ClinVar Miner

List of variants studied for complex neurodevelopmental disorder by Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Included ClinVar conditions (297):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 153
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HGVS dbSNP gnomAD frequency
NM_001040142.2(SCN2A):c.1269G>A (p.Val423=) rs139815570 0.00662
NM_004204.5(PIGQ):c.350C>T (p.Ala117Val) rs111753944 0.00508
NM_001365536.1(SCN9A):c.3767A>G (p.Asn1256Ser) rs141268327 0.00496
NM_021072.4(HCN1):c.140G>T (p.Gly47Val) rs544994462 0.00362
NM_021912.5(GABRB3):c.31C>T (p.Pro11Ser) rs25409 0.00354
NM_015192.4(PLCB1):c.3550C>T (p.Leu1184Phe) rs28390202 0.00270
NM_007254.4(PNKP):c.416G>A (p.Arg139His) rs34472250 0.00185
NM_001130438.3(SPTAN1):c.3720-5T>G rs200543425 0.00180
NM_001130438.3(SPTAN1):c.3051G>A (p.Pro1017=) rs140279996 0.00175
NM_001199107.2(TBC1D24):c.1327G>A (p.Glu443Lys) rs141399869 0.00163
NM_020822.3(KCNT1):c.2729G>A (p.Arg910Gln) rs151272083 0.00162
NM_015267.4(CUX2):c.4108G>A (p.Gly1370Arg) rs143575822 0.00124
NM_007254.4(PNKP):c.1029+2T>C rs199919568 0.00115
NM_152743.4(BRAT1):c.2041G>A (p.Glu681Lys) rs145833100 0.00079
NM_001127222.2(CACNA1A):c.5650G>A (p.Val1884Ile) rs201836062 0.00070
NM_001191061.2(SLC25A22):c.140C>T (p.Thr47Met) rs142220309 0.00068
NM_001191061.2(SLC25A22):c.876G>A (p.Ala292=) rs146300431 0.00058
NM_020822.3(KCNT1):c.3685A>G (p.Thr1229Ala) rs74533482 0.00057
NM_014334.4(FRRS1L):c.533T>C (p.Val178Ala) rs148986846 0.00047
NM_001365536.1(SCN9A):c.1277T>A (p.Met426Lys) rs200415928 0.00046
NM_001365999.1(SZT2):c.6185G>A (p.Arg2062Gln) rs200443293 0.00038
NM_152743.4(BRAT1):c.431G>A (p.Gly144Asp) rs199745325 0.00036
NM_001040142.2(SCN2A):c.1402_1404del (p.Ser468del) rs780584405 0.00027
NM_006279.5(ST3GAL3):c.1079G>A (p.Arg360Gln) rs553120567 0.00027
NM_006279.5(ST3GAL3):c.362G>A (p.Arg121Gln) rs201287443 0.00027
NM_001127222.2(CACNA1A):c.3227C>T (p.Ala1076Val) rs199512932 0.00024
NM_173354.5(SIK1):c.1246-5C>T rs371389145 0.00019
NM_001040142.2(SCN2A):c.5753G>A (p.Arg1918His) rs201718767 0.00015
NM_001110792.2(MECP2):c.1409G>A (p.Arg470His) rs185957513 0.00015
NM_020822.3(KCNT1):c.2595-9C>T rs369966222 0.00015
NM_001165963.4(SCN1A):c.5217C>T (p.Pro1739=) rs149315236 0.00014
NM_015192.4(PLCB1):c.28G>T (p.Ala10Ser) rs150241349 0.00012
NM_001040142.2(SCN2A):c.5752C>T (p.Arg1918Cys) rs139899756 0.00011
NM_001365999.1(SZT2):c.4892C>T (p.Thr1631Met) rs201312287 0.00009
NM_004975.4(KCNB1):c.1266G>C (p.Glu422Asp) rs755843579 0.00009
NM_001958.5(EEF1A2):c.183C>T (p.Asp61=) rs147929770 0.00008
NM_001130438.3(SPTAN1):c.5872G>T (p.Gly1958Cys) rs920545433 0.00007
NM_001165963.4(SCN1A):c.1803C>T (p.Asn601=) rs139403702 0.00006
NM_001365999.1(SZT2):c.8556A>C (p.Thr2852=) rs201027552 0.00006
NM_001367561.1(DOCK7):c.4867A>G (p.Ile1623Val) rs200800312 0.00006
NM_020822.3(KCNT1):c.2674G>A (p.Glu892Lys) rs376757326 0.00006
NM_031844.3(HNRNPU):c.1319C>A (p.Ala440Asp) rs373039242 0.00006
NM_001130438.3(SPTAN1):c.1806+4A>G rs770046688 0.00005
NM_001165963.4(SCN1A):c.1343T>C (p.Ile448Thr) rs755962326 0.00005
