ClinVar Miner

List of variants reported as pathogenic for Neurodevelopmental disorder

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ClinVar version:
Total variants: 225
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HGVS dbSNP gnomAD frequency
NM_001127701.1(SERPINA1):c.1096G>A (p.Glu366Lys) rs28929474 0.01282
NM_003754.3(EIF3F):c.694T>G (p.Phe232Val) rs141976414 0.00080
NM_001329943.3(KIAA0586):c.94dup (p.His32fs) rs555421894 0.00053
NM_000487.6(ARSA):c.465+1G>A rs80338815 0.00046
NM_001378615.1(CC2D2A):c.4667A>T (p.Asp1556Val) rs201502401 0.00020
NM_002180.3(IGHMBP2):c.1488C>A (p.Cys496Ter) rs145226920 0.00016
NM_017866.6(TMEM70):c.317-2A>G rs183973249 0.00011
NM_015665.6(AAAS):c.1432C>T (p.Arg478Ter) rs121918548 0.00007
NM_145207.3(AFG2A):c.251G>A (p.Arg84Gln) rs745858366 0.00006
NM_020778.5(ALPK3):c.3175C>T (p.Arg1059Ter) rs749465164 0.00004
NM_001114748.2(TMEM240):c.511C>T (p.Arg171Trp) rs606231455 0.00002
NM_001195518.2(MICU1):c.385C>T (p.Arg129Ter) rs369069489 0.00002
NM_001329943.3(KIAA0586):c.704_705del (p.Gln235fs) rs770566897 0.00002
NM_001378615.1(CC2D2A):c.3325C>T (p.Arg1109Ter) rs760676442 0.00002
NM_017736.5(THUMPD1):c.706C>T (p.Gln236Ter) rs778649204 0.00002
NM_000252.3(MTM1):c.1261C>T (p.Arg421Ter) rs587783771 0.00001
NM_001206744.2(TPO):c.1477G>A (p.Gly493Ser) rs778515113 0.00001
NM_013450.4(BAZ2B):c.628C>T (p.Arg210Ter) rs780189423 0.00001
NM_017736.5(THUMPD1):c.341T>G (p.Leu114Ter) rs1470272788 0.00001
NM_017872.5(THG1L):c.529C>T (p.Gln177Ter) rs1231208679 0.00001
NM_022552.5(DNMT3A):c.917G>A (p.Trp306Ter) rs1465829182 0.00001
NM_198576.4(AGRN):c.4744G>A (p.Gly1582Arg) rs1367262797 0.00001
GRCh37/hg19 2q24.2(chr2:160124451-160219840)x1
GRCh37/hg19 2q24.2(chr2:160124451-160511552)x1
GRCh37/hg19 9p13.2-13.1(chr9:36426622-38787479)x1
GRCh37/hg19 9p13.2-13.1(chr9:36442195-39156958)x1
GRCh37/hg19 9p13.3-13.1(chr9:36088563-39092820)x1
GRCh37/hg19 9p13.3-13.2(chr9:35059633-37660586)x1
GRCh38/hg38 14q32.31-32.33(chr14:102263440-106874929)x1
GRCh38/hg38 20q13.33(chr20:62632017-63794804)x1
GRCh38/hg38 4p16.3-11(chr4:1-49062177)x3
GRCh38/hg38 4p16.3-13(chr4:2904667-42963232)x3
GRCh38/hg38 4p16.3-q12(chr4:85624-57073230)x3
GRCh38/hg38 7q33-36.3(chr7:137463392-159345973)x3
GRCh38/hg38 8p23.3-21.2(chr8:449893-23854904)x1
GRCh38/hg38 8q23.3-24.23(chr8:115586904-135607135)x3
NM_000048.4(ASL):c.1045_1057del (p.Val349fs) rs796051933
NM_000329.3(RPE65):c.1430A>G (p.Asp477Gly) rs1571158279
NM_000548.5(TSC2):c.924del (p.Leu309fs) rs2151108081
