ClinVar Miner

Variants studied for brain disease

Included ClinVar conditions (2107):
Minimum submission review status: Collection method:
Minimum conflict level:
Gene type:
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If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells.

pathogenic likely pathogenic uncertain significance likely benign benign affects association protective risk factor other not provided total
17186 7991 39044 13161 7598 3 48 5 97 26 2689 83025

Gene and significance breakdown #

Total genes and gene combinations: 2167
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign affects association protective risk factor other not provided total
TSC2 235 47 1343 609 371 0 0 0 0 0 1602 3673
NF1 817 280 1530 531 60 0 0 0 0 0 2 3120
ATM 379 200 1649 455 62 0 0 0 0 0 0 2614
ATM, C11orf65 233 144 992 243 24 0 0 0 0 0 2 1566
TSC1 110 26 627 267 127 0 0 0 0 0 551 1512
SYNE1 34 10 500 271 142 0 0 0 0 0 1 851
VPS13B 73 280 310 84 53 0 0 0 0 0 4 720
MECP2 417 30 194 25 66 0 0 0 0 0 0 691
KMT2D 160 137 213 129 34 0 0 0 0 0 2 620
SPG11 149 15 329 69 42 0 0 0 0 0 1 582
POLG 91 51 254 181 60 0 0 0 0 0 2 579
CHD7 179 27 234 63 62 0 0 0 0 0 1 523
CACNA1H 0 0 301 110 106 0 0 0 4 0 2 521
ATP7B 122 181 210 43 33 0 0 0 0 0 12 503
SCN1A, SCN9A 24 9 308 116 72 0 0 0 0 0 0 494
PAH 197 230 106 21 12 0 0 0 0 0 4 473
LOC102724058, SCN1A 179 32 144 41 19 0 0 0 0 0 102 456
FLNA 51 24 207 77 92 0 0 0 0 0 3 447
SCN1A 206 38 115 34 16 0 0 0 1 0 86 446
SACS 39 206 180 19 7 1 0 0 0 0 2 442
KCNQ2 215 31 100 47 36 0 0 0 0 0 0 412
CACNA1A 73 13 202 48 54 0 0 0 0 0 38 403
FH 92 31 215 62 11 0 0 0 0 0 0 398
GRIN2A 37 9 197 137 35 0 0 0 0 0 0 397
CNTNAP2 23 2 260 72 53 0 0 0 0 0 0 391
NIPBL 214 56 92 31 8 0 0 0 0 0 0 388
FBXL4 27 32 320 1 7 0 0 0 0 0 0 381
NSD1 175 38 92 55 17 0 0 0 0 1 0 374
DEPDC5 89 12 167 68 30 0 0 0 0 0 0 355
GLDC 53 123 154 40 36 0 0 0 0 0 0 353
KIF1A 20 26 173 86 40 0 0 0 0 0 1 336
NRXN1 12 2 258 57 27 0 0 0 1 0 0 334
KCNT1 16 4 163 100 47 0 0 0 0 0 0 325
NPC1 69 113 125 40 31 0 0 0 0 0 1 324
SCN2A 50 29 157 76 34 0 0 0 0 0 1 317
MRE11 15 10 235 49 18 0 0 0 0 0 0 310
ZEB2 90 9 128 69 28 0 0 0 0 0 0 308
BTD 200 59 96 8 16 0 0 0 0 0 1 298