NM_000814.6(GABRB3):c.1269C>G (p.His423Gln) rs76962261 0.00004
NM_001130438.3(SPTAN1):c.1968G>A (p.Val656=) rs968327265 0.00004
NM_006922.4(SCN3A):c.4236A>G (p.Gln1412=) rs551837418 0.00004
NM_020822.3(KCNT1):c.1783C>T (p.Leu595Phe) rs950983477 0.00004
NM_000814.6(GABRB3):c.969G>A (p.Glu323=) rs77608123 0.00003
NM_001037.5(SCN1B):c.363C>G (p.Cys121Trp) rs104894718 0.00003
NM_001040142.2(SCN2A):c.4260G>T (p.Thr1420=) rs138241682 0.00003
NM_001130438.3(SPTAN1):c.2287G>A (p.Val763Met) rs372062686 0.00003
NM_001191061.2(SLC25A22):c.654G>A (p.Ala218=) rs769899113 0.00003
NM_015192.4(PLCB1):c.890G>A (p.Arg297His) rs775904184 0.00003
NM_020822.3(KCNT1):c.1110G>A (p.Thr370=) rs140367649 0.00003
NM_173354.5(SIK1):c.955C>T (p.Arg319Trp) rs759268634 0.00003
NM_177550.5(SLC13A5):c.998G>A (p.Arg333Gln) rs1379095103 0.00003
NM_001130438.3(SPTAN1):c.4785G>A (p.Gln1595=) rs746824729 0.00002
NM_001371246.1(SCN2A):c.687T>C (p.Ser229=) rs746904068 0.00002
NM_005249.5(FOXG1):c.271C>A (p.Pro91Thr) rs1555321245 0.00002
NM_016373.4(WWOX):c.517-108243C>T rs551189075 0.00002
NM_152296.5(ATP1A3):c.1176C>T (p.Thr392=) rs1353417724 0.00002
NM_000834.5(GRIN2B):c.2011-8C>G rs774971411 0.00001
NM_000834.5(GRIN2B):c.3118G>A (p.Gly1040Ser) rs202222002 0.00001
NM_000834.5(GRIN2B):c.3981G>A (p.Lys1327=) rs201670483 0.00001
NM_001037.5(SCN1B):c.373C>T (p.Arg125Cys) rs1135401736 0.00001
NM_001040142.2(SCN2A):c.2149+3A>C rs1474808070 0.00001
NM_001130438.3(SPTAN1):c.5672T>C (p.Ile1891Thr) rs961696023 0.00001
NM_001184880.2(PCDH19):c.695A>G (p.Asn232Ser) rs587784299 0.00001
NM_001199107.2(TBC1D24):c.734T>C (p.Leu245Pro) rs370477379 0.00001
NM_001271.4(CHD2):c.594G>C (p.Gln198His) rs374064833 0.00001
NM_001330260.2(SCN8A):c.2139A>C (p.Glu713Asp) rs1218269439 0.00001
NM_001330260.2(SCN8A):c.71A>G (p.Asn24Ser) rs769269501 0.00001
NM_001367561.1(DOCK7):c.691C>G (p.Arg231Gly) rs1254316274 0.00001
NM_003705.5(SLC25A12):c.67-6T>A rs1302626614 0.00001
NM_006279.5(ST3GAL3):c.781C>T (p.Arg261Ter) rs1195818093 0.00001
NM_006922.4(SCN3A):c.4G>A (p.Ala2Thr) rs772128810 0.00001
NM_007327.4(GRIN1):c.957G>A (p.Pro319=) rs766888803 0.00001
NM_000836.4(GRIN2D):c.2695_2697delinsACC (p.Ala899Thr)
NM_000836.4(GRIN2D):c.3847C>T (p.Pro1283Ser)
NM_001040142.2(SCN2A):c.2674G>A (p.Val892Ile) rs121917751
NM_001040142.2(SCN2A):c.3457G>A (p.Glu1153Lys) rs200138205
NM_001040142.2(SCN2A):c.4722C>A (p.Phe1574Leu) rs1558884200
NM_001099922.3(ALG13):c.2144A>T (p.Tyr715Phe) rs1569519563
NM_001110792.2(MECP2):c.1200_1243del (p.Pro400_Pro401insTer) rs61752992
NM_001110792.2(MECP2):c.352C>T (p.Arg118Trp) rs28934907
NM_001110792.2(MECP2):c.414-3C>G rs267608465
NM_001110792.2(MECP2):c.491C>G (p.Pro164Arg) rs61748404
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) rs28934906
NM_001110792.2(MECP2):c.641C>T (p.Ala214Val) rs587783138
NM_001110792.2(MECP2):c.6CGC[8] (p.Ala7_Ala8dup) rs398123566
NM_001110792.2(MECP2):c.799C>T (p.Arg267Ter) rs61749721
NM_001110792.2(MECP2):c.842del (p.Gly281fs) rs61750241
NM_001110792.2(MECP2):c.916C>T (p.Arg306Ter) rs61751362
NM_001110792.2(MECP2):c.952C>T (p.Arg318Cys) rs28935468