NM_000719.7(CACNA1C):c.1159dup (p.Thr387fs) rs2154577568
NM_001003694.2(BRPF1):c.362_363del (p.Glu121fs) rs1057519511
NM_001032221.6(STXBP1):c.795-1G>A rs1554777708
NM_001042475.3(CEP85L):c.232+1G>T rs1774227158
NM_001080517.3(SETD5):c.2302C>T (p.Arg768Ter) rs864321657
NM_001080517.3(SETD5):c.536del (p.Gly179fs) rs2125111475
NM_001083962.2(TCF4):c.514_517del (p.Lys172fs) rs398123561
NM_001110556.2(FLNA):c.7058T>C (p.Phe2353Ser) rs2148102210
NM_001110792.2(MECP2):c.455C>T (p.Ala152Val) rs28934908
NM_001110792.2(MECP2):c.953G>A (p.Arg318His) rs61751443
NM_001128126.3(AP4S1):c.138+3_138+6del rs876661295
NM_001163435.3(TBCK):c.658+1G>A rs1579395680
NM_001170629.2(CHD8):c.3724C>T (p.Arg1242Ter) rs1555314788
NM_001170629.2(CHD8):c.5856_5863dup (p.Phe1955fs)
NM_001172509.2(SATB2):c.1375C>T (p.Arg459Ter) rs1553547838
NM_001195518.2(MICU1):c.40del (p.Ala14fs) rs749124658
NM_001195553.2(DCX):c.608C>G (p.Thr203Arg) rs104894782
NM_001271.4(CHD2):c.1934C>T (p.Thr645Met) rs2053619460
NM_001281775.3(ZMYND8):c.1960_1964del (p.Lys654fs)
NM_001282531.3(ADNP):c.2156dup (p.Tyr719Ter) rs1135401808
NM_001291415.2(KDM6A):c.2128C>T (p.Arg710Ter) rs755440519
NM_001303052.2(MYT1L):c.1807del (p.Arg603fs) rs2149016192
NM_001303256.3(MORC2):c.394C>T (p.Arg132Cys) rs1064795559
NM_001303256.3(MORC2):c.79G>A (p.Glu27Lys) rs1602510200
NM_001318852.2(MAPK8IP3):c.1735C>T (p.Arg579Cys) rs1567203083
NM_001320.7(CSNK2B):c.410G>A (p.Cys137Tyr) rs2151188789
NM_001320.7(CSNK2B):c.495_496del (p.Met166fs) rs2151188957
NM_001321571.2(CAMK2D):c.236G>A (p.Ser79Asn)
NM_001321571.2(CAMK2D):c.275+1G>T
NM_001321571.2(CAMK2D):c.416C>T (p.Pro139Leu)
NM_001321571.2(CAMK2D):c.821A>C (p.Gln274Pro)
NM_001321571.2(CAMK2D):c.824G>A (p.Arg275His)
NM_001321571.2(CAMK2D):c.873G>C (p.Leu291Phe)
NM_001321571.2(CAMK2D):c.881T>C (p.Phe294Ser)
NM_001330260.2(SCN8A):c.755C>G (p.Ser252Ter)
NM_001348323.3(TRIP12):c.2118_2119insT (p.Thr707fs) rs2154278573
NM_001351169.2(NT5C2):c.1449+2T>C rs753295868
NM_001353345.2(SETD1B):c.22dup (p.His8fs)
NM_001356.5(DDX3X):c.488dup (p.Tyr163Ter) rs2147350843
NM_001356.5(DDX3X):c.614C>T (p.Pro205Leu) rs2147351801
NM_001366521.1(ATP2B1):c.2632C>T (p.Gln878Ter) rs1033577592
NM_001367479.1(DNAH14):c.6166C>T (p.Arg2056Ter)
NM_001367721.1(CASK):c.2252_2253del (p.Gly751fs) rs2147095950
NM_001367721.1(CASK):c.38_39del (p.Glu13fs)
NM_001371928.1(AHDC1):c.2432C>A (p.Ser811Ter)
NM_001375380.1(EBF3):c.616C>T (p.Arg206Ter) rs1057519522
NM_001375765.1(GIGYF1):c.2498dup (p.Gly834fs) rs776212530