EHMT1 27 9 162 73 41 0 0 0 0 0 0 290
KCNQ3 13 3 144 91 54 0 0 0 0 0 0 289
RELN 18 0 173 56 49 0 0 0 0 0 1 287
SPTAN1 12 6 150 75 46 0 0 0 0 0 0 277
SUFU 21 5 177 62 10 0 0 0 0 0 0 269
CDKL5 157 33 52 12 16 0 0 0 0 0 0 260
LRP2 17 3 173 41 24 0 0 0 0 0 3 260
AGXT 182 38 65 2 3 0 0 0 0 0 0 255
TBC1D24 28 6 169 51 19 0 0 0 0 0 0 252
LRRK2 16 1 204 46 20 0 0 0 1 0 0 248
HEXA 84 68 95 27 7 0 0 0 0 2 0 244
CEP290 76 12 119 26 29 0 0 0 0 0 0 243
CBS 37 67 109 41 16 0 0 0 0 0 1 240
BRAT1 19 2 149 36 29 0 0 0 0 0 0 235
CPLANE1 65 12 122 40 36 0 0 0 0 0 0 232
GALC 36 85 92 18 27 0 0 0 0 3 0 231
GLI3 44 1 85 80 38 0 0 0 0 0 0 231
TCF4 47 25 82 65 22 0 0 0 0 0 0 230
SCN8A 40 20 107 45 20 0 0 0 0 0 0 225
GLA, RPL36A-HNRNPH2 117 47 48 22 9 0 0 0 0 1 3 224
ATP1A2 18 8 114 81 21 0 0 0 0 0 0 222
ANKRD11 46 10 50 91 26 0 0 0 0 0 2 221
ARSA 52 64 101 18 13 0 0 0 0 1 0 220
SNHG14, UBE3A 116 18 78 7 11 0 0 0 0 0 1 220
DCTN1 10 0 147 55 21 0 0 0 0 0 0 219
CHD2 52 9 96 34 26 0 0 0 0 0 1 215
EP300 31 12 102 63 19 0 0 0 0 0 3 215
ABCD1 73 32 74 22 21 0 0 0 0 0 0 213
ATP7A 89 17 61 23 25 0 0 0 0 0 0 213
RANBP2 3 2 125 34 47 0 0 0 3 0 0 210
GNE 30 51 99 27 12 1 0 0 0 0 0 205
SYNGAP1 67 17 60 44 19 0 0 0 0 0 0 203
TPP1 32 48 81 21 19 0 0 0 0 0 25 201
FKTN 16 23 143 20 11 0 0 0 0 0 0 200
OFD1 133 7 27 7 26 0 0 0 0 0 0 200
FKRP 30 37 101 30 13 0 0 0 0 0 0 199
DHCR7 43 70 89 14 15 0 0 0 0 0 2 198
JMJD1C 0 0 139 32 26 0 0 0 0 0 0 197
CDON 4 0 111 58 23 0 0 0 0 0 0 190
SETX 18 2 112 28 27 0 0 0 0 0 0 187
ABCA1 16 1 51 79 37 0 0 0 0 0 0 184
MTM1 131 23 24 4 7 0 0 0 0 0 0 184
ALDH7A1 22 7 112 31 23 0 0 0 0 0 0 183
MAN2B1 24 52 103 15 10 0 0 0 0 0 0 183
MBD5 18 1 121 30 15 0 0 0 0 0 1 183
CLN3 22 78 69 16 8 0 0 0 0 0 0 182
SYNJ1 9 2 123 32 17 0 0 0 0 0 0 182
PCDH19 40 13 85 31 16 0 0 0 0 0 0 181
TP53 7 172 4 0 0 0 0 0 0 0 0 181
CREBBP 100 34 29 6 12 0 0 0 0 0 1 180
DOCK7 9 1 122 31 16 0 0 0 0 0 0 179
ITPR1 23 5 73 73 9 0 0 0 0 0 1 178
PNKP 16 4 119 34 20 0 0 0 0 0 0 177
UNC13D 16 6 121 22 23 0 0 0 0 0 0 175
GRIN2B 19 10 83 44 26 0 0 0 0 0 1 174
PIGO 14 5 132 17 13 0 0 0 0 0 1 174
ATRX 24 5 86 28 33 0 0 0 0 0 1 173
EFHC1 2 0 124 31 26 0 0 0 2 0 1 172
FREM1 4 1 102 43 23 0 0 0 0 0 0 172
