Indicators of HSV1 Infection, ECM–Receptor Interaction, and Chromatin Modulation in a Nuclear Family with Schizophrenia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Family Recruitment
2.2. WES
2.3. Mutation Validation with PCR-Based Sequencing
2.4. Bioinformatic Analysis
3. Results
3.1. Clinical Manifestations of SCZ in the Study Family
3.2. WES Analysis
3.3. Autosomal Dominant Analysis and Rare Mutation Identification
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene | Coding: Amino Acid Change | rs Number | Public Database MAF | In Silico Analysis | |||
---|---|---|---|---|---|---|---|
gnomAD | Taiwan BioBank | SIFT | Polyphen-2 | CADDraw/phred | |||
Herpes Simplex Virus 1 Infection Pathway # | |||||||
ZNF573:NM_001172692 | c.A1303G:p.M435V | rs3095726 | 0.831 | 0.3895 | T | B | −0.073/0.943 |
ZNF177:NM_001172651 | c.C335T:p.T112M | rs2217652 | 0.61 | 0.408 | T | B | −0.13/0.718 |
ZNF177:NM_001172651 | c.A1363T:p.I455F | rs2230752 | 0.566 | 0.4 | D | B | 0.744/8.855 |
ZNF132:NM_003433 | c.C755T:p.P252L | rs1465789 | 0.547 | 0.296 | T | B | 0.265/3.882 |
ZNF132:NM_003433 | c.G608A:p.G203D | rs1122955 | 0.174 | 0.0615 | T | B | −1.234/0.002 |
ZNF891:NM_001277291 | c.G1375C:p.V459L | rs2173970 | 0.189 | 0.1555 | T | B | 1.398/15.07 |
ZNF571:NM_001321272 | c.A1777G:p.K593E | rs16973890 | 0.0148 | 0.062 | T | P | 2.087/19.92 |
SP100:NM_001080391 | c.T2477C:p.M826T | rs836237 | 0.797 | 0.4545 | T | B | −1.434/0.001 |
ZNF790:NM_001242800 | c.A902G:p.Q301R | rs3745775 | 0.273 | 0.245 | D | B | 0.255/3.759 |
ZNF44:NM_001353551 | c.A394G:p.T132A | rs11879168 | 0.181 | 0.301 | D | B | 0.955/11.05 |
ZNF529:NM_001145650 | c.T337G:p.L113V | rs2912444 | 0.694 | 0.489 | T | B | −0.538/0.099 |
ZNF527:NM_032453 | c.A638G:p.H213R | rs4452075 | 0.272 | 0.304 | D | B | −0.35/0.245 |
ZNF229:NM_00127851 | c.G1966A:p.G656R | rs1434579 | 0.27 | 0.3265 | D | P | 2.495/22.4 |
ZNF229:NM_00127851 | c.C991T:p.R331C | rs12151338 | 0.274 | 0.3365 | T | P | 1.057/12.32 |
ZNF568:NM_001204839 | c.G1696C:p.G566R | rs1363753 | 0.57 | 0.3325 | T | B | −0.68/0.048 |
ZNF302:NM_001012320 | c.A266G:p.Y89C | rs2290652 | 0.303 | 0.234 | T | P | 2.082/19.88 |
ZNF565:NM_001366190 | c.G140T:p.G47V | rs75766177 | 0.00356 | 0.102 | T | B | −0.092/0.863 |
ZNF543:NM_213598 | c.C163G:p.P55A | rs6510057 | 0.528 | 0.295 | T | B | 0.407/5.505 |
ZNF268:NM_001165887 | c.A220T:p.M74L | rs61960670 | 0.182 | 0.137 | T | B | −0.68/0.049 |
ZNF268:NM_001165881 | c.G2579C:p.R860T | rs62644541 | 0.182 | 0.137 | D | B | 2.755/22.9 |
ZNF300:NM_052860 | c.5_7del:p.M2del | rs72332188 | 0.027317 | 0.038 | NA | NA | N/A |