NM_001378452.1(ITPR1):c.4684G>A (p.Val1562Met) rs397514535
NM_001378452.1(ITPR1):c.805C>T (p.Arg269Trp) rs886039392
NM_001378615.1(CC2D2A):c.2671G>A (p.Glu891Lys) rs863225178
NM_001791.4(CDC42):c.68A>G (p.Tyr23Cys) rs797044916
NM_001904.4(CTNNB1):c.1420C>T (p.Arg474Ter) rs1553631860
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_002373.6(MAP1A):c.5484_5485del (p.Met1829fs) rs2140209334
NM_002397.5(MEF2C):c.-8C>T rs2153222958
NM_002397.5(MEF2C):c.45dup (p.Asn16Ter) rs1554150552
NM_002830.4(PTPN4):c.2338C>T (p.Gln780Ter) rs2105059931
NM_002834.5(PTPN11):c.1507G>C (p.Gly503Arg) rs397507545
NM_003042.4(SLC6A1):c.919G>A (p.Gly307Arg) rs1553689696
NM_003070.5(SMARCA2):c.3602C>A (p.Ala1201Glu) rs281875189
NM_003128.3(SPTBN1):c.4718dup (p.Trp1574fs) rs2104068395
NM_003470.3(USP7):c.3052C>T (p.Arg1018Ter) rs1272068741
NM_003482.4(KMT2D):c.13889dup (p.Pro4631fs) rs2120403375
NM_004380.3(CREBBP):c.4133G>A (p.Arg1378Gln) rs121434626
NM_004491.5(ARHGAP35):c.2814dup (p.Lys939Ter)
NM_004539.4(NARS1):c.1600C>T (p.Arg534Ter) rs2051507892
NM_004656.4(BAP1):c.146T>C (p.Leu49Pro) rs2153228340
NM_004656.4(BAP1):c.176G>C (p.Arg59Pro) rs1298276806
NM_004656.4(BAP1):c.2153G>A (p.Arg718Gln) rs1440748203
NM_004656.4(BAP1):c.271T>C (p.Cys91Arg) rs1705222655
NM_004656.4(BAP1):c.271T>G (p.Cys91Gly) rs1705222655
NM_004656.4(BAP1):c.272G>C (p.Cys91Ser) rs1559591264
NM_004656.4(BAP1):c.34C>A (p.Pro12Thr) rs2153228682
NM_004656.4(BAP1):c.34C>G (p.Pro12Ala) rs2153228682
NM_004656.4(BAP1):c.506A>G (p.His169Arg) rs2153227828
NM_004656.4(BAP1):c.91G>A (p.Glu31Lys) rs2153228535
NM_004973.4(JARID2):c.176_177del (p.Val59fs) rs2127515878
NM_004974.4(KCNA2):c.890G>A (p.Arg297Gln) rs786205232
NM_005188.4(CBL):c.1111T>A (p.Tyr371Asn) rs267606706
NM_005249.5(FOXG1):c.1414_1417del (p.Ser472fs) rs1881828200
NM_005249.5(FOXG1):c.703C>T (p.Leu235Phe) rs1566445489
NM_006009.4(TUBA1A):c.5G>A (p.Arg2His) rs587784491
NM_006186.4(NR4A2):c.325dup (p.Gln109fs) rs774629025
NM_006245.4(PPP2R5D):c.751G>T (p.Asp251Tyr) rs1762178916
NM_006493.4:c.679C>T
NM_006521.6(TFE3):c.350G>A (p.Arg117Gln) rs2147777346
NM_006593.4(TBR1):c.381del (p.Gly128fs) rs2105278359
NM_006766.5(KAT6A):c.1506del (p.Asp503fs) rs2150871384
NM_006772.3(SYNGAP1):c.936dup (p.Glu313fs) rs2151168879
NM_006852.6(TLK2):c.968+1G>C rs1598620094
NM_007327.4(GRIN1):c.2479G>A (p.Gly827Arg) rs1451230055
NM_012309.5(SHANK2):c.601dup (p.Leu201fs) rs1555094999
NM_012330.4(KAT6B):c.3349_3350del (p.Gln1117fs)
NM_012330.4(KAT6B):c.5058C>A (p.Tyr1686Ter) rs1381894692
