ClinVar Miner

List of variants studied for X-linked syndromic intellectual disability by Baylor Genetics

Included ClinVar conditions (104):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 191
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HGVS dbSNP gnomAD frequency
NM_001394073.1(HS6ST2):c.652A>C (p.Lys218Gln) rs746316980 0.00005
NM_005120.3(MED12):c.4864-6C>T rs1018026145 0.00005
NM_001032382.2(PQBP1):c.541C>T (p.Arg181Trp) rs782792216 0.00004
NM_006950.3(SYN1):c.1321G>T (p.Ala441Ser) rs772106134 0.00004
NM_020717.5(SHROOM4):c.775C>A (p.Gln259Lys) rs373402338 0.00004
NM_000489.6(ATRX):c.2329G>C (p.Gly777Arg) rs1411348345 0.00003
NM_001289.6(CLIC2):c.103C>T (p.Arg35Cys) rs1446453794 0.00003
NM_004187.5(KDM5C):c.4334G>A (p.Arg1445His) rs782272528 0.00003
NM_001008537.3(NEXMIF):c.2786C>T (p.Thr929Ile) rs370164571 0.00002
NM_001015877.2(PHF6):c.688A>G (p.Ile230Val) rs794727879 0.00002
NM_001032382.2(PQBP1):c.671G>A (p.Arg224Gln) rs1249414837 0.00002
NM_001081550.2(THOC2):c.2734G>C (p.Ala912Pro) rs1256411821 0.00002
NM_004595.5(SMS):c.1019A>G (p.Glu340Gly) rs751460863 0.00002
NM_004606.5(TAF1):c.4821+3A>G rs760062431 0.00002
NM_005634.3(SOX3):c.20A>G (p.Asn7Ser) rs1262847980 0.00002
NM_014927.5(CNKSR2):c.1895G>A (p.Arg632His) rs750208984 0.00002
NM_015107.3(PHF8):c.-56C>T rs376594438 0.00002
NM_020717.5(SHROOM4):c.1589C>T (p.Ser530Phe) rs781981612 0.00002
NM_020717.5(SHROOM4):c.724C>T (p.Arg242Cys) rs782548063 0.00002
NM_000489.6(ATRX):c.1766A>C (p.Lys589Thr) rs1557140828 0.00001
NM_001081550.2(THOC2):c.2414A>G (p.Asn805Ser) rs769718049 0.00001
NM_001830.4(CLCN4):c.2000G>A (p.Gly667Asp) rs953773970 0.00001
NM_002547.3(OPHN1):c.1201+3A>G rs1482683297 0.00001
NM_003491.4(NAA10):c.534C>A (p.Asn178Lys) rs1360898468 0.00001
NM_004187.5(KDM5C):c.2866G>A (p.Ala956Thr) rs1392496114 0.00001
NM_004187.5(KDM5C):c.4566C>A (p.Asn1522Lys) rs1245355138 0.00001
NM_004187.5(KDM5C):c.893T>A (p.Leu298Gln) rs137861376 0.00001
NM_005120.3(MED12):c.3692-7A>G rs1014804538 0.00001
NM_005634.3(SOX3):c.337G>A (p.Ala113Thr) rs1927341730 0.00001
NM_020717.5(SHROOM4):c.4322G>A (p.Arg1441His) rs781832862 0.00001
NM_080632.3(UPF3B):c.763A>G (p.Arg255Gly) rs985384811 0.00001
GRCh37/hg19 Xq24(chrX:118714474-118718137)
GRCh37/hg19 Xq28(chrX:153174571-153609996)
NM_000489.6(ATRX):c.109C>T (p.Arg37Ter) rs122445108
NM_000489.6(ATRX):c.1219C>G (p.Leu407Val) rs1557142145
NM_000489.6(ATRX):c.1655C>G (p.Thr552Ser) rs2071378519
NM_000489.6(ATRX):c.2323G>C (p.Asp775His) rs2071322741
NM_000489.6(ATRX):c.3196A>G (p.Lys1066Glu)
NM_000489.6(ATRX):c.4317G>A (p.Lys1439=) rs1569535642
NM_000489.6(ATRX):c.4654G>T (p.Val1552Phe) rs1602995714