ZIM3:NM_052882 | c.A1135G:p.I379V | rs4801433 | 0.451 | 0.363 | T | P | 1.731/17.24 |
ZIM3:NM_052882 | c.T205A:p.L69M | rs4801200 | 0.45 | 0.363 | T | P | 0.283/4.096 |
ZIM3:NM_052882 | c.G82A:p.E28K | rs2370134 | 0.143 | 0.2665 | T | P | 0.174/2.83 |
ZNF584:NM_001318002 | c.C298T:p.R100C | rs200779956 | 0.000105 | 0.0615 | T | B | 0.202/3.141 |
ZNF584:NM_001363680 | c.C289T:p.P97S | rs11668789 | 0.178 | 0.061 | T | B | −0.063/0.991 |
ZNF484:NM_001007101 | c.G1397A:p.G466D | rs3739602 | 0.0239 | 0.2785 | D | P | 2.451/22.3 |
ZNF440:NM_152357 | c.A371G:p.N124S | rs427880 | 0.515 | 0.3965 | D | B | 0.11/2.181 |
ZNF440:NM_152357 | c.G1561A:p.G521R | rs117998813 | 0.00385 | 0.0755 | D | B | 1.105/12.82 |
ZNF285:NM_001291491 | c.G158A:p.S53N | rs2571089 | 0.192 | 0.362 | T | B | −0.604/ 0.071 |
ZNF460:NM_001330622 | c.A568G:p.K190E | ND | ND | ND | D | P | 3/23.4 |
ZNF284:NM_001037813 | c.369_371del:p.S124del | rs139900131 | 0.473322 | 0.3493 | NA | NA | N/A |
ZNF382:NM_001256838 | c.C1637T:p.T546M | rs61732180 | 0.162 | 0.188 | T | B | 0.854/9.938 |
ZNF180:NM_001278508 | c.C740G:p.S247C | rs1897820 | 0.532 | 0.59 | D | B | 1.601/16.38 |
ZNF180:NM_001278508 | c.C192G:p.C64W | rs2253563 | 0.517 | 0.5765 | D | P | 1.158/13.3 |
ZNF180:NM_001278508 | c.T122C:p.V41A | rs2571108 | 0.692 | 0.697 | T | B | 0.209/3.23 |
ZNF57:NM_001319083 | c.C572A:p.T191N | rs2288958 | 0.418 | 0.6085 | T | B | −1.136/0.003 |
ZNF816:NM_001202456 | c.C485T:p.S162L | rs11084210 | 0.0929 | 0.2365 | T | B | −0.468/0.138 |
ZNF30:NM_001099437 | c.A1202G:p.Y401C | rs765746 | 0.188 | 0.403 | D | P | 1.728/17.22 |
ZNF439:NM_001348724 | c.C1013G:p.A338G | rs72994214 | 0.023 | 0.08 | D | B | 0.772/9.12 |
ZNF317:NM_00119079 | c.G57T:p.Q19H | rs3752199 | 0.154 | 0.117 | T | B | 0.43/5.76 |
ZNF416:NM_001353405 | c.C284T:p.S95L | rs151324898 | 0.000952 | 0.035 | T | P | 0.947/10.97 |
ZNF735:NM_001159524 | c.C670A:p.H224N | rs4320434 | 0.224 | 0.2575 | T | B | −1.599/0.001 |
ZNF875:NM_001329773 | c.G1358T:p.S453I | rs3745765 | 0.278 | 0.318 | T | B | −0.005/1.302 |
ZNF460:NM_001330622 | c.A568G:p.K190E | ND | ND | ND | D | P | 3/23.4 |
ZNF333:NM_001352243 | c.C917T:p.A306V | rs3764626 | 0.357 | 0.5945 | T | B | 0.635/7.848 |
TLR3:NM_00326 | c.C1234T:p.L412F | rs3775291 | 0.236 | 0.361 | D | P | 2.844/23.1 |
IFNAR1:NM_000629 | c.G502C:p.V168 | rs2257167 | 0.156081 | 0.354 | T | P | 1.153/13.25 |
ECM–receptor interaction pathway $ | |||||||
LAMA2:NM_000426 | c.G1856A:p.R619H | rs3816665 | 0.257227 | 0.0725 | T | B | −1.085/0.004 |
LAMA2:NM_00107982 | c.C7748T:p.A2583V | rs2229848 | 0.370535 | 0.587 | T | P | 4.105/27.8 |
