ClinVar Miner

Variants studied for central nervous system disease

Included ClinVar conditions (2722):
Minimum submission review status: Collection method:
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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
27901 13824 94243 37019 18379 21 94 5 160 41 2818 183059

Gene and significance breakdown #

Total genes and gene combinations: 3115
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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 449 103 2186 1219 610 0 0 0 0 0 1602 5414
ATM 737 276 2687 856 97 0 0 0 0 0 0 4415
ATM, C11orf65 417 184 1666 460 67 0 0 0 0 0 2 2667
TSC1 227 48 1066 471 270 0 0 0 0 0 551 2348
SMARCA4 68 30 1290 815 107 0 0 0 0 1 0 2277
VPS13B 238 324 952 514 93 0 0 0 0 0 4 1921
SYNE1 61 23 1179 349 165 0 0 0 0 0 2 1654
SDHA 72 35 801 292 37 0 0 0 0 0 1 1196
CACNA1H 0 0 664 382 134 0 0 0 4 0 2 1174
SPG11 223 33 740 200 43 1 1 0 0 0 2 1167
CACNA1A 93 35 558 250 62 0 0 0 0 0 18 988
ATP7B 229 228 413 268 53 0 0 0 0 0 12 982
CHD7 262 63 415 173 70 0 0 0 0 0 1 949
KMT2D 319 183 258 164 84 0 0 0 0 0 3 939
RELN 24 11 656 219 66 0 0 0 0 0 1 915
CEP290 214 42 383 278 43 0 0 0 0 0 0 911
MECP2 477 48 268 87 83 0 0 0 0 0 1 897
POLG 116 69 448 261 64 0 0 0 0 0 3 864
FLNA 78 32 397 242 123 0 0 0 0 0 3 862
SCN1A, SCN9A 44 14 589 181 46 0 0 0 0 0 0 854
LYST 54 7 615 176 55 0 0 0 0 0 0 852
KIF1A 59 57 527 244 62 0 0 0 0 0 3 850
PAH 385 331 231 94 25 0 0 0 0 0 3 848
LOC102724058, SCN1A 289 91 332 113 26 0 0 0 0 0 102 837
SCN1A 341 102 287 93 19 0 0 0 1 0 86 837
GRIN2A 72 34 425 180 131 0 0 0 0 0 1 805
KCNQ2 295 97 274 132 45 0 0 0 0 0 0 801
DEPDC5 147 35 422 168 32 0 0 0 0 0 0 782
FH 163 52 424 141 17 0 0 0 0 0 0 772
CNTNAP2 37 12 533 174 66 0 0 0 0 0 2 763
SCN2A 101 92 379 167 61 0 0 0 0 0 2 754
GLDC 138 166 292 220 48 0 0 0 0 0 0 742
NRXN1 19 8 517 183 43 0 0 0 1 0 0 735
SACS 71 219 394 67 30 1 0 0 0 0 2 717
KCNT1 23 15 345 288 61 0 0 0 0 0 0 716
JMJD1C 0 0 471 162 31 0 1 0 0 0 0 665
SPTAN1 14 14 288 272 82 0 0 0 0 0 1 656
EHMT1 47 26 279 212 80 0 0 0 0 0 0 635
IGHMBP2 50 32 413 125 52 0 0 0 0 0 0 598
SDHB 106 39 340 103 10 0 0 0 0 0 1 589
CHD2 85 42 258 172 43 0 0 0 0 0 2 587
SCN8A 46 55 273 187 36 0 0 0 0 0 0 579
MRE11 32 20 423 98 34 0 0 0 0 0 1 573
KCNQ3 25 10 344 126 111 0 0 0 0 0 1 562