NM_013275.6(ANKRD11):c.5469del (p.Met1825fs)
NM_013275.6(ANKRD11):c.6923del (p.Gly2308fs) rs2151732245
NM_013275.6(ANKRD11):c.6928_6934del (p.Ile2310fs) rs2151732133
NM_013450.4(BAZ2B):c.2126G>A (p.Cys709Tyr) rs1576949430
NM_013450.4(BAZ2B):c.242C>G (p.Ser81Ter) rs767318278
NM_013450.4(BAZ2B):c.5036A>T (p.Glu1679Val) rs1575883384
NM_014009.4(FOXP3):c.1010G>A (p.Arg337Gln) rs2066044949
NM_014681.6(DHX34):c.2327G>C (p.Arg776Pro) rs764483792
NM_014712.3(SETD1A):c.1256_1259dup (p.Thr421fs) rs2143491920
NM_014795.4(ZEB2):c.3088C>T (p.Gln1030Ter) rs903815010
NM_014795.4(ZEB2):c.3149C>G (p.Ser1050Trp) rs1226638635
NM_014991.6(WDFY3):c.3579G>A (p.Trp1193Ter)
NM_015021.3(ZNF292):c.4839_4840del (p.Asn1614fs) rs2127867376
NM_015021.3(ZNF292):c.6160_6161del (p.Glu2054fs) rs1301328139
NM_015100.4(POGZ):c.1180_1181del (p.Met394fs) rs1057518170
NM_015100.4(POGZ):c.3456_3457del (p.Glu1154fs) rs869320764
NM_015100.4(POGZ):c.712C>T (p.Arg238Ter) rs1557910873
NM_015335.5(MED13L):c.2071C>T (p.Gln691Ter) rs2137378964
NM_015335.5(MED13L):c.2950C>T (p.Gln984Ter) rs1376289620
NM_015335.5(MED13L):c.3760_3761del (p.Leu1254fs) rs2137305263
NM_015909.4(NBAS):c.603_605del (p.Leu202del) rs796065038
NM_016333.4(SRRM2):c.1882C>T (p.Arg628Ter) rs1464581573
NM_016333.4(SRRM2):c.2214_2215del (p.Arg739fs) rs2150775947
NM_016333.4(SRRM2):c.2782_2785del (p.Arg928fs) rs2150776380
NM_016333.4(SRRM2):c.2970_2971del (p.Gly991fs) rs2150776534
NM_016333.4(SRRM2):c.3346C>T (p.Gln1116Ter) rs2150776793
NM_016333.4(SRRM2):c.3426_3427del (p.Ser1143fs) rs2150776824
NM_016333.4(SRRM2):c.4200_4203dup (p.Ile1402fs) rs2150777403
NM_016333.4(SRRM2):c.4512_4578del (p.Asn1506fs) rs2150777611
NM_016333.4(SRRM2):c.4528_4529del (p.Leu1510fs) rs2150777620
NM_016333.4(SRRM2):c.4616C>A (p.Ser1539Ter) rs760736029
NM_016333.4(SRRM2):c.4913C>G (p.Ser1638Ter) rs2150777933
NM_016333.4(SRRM2):c.5074C>T (p.Arg1692Ter) rs2150778065
NM_016333.4(SRRM2):c.5410_5411dup (p.Ser1804fs) rs2150778293
NM_016333.4(SRRM2):c.58C>T (p.Gln20Ter) rs764663923
NM_016333.4(SRRM2):c.6042_6043del (p.Arg2015fs) rs2150778741
NM_016333.4(SRRM2):c.6127C>T (p.Arg2043Ter) rs747576963
NM_016333.4(SRRM2):c.6265C>T (p.Arg2089Ter) rs2150778921
NM_016333.4(SRRM2):c.6709dup (p.Ala2237fs) rs2150779172
NM_016333.4(SRRM2):c.7254_7257del (p.Met2419fs) rs2150779549
NM_016604.4(KDM3B):c.331C>T (p.Arg111Ter) rs2126922810
NM_016628.5(WAC):c.485_486del (p.Glu162fs)
NM_016734.3(PAX5):c.1129C>T (p.Arg377Ter) rs377685637
NM_016734.3(PAX5):c.157G>C (p.Asp53His) rs1337956293