VWF:NM_000552 | c.G6104A:p.G2035D | rs186806674 | 0.000157 | 0.0045 | T | B | 0.811/9.502 |
ITGA4:NM_000885 | c.G2633A:p.R878Q | rs1143676 | 0.288230 | 0.8475 | T | B | −0.899/0.014 |
LAMC3:NM_006059 | c.C1564T:p.P522S | rs869457 | 0.282728 | 0.2955 | T | B | 0.839/9.786 |
LAMC3:NM_006059 | c.A1631G:p.E544G | rs10901333 | 0.477113 | 0.471 | T | B | 2.173/20.7 |
LAMC3:NM_006059 | c.C2308G:p.R770G | rs3739510 | 0.845 | 0.6075 | T | B | −0.095/0.851 |
LAMC3:NM_006059 | c.A3244G:p.S1082G | rs2275140 | 0.243787 | 0.663 | T | B | 0.421/5.661 |
LAMA4:NM_001105206 | c.G5443A:p.V1815I | rs3734292 | 0.001740 | 0.0755 | D | P | 3.647/25.2 |
DMP1:NM_001079911 | c.A157T:p.S53C | rs10019009 | 0.281 | 0.4205 | D | P | 3.056/23.5 |
HMMR:NM_001142557 | c.G737A:p.R246H | rs2303078 | 0.037807 | 0.04 | T | B | 0.075/1.873 |
FRAS1:NM_001166133 | c.T1396A:p.L466I | rs12504081 | 0.350818 | 0.3855 | T | P | 2.658/22.7 |
FRAS1:NM_001166133 | c.A2060G:p.D687G | rs345513 | 0.425 | 0.4485 | T | B | 0.327/4.597 |
FRAS1:NM_001166133 | c.C2450T:p.A817V | rs6835769 | 0.433817 | 0.197 | T | B | 0.351/4.87 |
FRAS1:NM_001166133 | c.G3406A:p.E1136K | rs12512164 | 0.242134 | 0.207 | T | P | 1.844/18.06 |
TNN:NM_022093 | c.C3467T:p.A1156V | rs2072036 | 0.114564 | 0.178 | D | B | 0.296/4.24 |
COL6A2:NM_001849 | c.G2039A:p.R680H | rs1042917 | 0.478396 | 0.43 | D | P | 3.684/25.3 |
COL9A1:NM_001377290 | c.A1133G:p.Q378R | rs1135056 | 0.382833 | 0.2785 | T | B | 0.922/10.68 |
TNR:NM_003285 | c.G382T:p.A128S | rs2239819 | 0.241553 | 0.514 | T | B | 1.383/14.97 |
COL6A6:NM_001102608 | c.G5216A:p.R1739Q | rs16830494 | 0.095544 | 0.1835 | D | B | 2.068/19.77 |
Gene | Coding: Amino Acid Change | rs Number | Public Database MAF | In Silico Analysis | |||
---|---|---|---|---|---|---|---|
gnomAD | Taiwan BioBank | SIFT | Polyphen-2 | CADDraw/phred | |||
SSX2IP:NM_001166294 | c.G1492C:p.G498R | rs191448293 | 0.0002900 | 0.001648 | D | P | 1.85/18.1 |
SPAG17:NM_206996 | c.A4837G:p.N1613D | rs200562117 | 0.00008007 | 0.000660 | T | B | 0.468/6.162 |
STYXL2:NM_001080426 | c.C91T:p.R31X | rs377245710 | 0.00005664 | 0.001318 | NA | NA | 7.113/37 |
ZNF648:NM_001009992 | c.T1105C:p.C369R | rs765064028 | 0.00005709 | 0.000668 | D | P | 3.636/25.2 |
RGSL1:NM_001137669 | c.T226C:p.F76L | rs1403931074 | 0.00004728 | ND | D | P | 3.83/26 |
EMILIN1:NM_007046 | c.G2366A:p.R789Q | rs566620372 | 0.00007649 | ND | T | P | 3.552/24.9 |
ARHGEF33:NM_001145451 | c.C484G:p.P162A | rs190587324 | 0.0001200 | 0.000989 | T | P | 2.677/22.8 |
USP34:NM_014709 | c.A3444G:p.I1148M | rs769808228 | 0.00007653 | 0.002307 | T | B | 1.537/15.97 |