DOCK7 16 8 379 132 18 0 0 0 0 0 0 551
ATRX 35 17 238 196 83 0 0 0 0 0 2 546
RPGRIP1L 88 25 294 151 29 0 0 0 0 0 0 543
NSD1 257 67 188 39 4 0 0 0 0 1 0 539
SUFU 36 6 352 135 21 0 0 0 1 0 0 537
NIPBL 246 71 151 50 30 0 0 0 0 0 0 526
SETX 31 8 350 122 80 0 0 0 0 0 0 523
RANBP2 3 2 333 128 60 0 0 0 3 0 0 522
PCNT 41 12 318 61 104 0 0 0 0 0 1 515
ABCD1 138 72 185 104 50 0 0 0 0 0 0 511
SYNJ1 18 4 346 117 21 0 0 0 0 0 0 505
SPAST 271 47 143 28 34 0 0 0 0 0 4 496
BRAT1 30 5 320 115 32 0 0 0 0 0 0 495
PCDH19 129 44 235 81 17 0 0 0 0 0 0 494
SYNGAP1 114 43 168 142 33 0 0 0 0 0 0 486
GRIN2B 42 72 179 159 54 0 0 0 0 0 1 480
MAN2B1 71 88 194 178 35 0 0 0 0 0 0 479
MBD5 39 6 232 168 40 0 0 0 0 0 1 479
PLEKHG5 18 4 327 104 49 0 0 0 0 0 2 479
GALC 92 115 177 127 43 0 0 0 0 3 0 478
ATP7A 102 24 156 148 54 0 0 0 0 0 0 468
DNMT1 7 7 266 154 65 0 0 0 0 0 0 465
CBS 74 81 203 141 30 0 0 0 0 0 2 462
AP5Z1 17 6 320 105 52 0 0 0 0 0 0 461
CC2D2A 74 20 288 96 28 0 0 0 0 0 0 460
ZEB2 126 18 181 97 46 0 0 0 0 0 0 457
CDKL5 221 59 117 50 26 0 0 0 0 0 1 453
GLA, RPL36A-HNRNPH2 191 103 121 68 13 0 0 0 0 1 3 452
TBC1D24 36 13 292 100 40 0 0 0 0 0 0 449
PIGO 30 11 317 89 16 0 0 0 0 0 1 445
ATP1A2 26 14 263 104 75 0 0 0 0 0 0 439
LRP2 17 6 269 66 87 0 0 0 0 0 3 435
CLN3 50 91 200 122 12 0 0 0 0 0 0 433
UNC13D 35 9 294 86 41 0 0 0 0 0 0 433
ARSA 112 97 173 89 37 0 0 0 0 1 2 429
ANKRD11 112 26 107 143 59 0 0 0 0 0 2 426
DCTN1 10 2 275 111 60 0 0 0 0 0 0 426
ATP1A3 63 23 176 140 49 0 0 0 0 0 0 422
AHI1 79 18 233 79 37 0 0 0 0 0 0 419
CREBBP 207 68 75 34 45 0 0 0 0 0 1 415
PEX6 65 48 172 137 31 0 0 0 0 0 1 413
PLCB1 7 2 287 112 29 0 0 0 0 0 0 413
PNPLA6 24 7 274 106 30 0 0 0 0 0 0 412
TCF4 75 32 182 66 70 0 0 0 0 0 0 408
IDUA 88 74 139 130 29 0 0 0 0 2 1 407
HGSNAT 53 38 209 114 27 0 0 0 0 0 0 402
PNKP 35 13 268 93 26 0 0 0 0 0 1 398
KCNMA1 6 3 255 132 25 0 0 0 0 0 0 394
FKRP 48 43 214 91 14 0 0 0 0 0 0 393
FBXL4 32 37 324 1 7 0 0 0 0 0 0 390
HEXA 117 94 135 95 11 0 0 0 0 2 1 388
FKTN 36 25 243 77 24 0 0 0 0 0 0 382
TECPR2 17 13 130 214 32 0 0 0 0 0 3 379
SMPD1 94 114 106 101 35 0 0 0 0 0 0 378
BTD 220 73 123 54 19 0 0 0 0 0 3 376
SIK1 5 0 174 147 55 0 0 0 0 0 0 375
ALDH7A1 44 14 237 57 37 0 0 0 0 0 0 373
DHCR7 77 97 153 101 29 0 0 0 0 0 2 373
PEX1 57 88 151 103 27 0 0 0 0 0 0 373