ERCC6 30 33 59 50 14 0 0 0 0 0 0 171
LRPPRC 7 38 106 19 5 0 0 0 0 0 1 171
BBS10 43 65 64 10 7 0 0 0 0 0 0 169
CC2D2A 49 7 95 20 8 0 0 0 0 0 0 168
ABAT 15 0 93 35 32 0 0 0 0 0 1 166
ERCC4 8 1 104 35 26 0 0 0 0 0 0 166
LAMP2 36 8 74 41 12 0 0 0 0 0 0 165
ATP1A3 25 7 78 49 21 0 0 0 0 0 0 164
CHRNA4 6 1 104 30 25 0 0 0 0 0 1 163
IDUA 45 46 60 12 11 0 0 0 0 2 0 162
SKI 13 6 92 39 17 0 0 0 0 0 0 161
PTPN11 62 21 57 11 15 0 0 0 0 0 6 160
APOB 21 0 101 37 0 0 0 0 0 0 0 159
KCNMA1 3 2 108 46 17 0 0 0 0 0 0 159
GCDH 45 74 53 6 7 0 0 0 0 0 0 157
NAGLU 28 56 78 7 6 0 0 0 0 0 0 157
POLH 18 3 112 19 7 0 0 0 0 0 0 157
ATP13A2 14 3 110 20 21 0 0 0 0 0 2 156
HLCS 17 21 97 15 20 0 0 0 0 0 0 156
WWOX 22 5 91 20 20 0 1 0 0 0 1 156
ALDH5A1 15 1 99 33 15 0 0 0 0 0 2 155
POMGNT1, TSPAN1 19 70 63 11 5 0 0 0 0 0 0 155
GLB1 35 53 66 10 3 0 0 0 0 0 6 154
MED12 11 5 75 36 25 0 0 0 0 0 0 152
PIGN 22 12 89 19 12 0 0 0 0 0 0 152
SMC1A 33 27 63 32 10 0 0 0 0 0 0 152
SMPD1 33 65 45 6 8 0 0 0 0 0 0 150
KCNA1 15 1 71 42 20 0 0 0 0 0 1 149
PPT1 21 85 47 7 2 0 0 0 0 0 1 149
AHI1 50 8 56 22 23 0 0 0 0 0 0 147
SMAD4 7 0 82 47 8 0 0 0 0 0 1 143
CCBE1 6 0 98 19 19 0 0 0 0 0 5 142
PEX1 22 71 50 4 7 0 0 0 0 0 0 142
PRICKLE1 6 2 100 29 19 0 0 0 0 0 0 142
SETBP1 13 2 57 58 13 0 0 0 0 0 0 141
COL4A1 18 5 41 47 27 0 0 0 2 0 1 140
RPGRIP1L 32 8 79 14 12 0 0 0 0 0 0 139
SGSH 36 36 71 5 10 0 0 0 0 0 0 139
CACNB4 2 0 70 54 18 0 0 0 1 0 0 138
CYP27A1 61 30 57 7 9 0 0 0 0 0 0 138
BBS2 29 36 65 21 10 0 0 0 0 0 0 136
COL4A2 5 1 40 58 32 0 0 0 3 0 0 136
PIGG 7 0 86 25 18 0 0 0 0 0 0 136
VPS13A 11 0 84 45 6 0 0 0 0 0 0 136
XPC 28 40 62 5 5 0 0 0 0 0 0 136
PRICKLE2 3 0 92 20 23 0 0 0 0 0 0 135
DYNC1H1 10 10 86 26 0 0 0 0 0 0 0 132
SOS1 21 10 72 21 12 0 0 0 0 0 2 131
POMT2 19 7 78 11 14 0 0 0 0 0 3 130
HGSNAT 25 21 78 8 7 0 0 0 0 0 0 129
ACADSB 8 4 92 14 15 0 0 0 0 0 0 127
AP5Z1 10 3 75 19 21 0 0 0 0 0 0 127
CP 55 4 54 14 11 0 0 0 0 0 0 127
POMT1 21 6 63 18 21 0 0 0 0 0 0 127
KIF7 16 2 74 16 31 0 0 0 0 0 0 126
MLC1 19 27 54 27 8 0 0 0 0 0 0 126
GLI2 11 2 72 36 15 0 0 0 0 0 0 125
PCNT 33 3 66 7 17 0 0 0 0 0 1 125
SLC2A1 38 11 45 24 12 0 0 0 0 0 2 125
GABRG2 14 9 69 29 9 0 0 0 2 0 0 124
PEX6 29 34 49 9 10 0 0 0 0 0 1 123