NM_000489.6(ATRX):c.477del (p.Lys159fs) rs1603240572
NM_000489.6(ATRX):c.485-7C>A rs1225852818
NM_000489.6(ATRX):c.5449-7A>G rs2067371776
NM_000489.6(ATRX):c.569C>T (p.Pro190Leu) rs1057518708
NM_000489.6(ATRX):c.715T>C (p.Phe239Leu) rs2071445748
NM_000489.6(ATRX):c.758T>C (p.Leu253Ser)
NM_001008537.3(NEXMIF):c.1159G>T (p.Glu387Ter) rs2080114203
NM_001008537.3(NEXMIF):c.1376_1377del (p.Asp458_Cys459insTer) rs1057518730
NM_001008537.3(NEXMIF):c.1417T>C (p.Ser473Pro) rs891017786
NM_001008537.3(NEXMIF):c.1690A>G (p.Ser564Gly)
NM_001008537.3(NEXMIF):c.2888_2889del (p.Ser963fs) rs1569335265
NM_001008537.3(NEXMIF):c.3202C>T (p.Leu1068Phe) rs1556016358
NM_001008537.3(NEXMIF):c.3437C>A (p.Ser1146Tyr) rs2080101583
NM_001008537.3(NEXMIF):c.3728G>A (p.Arg1243His) rs1256402686
NM_001008537.3(NEXMIF):c.4055A>G (p.Asn1352Ser) rs1299106178
NM_001008537.3(NEXMIF):c.4248dup (p.Gly1417fs) rs1057518728
NM_001008537.3(NEXMIF):c.4271C>T (p.Ser1424Phe) rs2080097689
NM_001008537.3(NEXMIF):c.4397A>C (p.His1466Pro) rs2080097127
NM_001008537.3(NEXMIF):c.466G>A (p.Ala156Thr) rs2080117655
NM_001008537.3(NEXMIF):c.862G>T (p.Glu288Ter) rs2080115999
NM_001015877.2(PHF6):c.947A>T (p.Asn316Ile)
NM_001015877.2(PHF6):c.969-6T>G rs2077504087
NM_001032382.2(PQBP1):c.32T>C (p.Leu11Ser) rs2063344708
NM_001032382.2(PQBP1):c.586C>T (p.Arg196Ter) rs1557041672
NM_001032382.2(PQBP1):c.640dup (p.Arg214fs) rs606231196
NM_001032382.2(PQBP1):c.784A>G (p.Lys262Glu) rs1569510706
NM_001039591.3(USP9X):c.1315-4A>G rs1057522024
NM_001039591.3(USP9X):c.1782C>G (p.Pro594=) rs2062543205
NM_001039591.3(USP9X):c.2089T>C (p.Cys697Arg)
NM_001039591.3(USP9X):c.2276G>A (p.Arg759Lys)
NM_001039591.3(USP9X):c.4881A>T (p.Lys1627Asn)
NM_001079872.2(CUL4B):c.1588T>C (p.Phe530Leu) rs1923920343
NM_001079872.2(CUL4B):c.1598T>G (p.Phe533Cys) rs1923919394
NM_001079872.2(CUL4B):c.341C>G (p.Ala114Gly)
NM_001079872.2(CUL4B):c.43G>A (p.Ala15Thr) rs1925231122
NM_001079872.2(CUL4B):c.911C>T (p.Pro304Leu)
NM_001081550.2(THOC2):c.195G>C (p.Gln65His) rs2050956716
NM_001081550.2(THOC2):c.2993G>A (p.Arg998His) rs1326074013
NM_001110792.2(MECP2):c.1174_1178del (p.Val392fs)
NM_001110792.2(MECP2):c.1191_1236del (p.Leu398fs) rs267608329
NM_001110792.2(MECP2):c.842del (p.Gly281fs) rs61750241
NM_001110792.2(MECP2):c.961C>T (p.Arg321Trp) rs61751444
NM_001184880.2(PCDH19):c.1225G>C (p.Gly409Arg) rs1928402131
NM_001184880.2(PCDH19):c.1676del (p.Asn559fs) rs1569314475
NM_001184880.2(PCDH19):c.1849del (p.Glu616_Ile617insTer)
NM_001184880.2(PCDH19):c.676A>G (p.Ile226Val) rs1248114037
NM_001184880.2(PCDH19):c.798C>G (p.Asp266Glu) rs369638371
NM_001184880.2(PCDH19):c.919G>A (p.Glu307Lys) rs1569315225
