cellular tumor antigen p53, TP53; Hamartin, TSC1.