NM_016734.3(PAX5):c.419G>A (p.Arg140Gln) rs2132424384
NM_016734.3(PAX5):c.661C>T (p.Arg221Trp) rs2132194720
NM_016734.3(PAX5):c.962C>A (p.Pro321His) rs577863510
NM_017736.5(THUMPD1):c.303_306del (p.Glu102fs) rs2152419456
NM_017736.5(THUMPD1):c.469C>T (p.Arg157Ter) rs2152417926
NM_017736.5(THUMPD1):c.490C>T (p.Pro164Ser) rs151261045
NM_017736.5(THUMPD1):c.495dup (p.Ser166fs) rs2152417882
NM_017736.5(THUMPD1):c.634dup (p.Glu212fs) rs2152417708
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_018489.3(ASH1L):c.3860_3861del (p.Phe1287fs)
NM_019066.5(MAGEL2):c.1996dup (p.Gln666fs) rs770374710
NM_019597.5(HNRNPH2):c.616C>T (p.Arg206Trp) rs886039763
NM_020719.3(PRR12):c.4344del (p.Glu1449fs) rs2122311106
NM_020778.5(ALPK3):c.4154del (p.Pro1385fs) rs568699617
NM_020791.4(TAOK1):c.1303C>T (p.Arg435Ter) rs2153028697
NM_020791.4(TAOK1):c.2125C>T (p.Arg709Ter) rs1347078601
NM_020791.4(TAOK1):c.2161C>T (p.Gln721Ter) rs2150772043
NM_020922.5(WNK3):c.1089+1G>A
NM_020922.5(WNK3):c.1820A>T (p.Glu607Val)
NM_020922.5(WNK3):c.538-2A>G
NM_020922.5(WNK3):c.611C>G (p.Pro204Arg)
NM_020922.5(WNK3):c.721C>T (p.Arg241Ter)
NM_020922.5(WNK3):c.899T>C (p.Leu300Ser)
NM_022455.5(NSD1):c.2615T>G (p.Leu872Ter) rs1581321573
NM_022455.5(NSD1):c.6559C>T (p.Arg2187Ter) rs587784209
NM_022552.5(DNMT3A):c.2644C>T (p.Arg882Cys) rs377577594
NM_024721.5(ZFHX4):c.5695C>T (p.Arg1899Ter) rs1563560495
NM_030632.3(ASXL3):c.3403_3405delinsCC (p.Ser1135fs) rs2145424188
NM_030632.3(ASXL3):c.4399C>T (p.Arg1467Ter) rs1204482456
NM_030954.4(RNF170):c.342C>G (p.Tyr114Ter) rs2128929811
NM_033109.5:c.652A>T
NM_033517.1(SHANK3):c.3679dup (p.Ala1227fs) rs762292772
NM_052867.4(NALCN):c.4654G>A (p.Glu1552Lys) rs2139408863
NM_052874.5(STX1B):c.140C>A (p.Ser47Ter) rs200979563
NM_057175.5(NAA15):c.430C>T (p.Arg144Ter) rs1560966086
NM_130837.3(OPA1):c.1051G>C (p.Asp351His) rs1577228080
NM_130839.5(UBE3A):c.2540C>T (p.Pro847Leu) rs587781239
NM_138572.3(TAF8):c.719_720del (p.Thr240fs) rs2127459499
NM_138572.3(TAF8):c.806_809del (p.Asn269fs) rs2127464524
NM_152269.5(MTRFR):c.-28-1489_283-968del
NM_152641.4(ARID2):c.2734C>T (p.Gln912Ter) rs2138165644
NM_170606.3(KMT2C):c.7825C>T (p.Arg2609Ter) rs2129115127
NM_172107.4(KCNQ2):c.1678C>T (p.Arg560Trp) rs773171451
NM_172362.3(KCNH1):c.1136T>C (p.Leu379Pro) rs878853026
NM_181552.4(CUX1):c.1687C>T (p.Gln563Ter) rs1794879475
NM_182931.3(KMT2E):c.2107G>T (p.Glu703Ter) rs1798679896
NM_197968.4(ZMYM2):c.1013T>G (p.Leu338Ter)
Single allele

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