PLCB1 3 1 70 27 24 0 0 0 0 0 0 123
PRF1 16 8 75 11 19 0 0 0 0 0 0 123
BBS12 22 27 57 20 22 0 0 0 0 0 0 122
HRAS, LRRC56 17 8 59 35 7 0 0 0 0 0 0 122
ACOX1 10 2 91 14 6 0 0 0 0 0 0 121
PTCH1 3 3 61 51 4 0 0 0 0 0 0 121
CLN6 28 16 62 12 12 0 0 0 0 0 0 120
ASXL1 13 3 49 39 15 0 0 0 0 0 0 119
KCTD7 8 7 77 25 8 0 0 0 0 0 0 119
QARS1 10 3 66 28 12 0 0 0 0 0 0 119
STXBP1 47 13 28 25 15 0 0 0 0 0 0 119
SMARCA4 7 7 43 44 16 0 0 0 0 1 0 118
SPG7 37 15 46 10 16 0 0 0 0 0 3 117
HSD17B4 14 43 46 14 8 0 0 0 0 0 1 116
SIK1 5 0 60 23 28 0 0 0 0 0 0 116
TMEM67 47 12 55 3 7 0 0 0 0 0 0 116
ALDH3A2 25 47 39 9 3 0 0 0 0 0 1 115
FOXG1 41 16 41 19 5 0 0 0 0 0 0 115
NSD2 1 0 56 56 2 0 0 0 0 0 0 115
RAB3GAP2 7 2 86 18 6 0 0 0 0 0 0 115
IQSEC2 31 9 37 19 18 0 0 0 0 0 1 114
SPTBN2 6 5 58 40 8 0 0 0 0 0 2 114
PMM2 44 58 31 2 4 0 0 0 0 0 0 113
AGPS 4 0 88 13 8 0 0 0 0 0 0 112
BBS9 24 3 49 27 25 0 0 0 0 0 0 112
KRAS 18 11 48 36 0 0 0 0 0 0 1 112
MKS1 24 23 62 10 4 0 0 0 0 0 0 112
PAFAH1B1 89 17 4 0 2 0 0 0 0 0 1 112
C19orf12 16 5 50 31 14 0 0 0 0 0 1 110
DYRK1A 34 12 40 19 8 0 0 0 0 0 0 110
ARHGEF15 0 1 65 18 25 0 0 0 0 0 0 109
HCN1 7 3 56 32 12 0 0 0 0 0 0 109
TRAPPC11 6 4 73 11 17 0 0 0 0 0 0 109
PIGQ 0 0 76 22 10 0 0 0 0 0 0 108
DAG1 7 1 71 19 10 0 0 0 0 0 0 107
FLVCR1 4 0 66 10 29 0 0 0 0 0 0 107
NEXMIF 32 1 43 9 23 0 0 0 0 0 1 107
SRCAP 7 0 48 51 2 0 0 0 0 0 0 107
GABRA1 7 4 68 21 7 0 0 0 4 0 0 106
SPATA5 15 6 64 12 10 0 0 0 0 0 0 106
CLN8 13 38 44 18 4 0 0 0 0 0 1 105
PLA2G6 28 12 60 10 4 0 0 0 0 0 0 105
SLC6A1 14 7 49 20 16 0 0 0 0 0 1 105
SMARCA2 15 9 20 51 10 0 0 0 0 0 0 105
AMT 21 31 52 6 7 0 0 0 0 0 0 104
TH 14 31 54 7 4 0 0 0 0 0 1 104
CTSD 7 1 49 39 14 0 0 0 0 0 0 103
BRAF 33 41 19 17 2 0 0 0 0 0 1 102
CHRNA2 3 0 68 24 9 0 0 0 0 0 0 102
SLC6A8 26 1 26 20 29 0 0 0 0 0 1 102
TFAP2B 9 1 39 31 23 0 0 0 0 0 0 102
CACNA2D2 4 1 54 35 7 0 0 0 0 0 0 101
CLN5, FBXL3 23 41 43 3 5 0 0 0 0 0 0 101
IFIH1 11 5 60 12 15 0 0 0 0 0 0 101
SLC17A5 18 39 40 5 4 0 0 0 0 0 0 101
STX11 5 1 71 21 7 0 0 0 0 0 1 101
HEXB 21 33 45 5 5 0 0 0 0 0 0 100
ADSL 14 5 69 13 8 0 0 0 0 0 0 99
GLRA1 29 7 49 8 9 0 0 0 0 0 1 99
SLC12A5 14 0 56 13 16 0 0 0 0 0 0 99
ATR 5 3 71 14 5 0 0 0 0 0 0 98
COQ8A 23 10 48 12 10 0 0 0 0 0 0 98