NM_001330360.2(POLA1):c.3050A>G (p.Asn1017Ser) rs2045884809
NM_001353921.2(ARHGEF9):c.1061T>G (p.Met354Arg)
NM_001353921.2(ARHGEF9):c.1306del (p.Glu436fs) rs1602253296
NM_001353921.2(ARHGEF9):c.402+1G>A rs2052538764
NM_001353921.2(ARHGEF9):c.816-9T>C rs1057522347
NM_001356.5(DDX3X):c.1052G>A (p.Arg351Gln) rs1057518707
NM_001356.5(DDX3X):c.1180_1185dup (p.Arg394_Asp395dup) rs1602134468
NM_001356.5(DDX3X):c.1537G>C (p.Val513Leu) rs2063927856
NM_001356.5(DDX3X):c.1595C>T (p.Thr532Met) rs1064795387
NM_001356.5(DDX3X):c.1600C>T (p.Arg534Cys) rs1555954284
NM_001356.5(DDX3X):c.1675CTT[1] (p.Leu560del) rs1555954380
NM_001356.5(DDX3X):c.1703C>T (p.Pro568Leu) rs1057519430
NM_001356.5(DDX3X):c.544T>G (p.Phe182Val) rs2063875155
NM_001356.5(DDX3X):c.589_590dup (p.Thr198fs)
NM_001356.5(DDX3X):c.596G>A (p.Arg199His)
NM_001356.5(DDX3X):c.824C>T (p.Thr275Met) rs2063889558
NM_001356.5(DDX3X):c.846C>A (p.Ile282=) rs2063889864
NM_001356.5(DDX3X):c.931C>T (p.Arg311Ter) rs1453153749
NM_001367721.1(CASK):c.1690_1691del (p.Thr564fs)
NM_001367721.1(CASK):c.56G>A (p.Gly19Glu) rs2072812741
NM_001367721.1(CASK):c.589G>T (p.Gly197Ter)
NM_001367721.1(CASK):c.709-3C>T rs2067016459
NM_001367721.1(CASK):c.79C>T (p.Arg27Ter) rs794727270
NM_001367721.1(CASK):c.913_914dup (p.Gly306fs) rs1602386709
NM_001415.4(EIF2S3):c.1183-15A>G rs1379305185
NM_001551.3(IGBP1):c.37C>G (p.Pro13Ala) rs2085079076
NM_001551.3(IGBP1):c.995A>G (p.Tyr332Cys) rs2085295702
NM_001830.4(CLCN4):c.1561G>A (p.Ala521Thr) rs1924590136
NM_001830.4(CLCN4):c.2038C>A (p.Pro680Thr) rs142375213
NM_002139.4(RBMX):c.591A>G (p.Glu197=) rs1261521581
NM_002547.3(OPHN1):c.1489C>T (p.Arg497Ter) rs1569215382
NM_002547.3(OPHN1):c.1714G>C (p.Ala572Pro)
NM_002547.3(OPHN1):c.1889C>A (p.Pro630His) rs866834118
NM_002547.3(OPHN1):c.598-1G>C
NM_002547.3(OPHN1):c.833G>C (p.Trp278Ser)
NM_003491.4(NAA10):c.215T>C (p.Ile72Thr) rs1057519448
NM_003491.4(NAA10):c.247C>T (p.Arg83Cys)
NM_003491.4(NAA10):c.472-2A>C rs2065158556
NM_003491.4(NAA10):c.494_495del (p.Lys165fs) rs1569546255
NM_004187.5(KDM5C):c.1267_1269del (p.Lys423del)
NM_004187.5(KDM5C):c.1318T>G (p.Tyr440Asp)
NM_004187.5(KDM5C):c.1439C>T (p.Pro480Leu) rs1057518697
NM_004187.5(KDM5C):c.2768G>A (p.Arg923Gln) rs1556837428
NM_004187.5(KDM5C):c.3244dup (p.Arg1082fs) rs1934751829
NM_004187.5(KDM5C):c.3965_3985del (p.Glu1322_Pro1328del) rs2146819410
NM_004586.3(RPS6KA3):c.1443+6T>C rs2067519822
NM_004595.5(SMS):c.700C>T (p.Arg234Ter)
NM_004606.5(TAF1):c.1632G>T (p.Gly544=)
NM_004606.5(TAF1):c.2120G>A (p.Arg707Gln) rs1602490113
NM_004606.5(TAF1):c.290C>T (p.Ala97Val) rs2032706255
NM_004606.5(TAF1):c.4452+3A>G rs2036334224