CLEC4F:NM_001258027 | c.1421delA:p.K474Sfs*44 | rs781870818 | 0.00003535 | 0.000330 | NA | NA | NA |
STEAP3:NM_001008410 | c.G982A:p.A328T | rs376635282 | 0.00002651 | ND | T | P | 0.49/6.395 |
MYO7B:NM_001080527 | c.A694C:p.I232L | rs559170047 | 0.0001176 | 0.001979 | D | P | 3.607/25.1 |
USF3:NM_001009899 | c.A934G:p.T312A | rs192213473 | 0.0001033 | 0.000659 | T | B | 0.336/4.707 |
FIP1L1:NM_001134938 | c.1225_1226del:p.R413Gfs*3 | rs143671659 | 0.000160 | ND | NA | NA | NA |
NDST3:NM_004784 | c.A2027T:p.E676V | rs757955201 | 0.00003188 | 0.000330 | T | B | 2.585/22.6 |
UCP1:NM_021833 | c.G242A:p.G81E | rs555800104 | 0.0001272 | 0.000659 | D | P | 3.426/24.5 |
SLC6A19:NM_001003841 | c.T1622G:p.L541R | rs1176698743 | ND | ND | D | P | 3.562/24.9 |
CENPK:NM_001349368 | c.G487A:p.V163I | rs769017086 | 0.00008767 | 0.001649 | T | P | 2.989/23.4 |
DMGDH:NM_013391 | c.T2324G:p.L775R | rs201416183 | 0.000003992 | ND | D | P | 4.262/29.2 |
ZFYVE16:NM_001284237 | c.C2189T:p.T730I | rs140823634 | 0.00006367 | ND | T | B | 1.397/15.06 |
SLC22A4:NM_003059 | c.442_443del:p.L148Vfs*131 | rs765247850 | 0.00001988 | 0.000330 | NA | NA | NA |
TCOF1:NM_000356 | c.C122T:p.A41V | rs56180593 | 0.002966 | 0.003 | D | P | 1.682 |
CRYBG1:NM_001624 | c.G166C:p.E56Q | rs201789082 | 0.0005189 | 0.002444 | D | P | 3.799/25.8 |
COL10A1:NM_000493 | c.T788C:p.I263T | rs200461789 | 0.00008876 | 0.000989 | T | B | 0.282/4.078 |
CREB5:NM_001011666 | c.G671T:p.G224V | rs142716067 | 0.0002903 | 0.006338 | D | P | 4.015/27.1 |
SEMA3E:NM_001178129 | c.G1552A:p.V518I | rs200779956 | 0.0001667 | 0.003626 | T | B | 1.179/13.47 |
ATP6V1B2:NM_001693 | c.C7A:p.L3M | rs201057159 | 0.0001301 | 0.001252 | T | P | 2.71/22.8 |
MTSS1:NM_001363300 | c.G1181A:p.R394Q | rs780673847 | 0.00001990 | 0.000330 | D | P | 3.739/25.6 |
EXD3:NM_017820 | c.C707T:p.A236V | rs370748438 | 0.0001587 | 0.000660 | T | B | −0.38/0.212 |
KIAA1217:NM_001282769 | c.T1169G:p.V390G | rs780371689 | 0.00006011 | 0.000330 | D | P | 4.244/29.1 |
SORBS1:NM_001290296 | c.C649G:p.R217G | rs371784791 | 0.0002812 | 0.001995 | D | B | 0.928/10.74 |
CYP2E1:NM_000773 | c.C1127G:p.T376S | ND | ND | ND | D | B | 1.605/16.41 |
NAT10:NM_001144030 | c.G2433T:p.E811D | ND | ND | ND | D | P | 3.284/24.1 |
PACSIN3:NM_001184974 | c.C82T:p.R28W | rs185936979 | 0.0004014 | 0.002970 | D | P | 4.48/32 |
OR8K5:NM_001004058 | c.C821A:p.A274D | rs201996541 | 0.00005177 | 0.000989 | D | P | 1.472/15.55 |
VWF:NM_000552 | c.G6104A:p.G2035D | rs186806674 | 0.0004034 | 0.003626 | T | B | 0.811/9.502 |
SLC39A5:NM_001135195 | c.C1517T:p.T506M | rs2293511 | 0.0007447 | 0.004293 | T | B | −0.791/0.027 |