NM_001110792.2(MECP2):c.991G>A (p.Val331Met) rs1569548388
NM_001127222.2(CACNA1A):c.1839C>G (p.Ile613Met) rs374686479
NM_001127222.2(CACNA1A):c.2088G>A (p.Leu696=) rs908321451
NM_001127222.2(CACNA1A):c.3085A>G (p.Arg1029Gly)
NM_001127222.2(CACNA1A):c.6271G>A (p.Ala2091Thr)
NM_001127222.2(CACNA1A):c.7266_7271del (p.Ser2423_Gly2424del) rs775428832
NM_001127644.2(GABRA1):c.80G>A (p.Gly27Glu) rs866861998
NM_001165963.4(SCN1A):c.1702C>T (p.Arg568Ter) rs886039430
NM_001165963.4(SCN1A):c.2589+3A>T rs794726775
NM_001165963.4(SCN1A):c.5263G>A (p.Asp1755Asn)
NM_001165963.4(SCN1A):c.602+1G>A
NM_001184880.2(PCDH19):c.528G>T (p.Leu176=) rs971048873
NM_001184880.2(PCDH19):c.707C>T (p.Pro236Leu) rs1060502176
NM_001271.4(CHD2):c.1613T>G (p.Ile538Arg) rs1567139944
NM_001271.4(CHD2):c.1805A>G (p.Asp602Gly) rs1567140845
NM_001271.4(CHD2):c.361C>T (p.Arg121Ter) rs397514740
NM_001323289.2(CDKL5):c.1147_1151del (p.Thr383fs) rs1569219331
NM_001330260.2(SCN8A):c.4282-10C>G rs369145855
NM_001330260.2(SCN8A):c.5740G>A (p.Gly1914Ser)
NM_001353921.2(ARHGEF9):c.928_935del (p.Ser310fs)
NM_001365536.1(SCN9A):c.4482A>G (p.Gln1494=) rs1558945594
NM_001365999.1(SZT2):c.8276T>C (p.Leu2759Pro)
NM_001365999.1(SZT2):c.9640A>G (p.Lys3214Glu)
NM_001367561.1(DOCK7):c.3743T>C (p.Ile1248Thr)
NM_001958.5(EEF1A2):c.1286T>G (p.Met429Arg)
NM_001958.5(EEF1A2):c.532A>T (p.Ile178Phe) rs765056369
NM_002641.4(PIGA):c.248T>C (p.Leu83Pro) rs1569180063
NM_004204.5(PIGQ):c.1012C>G (p.Arg338Gly) rs559762174
NM_004204.5(PIGQ):c.503C>T (p.Thr168Met) rs771796362
NM_004204.5(PIGQ):c.880T>C (p.Ser294Pro) rs2151045576
NM_004408.4(DNM1):c.1872C>T (p.Gly624=) rs1367619284
NM_004975.4(KCNB1):c.2279C>A (p.Thr760Lys)
NM_005249.5(FOXG1):c.1123G>A (p.Ala375Thr) rs1594384127
NM_006922.4(SCN3A):c.5734A>C (p.Arg1912=) rs1553517046
NM_007254.4(PNKP):c.1360C>A (p.Leu454Met) rs200611702
NM_007327.4(GRIN1):c.734A>T (p.Tyr245Phe) rs893141433
NM_015192.4(PLCB1):c.2036_2039del (p.Ser679fs) rs1568577135
NM_015267.4(CUX2):c.4124C>T (p.Pro1375Leu)
NM_020708.5(SLC12A5):c.3193C>T (p.Arg1065Trp) rs774675766
NM_020822.3(KCNT1):c.2896G>A (p.Ala966Thr)
NM_020822.3(KCNT1):c.3174C>T (p.Ala1058=) rs2131577612
NM_020822.3(KCNT1):c.3247G>C (p.Ala1083Pro) rs917893164
NM_020822.3(KCNT1):c.862G>A (p.Gly288Ser) rs587777264
NM_020988.3(GNAO1):c.723+9C>T
NM_021072.4(HCN1):c.192_206dup (p.Gly70_Gly74dup) rs1485709375
NM_021072.4(HCN1):c.2019G>A (p.Leu673=) rs767602409
NM_021072.4(HCN1):c.203GCG[6] (p.Gly74del) rs747975797
NM_031844.2(HNRNPU):c.2166_2167+1delAGG rs575582638
NM_031844.3(HNRNPU):c.1368A>C (p.Glu456Asp) rs1558187433
NM_139058.3(ARX):c.229G>A (p.Ala77Thr)
NM_152296.5(ATP1A3):c.1192+7G>A rs374826826
NM_172107.4(KCNQ2):c.2030G>C (p.Arg677Pro) rs1326189284
NM_172107.4(KCNQ2):c.593G>A (p.Arg198Gln) rs796052621
NM_172107.4(KCNQ2):c.773A>T (p.Asn258Ile)
NM_172107.4(KCNQ2):c.794C>T (p.Ala265Val) rs587777219
NM_173354.5(SIK1):c.1538C>T (p.Ala513Val) rs200402559
NM_198904.4(GABRG2):c.316G>A (p.Ala106Thr) rs796052505
NM_198904.4(GABRG2):c.690C>A (p.Gly230=) rs747988447

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