GAMT 10 2 66 18 7 0 0 0 0 0 0 98
NGLY1 20 5 52 17 6 0 0 0 0 0 0 98
STXBP2 12 1 58 15 19 0 0 0 0 0 0 98
MFSD8 19 4 55 12 10 0 0 0 0 0 0 97
TBX3 7 0 40 36 16 0 0 0 0 0 0 97
ASTN2, TRIM32 4 2 80 9 3 0 0 0 0 0 0 96
BBS1, ZDHHC24 25 23 46 5 8 0 0 0 0 0 0 96
GLUL 3 0 67 16 11 0 0 0 0 0 0 96
PEX26 9 2 55 23 9 0 0 0 0 0 0 96
SCN9A 5 1 63 23 8 0 0 0 0 0 0 96
WNT5A 5 3 46 29 16 0 0 0 0 0 0 96
ARFGEF2 3 0 80 10 1 0 0 0 0 0 1 94
FAM126A 5 1 59 12 16 0 0 0 0 0 1 94
AGA 16 42 39 4 6 0 0 0 0 0 0 93
AIP 14 49 13 24 5 0 0 0 0 0 0 93
ALG13 2 0 53 19 19 0 0 0 0 0 0 93
CNTN2 1 0 63 13 15 0 0 0 0 0 0 92
INPP5E 18 3 40 23 20 0 0 0 0 0 0 92
PEX12 16 30 40 6 5 0 0 0 0 0 0 92
POMGNT2 4 1 63 14 10 0 0 0 0 0 0 92
SOS2 2 4 47 23 16 0 0 0 0 0 1 92
DBH 9 0 57 15 12 0 0 0 0 0 0 91
KCNB1 11 8 45 17 12 0 0 0 0 0 0 91
MCOLN1 32 22 36 4 2 0 0 0 0 0 0 91
MOCS1 5 2 55 29 2 0 0 0 0 0 0 91
GOSR2, LRRC37A2 4 3 58 19 11 0 0 0 0 0 0 90
GRIN1 14 8 40 18 12 0 0 0 0 0 0 90
HBA-LCR, NPRL3 16 3 48 12 11 0 0 0 0 0 0 90
IRF6 13 4 36 18 19 0 0 0 0 0 0 90
PEX7 18 32 42 3 3 0 0 0 0 0 0 90
ARX 31 5 31 15 7 0 0 0 0 0 0 89
SCARB2 23 1 49 15 6 0 0 0 0 0 0 89
SLC13A5 11 6 53 19 6 0 0 0 0 0 0 89
SNAP29 3 0 59 17 10 0 0 0 0 0 0 89
BCHE 9 42 41 1 3 0 0 0 0 0 1 88
LGI1 24 1 48 13 4 0 0 0 0 0 0 88
SLC19A3 21 2 45 12 13 0 0 0 0 0 0 88
​intergenic 43 21 20 0 4 0 0 0 0 0 1 86
CEP41 4 0 65 13 6 0 0 0 0 0 0 86
D2HGDH 11 2 49 16 9 0 0 0 0 0 0 86
MAT1A 12 2 51 9 13 0 0 0 0 0 0 86
ROR2 8 0 23 45 14 0 0 0 0 0 0 86
CARS2 3 0 47 21 13 0 0 0 0 0 1 85
DLD 14 20 39 6 11 0 0 0 0 0 0 85
BIVM-ERCC5, ERCC5 16 3 46 18 13 0 0 0 0 0 0 84
PEX2 12 7 54 8 6 0 0 0 0 0 0 84
SMC3 10 14 39 22 10 0 0 0 0 0 0 84
CD96 2 0 41 29 11 0 0 0 0 0 0 83
CRPPA 26 6 34 6 12 0 0 0 0 0 0 83
KCNH5 1 0 43 25 14 0 0 0 0 0 0 83
MTTP 12 3 43 23 12 0 0 0 0 0 0 83
XPA 13 37 30 4 2 0 0 0 0 0 0 83
LMNB2 1 0 64 12 5 0 0 0 0 0 0 82
BBS4 23 6 29 10 17 0 0 0 0 0 0 81
KANSL1 0 0 38 26 17 0 0 0 0 0 0 81
RAB18 5 0 54 13 9 0 0 0 0 0 0 81
SUMF1 24 7 35 9 11 0 0 0 0 0 0 81
ARID1B 59 15 4 2 0 0 0 0 0 1 0 80
DCAF17 9 1 47 10 15 0 0 0 0 0 0 80
OTC 40 16 17 8 7 0 0 0 0 0 0 80
PNPO 8 3 48 15 7 0 0 0 0 0 0 80
TTC21B 1 0 59 14 5 0 0 0 0 0 0 79
MEGF8 6 0 36 15 21 0 0 0 0 0 0 78
SLC25A22 9 <