DNAH3:NM_00134788 | c.G10796A:p.R3599H | rs750487156 | 0.0001485 | 0.001320 | D | P | 2.868/23.1 |
PRSS53:NM_001039503 | c.C1004T:p.A335V | rs188342896 | 0.0005128 | 0.003955 | T | B | 0.433/5.786 |
N4BP1:NM_153029 | c.C19G:p.L7V | ND | ND | ND | T | P | 2.527/22.5 |
CBX2:NM_005189 | c.C1559G:p.S520C | ND | ND | ND | D | P | 4.002/27 |
GDF15:NM_004864 | c.G763A:p.A255T | rs779865510 | 0.000008450 | ND | D | P | 2.955/23.3 |
ZNF784:NM_203374 | c.C298A:p.P100T | rs558625495 | 0.0002610 | 0.004529 | D | B | 1.118/12.94 |
NLRP13:NM_001321057 | c.C2764G:p.P922A | rs181274636 | 0.0001805 | 0.004285 | T | B | 0.173/2.827 |
PEG3:NM_001369735 | c.G1736A:p.S579N | rs532173382 | 0.00009551 | 0.000989 | T | P | 3.266/24 |
ZNF460:NM_001330622 | c.A568G:p.K190E | ND | ND | ND | D | P | 3/23.4 |
C20orf96:NM_080571 | c.C58G:p.Q20E | rs756843278 | 0.00002503 | 0.001978 | D | P | 1.474/15.57 |
SALL4:NM_001318031 | c.T1262G:p.L421W | rs758373411 | 0.0001061 | ND | D | P | 3.88/26.2 |
ZNF831:NM_178457 | c.G3106A:p.A1036T | rs749543585 | 0.0001320 | 0.000330 | T | B | 0.618/7.683 |
MCM3AP:NM_003906 | c.T5555C:p.M1852T | rs182565117 | 0.0002757 | 0.004614 | T | B | 0.393/5.345 |
IL17RA:NM_001289905 | c.G1817A:p.G606E | rs761619526 | 0.0001468 | 0.003067 | T | P | −0.335/0.264 |
AIFM3:NM_001018060 | c.A151C:p.T51P | rs753362705 | 0.00009996 | 0.003014 | T | B | 0.363/5.011 |
MYO18B:NM_001318245 | c.G5399A:p.R1800Q | rs371283219 | 0.00004649 | 0.000659 | D | P | 4.151/28.2 |
ELFN2:NM_052906 | c.G62A:p.R21H | rs368781861 | 0.0001428 | 0.002125 | T | B | 0.686/8.33 |
SCUBE1:NM_173050 | c.G2146A:p.G716S | rs550015784 | 0.0001239 | 0.000342 | T | B | −0.44/0.159 |
SCUBE1:NM_173050 | c.G2141A:p.R714H | rs535650437 | 0.00003703 | 0.000341 | D | P | 3.831/26 |
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Huang, Y.-C.; Ping, L.-Y.; Hsu, S.-H.; Tsai, H.-Y.; Cheng, M.-C. Indicators of HSV1 Infection, ECM–Receptor Interaction, and Chromatin Modulation in a Nuclear Family with Schizophrenia. J. Pers. Med. 2023, 13, 1392. https://doi.org/10.3390/jpm13091392
Huang Y-C, Ping L-Y, Hsu S-H, Tsai H-Y, Cheng M-C. Indicators of HSV1 Infection, ECM–Receptor Interaction, and Chromatin Modulation in a Nuclear Family with Schizophrenia. Journal of Personalized Medicine. 2023; 13(9):1392. https://doi.org/10.3390/jpm13091392
Chicago/Turabian StyleHuang, Yen-Chen, Lieh-Yung Ping, Shih-Hsin Hsu, Hsin-Yao Tsai, and Min-Chih Cheng. 2023. "Indicators of HSV1 Infection, ECM–Receptor Interaction, and Chromatin Modulation in a Nuclear Family with Schizophrenia" Journal of Personalized Medicine 13, no. 9: 1392. https://doi.org/10.3390/jpm13091392