NM_004606.5(TAF1):c.4576-9A>G
NM_005120.3(MED12):c.2881C>T (p.Arg961Trp) rs80338758
NM_005120.3(MED12):c.3613C>T (p.Arg1205Cys) rs2092311027
NM_005120.3(MED12):c.6211del (p.Gln2071fs)
NM_005120.3(MED12):c.6408+1G>A rs2092347488
NM_005634.3(SOX3):c.1265G>A (p.Arg422His)
NM_005634.3(SOX3):c.791T>G (p.Val264Gly) rs1927323032
NM_006013.5(RPL10):c.191-5C>T rs1286783643
NM_006013.5(RPL10):c.347G>A (p.Arg116Gln) rs2068007021
NM_006517.5(SLC16A2):c.1070G>A (p.Trp357Ter) rs1380635081
NM_006517.5(SLC16A2):c.334G>C (p.Gly112Arg) rs1928309226
NM_006517.5(SLC16A2):c.511C>T (p.Arg171Ter) rs1930398120
NM_006517.5(SLC16A2):c.972G>A (p.Trp324Ter) rs1930463806
NM_006950.3(SYN1):c.1110C>G (p.Cys370Trp) rs141925310
NM_006950.3(SYN1):c.121G>A (p.Gly41Arg) rs2057941966
NM_006950.3(SYN1):c.1647_1650dup (p.Ser551fs)
NM_007325.5(GRIA3):c.1209A>C (p.Glu403Asp) rs2045453992
NM_007325.5(GRIA3):c.2116A>C (p.Met706Leu) rs1569441235
NM_007325.5(GRIA3):c.2408G>A (p.Gly803Glu) rs1569442989
NM_007325.5(GRIA3):c.2447C>T (p.Thr816Ile) rs1569443329
NM_007325.5(GRIA3):c.268+16792G>A rs1927781157
NM_007325.5(GRIA3):c.69G>A (p.Leu23=) rs759740734
NM_014927.5(CNKSR2):c.1447A>G (p.Met483Val) rs2092208925
NM_014927.5(CNKSR2):c.2749G>C (p.Glu917Gln) rs1288431232
NM_015107.3(PHF8):c.1185T>C (p.His395=) rs1468021929
NM_015107.3(PHF8):c.1233+6T>C
NM_015107.3(PHF8):c.1349A>G (p.Lys450Arg) rs2065708006
NM_015107.3(PHF8):c.197G>A (p.Arg66His) rs1557110261
NM_015107.3(PHF8):c.2129+39G>C rs2065554551
NM_015107.3(PHF8):c.2345G>C (p.Arg782Pro) rs782358977
NM_015107.3(PHF8):c.377del (p.Leu126fs) rs1057518729
NM_016032.4(ZDHHC9):c.421T>C (p.Cys141Arg) rs1927945327
NM_019597.5(HNRNPH2):c.617G>A (p.Arg206Gln) rs886039764
NM_020717.5(SHROOM4):c.1157A>G (p.Glu386Gly) rs1931268073
NM_020717.5(SHROOM4):c.1859T>C (p.Val620Ala) rs1931218179
NM_020717.5(SHROOM4):c.2519C>T (p.Thr840Ile) rs782154529
NM_020717.5(SHROOM4):c.3166C>T (p.Arg1056Cys)
NM_020717.5(SHROOM4):c.326G>T (p.Gly109Val)
NM_020717.5(SHROOM4):c.3541G>C (p.Glu1181Gln) rs1929724067
NM_024528.4(NKAP):c.550A>G (p.Lys184Glu)
NM_031206.7(LAS1L):c.1961G>T (p.Arg654Leu) rs1556298998
NM_031206.7(LAS1L):c.2057A>G (p.Glu686Gly)
NM_031407.7(HUWE1):c.-24-2A>G rs1569511527
NM_031407.7(HUWE1):c.10111G>A (p.Ala3371Thr)
NM_031407.7(HUWE1):c.1940G>A (p.Arg647Lys)
NM_031407.7(HUWE1):c.212C>T (p.Thr71Ile)
NM_031407.7(HUWE1):c.2803A>G (p.Ser935Gly)
NM_031407.7(HUWE1):c.286G>A (p.Val96Met)
NM_031407.7(HUWE1):c.3239G>A (p.Arg1080His) rs1057518704
NM_203475.3(PORCN):c.1076dup (p.Tyr359Ter)
NM_203475.3(PORCN):c.727C>T (p.Arg243Ter)
NM_203475.3(PORCN):c.964C>G (p.Leu322Val) rs782200118

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