PIGN 44 30 216 76 14 0 0 0 0 0 0 370
GNE 58 68 190 84 31 1 0 0 0 0 1 367
CHRNA4 6 1 200 130 34 0 0 0 0 0 1 360
POMT2 26 12 236 60 32 0 0 0 0 0 2 353
HLCS 32 37 165 107 42 0 0 0 0 0 0 352
BBS10 73 75 160 76 17 0 0 0 0 0 0 351
BBS2 55 62 158 102 23 0 0 0 0 0 0 350
POMGNT1, TSPAN1 30 84 163 102 9 0 0 0 0 0 0 348
LRRK2 16 1 268 60 64 0 0 0 2 0 0 344
GLI3 58 3 103 82 110 0 0 0 0 0 0 340
PHOX2B 10 1 228 81 23 0 0 0 0 0 0 340
NAGLU 59 70 134 117 14 0 0 0 0 0 0 337
SDHC 33 15 219 68 5 0 0 0 0 0 0 337
SDHD 59 16 192 64 8 0 0 0 0 0 0 334
CPLANE1 74 23 180 38 51 0 0 0 0 0 0 330
WWOX 42 17 203 54 21 0 1 0 0 0 1 330
TH 28 48 157 123 17 0 0 0 0 0 1 327
EFHC1 3 0 227 79 29 0 1 0 7 0 1 326
SGSH 49 46 150 113 29 0 0 0 0 0 0 326
IFIH1 30 6 208 60 29 0 0 0 0 0 1 325
CHRNA2 3 1 205 72 56 0 0 0 0 0 0 323
ERCC4 11 5 213 62 43 0 0 0 0 0 0 320
MFSD8 43 19 179 75 20 0 0 0 0 0 0 320
SMC1A 64 40 151 53 26 0 0 0 0 0 0 319
SPATA5 42 14 196 61 10 0 0 0 0 0 0 318
STXBP1 105 50 93 62 25 0 0 0 0 0 0 317
MED12 13 8 157 101 39 0 0 0 0 1 0 315
SNHG14, UBE3A 128 29 122 36 11 0 0 0 0 0 1 315
MKS1 45 35 155 99 13 0 0 0 0 0 0 313
POMT1 33 16 186 65 37 0 0 0 0 0 0 312
VPS13A 18 2 193 54 71 0 0 0 0 0 0 310
ATP13A2 24 9 193 79 39 0 0 0 0 0 2 308
IQSEC2 60 19 126 80 28 0 0 0 0 0 1 308
AGXT 182 48 104 19 19 0 0 0 0 0 0 307
PMM2 81 78 128 60 19 0 0 0 0 0 0 305
SMARCE1 14 7 191 85 6 0 0 0 4 0 0 305
CLN6 37 30 168 77 20 0 0 0 0 0 0 303
PRICKLE2 3 0 219 56 38 0 0 0 0 0 0 303
ALDH5A1 31 5 186 59 35 0 0 0 0 0 2 302
PIGG 17 2 193 75 20 0 0 0 0 0 0 302
SLC12A5 23 1 178 84 18 0 0 0 2 0 0 301
GCDH 96 99 84 72 11 0 0 0 0 0 0 300
DYNC1H1 19 33 147 54 54 0 0 0 0 0 1 299
ZFYVE26 22 45 193 18 26 0 0 0 0 0 0 299
BBS9 34 6 183 57 40 0 0 0 0 0 0 298
ZNF423 1 2 185 83 30 0 0 0 0 0 0 297
ALS2 40 21 174 54 28 0 0 0 0 0 0 296
PPT1 41 90 127 42 17 0 0 0 0 0 1 294
CARS2 4 1 204 71 15 0 0 0 0 0 1 291
CYP27A1 78 42 102 107 21 0 0 0 0 0 1 291
GLB1 74 70 94 91 11 0 0 0 0 0 15 291
BICD2 12 10 179 75 18 0 0 0 0 0 1 289
ABAT 15 1 175 52 55 0 0 0 0 0 1 287
FREM1 4 1 176 31 76 0 0 0 0 0 0 285
LAMP2 48 10 129 45 61 0 0 0 0 0 0 285
MTM1 144 38 46 43 22 0 0 0 0 0 0 285
ITPR1 23 11 130 43 81 0 0 0 0 0 1 282
SPG7 81 21 142 44 20 0 0 0 0 0 3 282
CDON 4 0 157 37 86 0 0 0 0 0 0 281
QARS1 22 9 202 51 1 0 0 0 0 0 0 281
TPP1 37 52 145 36 27 0 0 0 0 0 25 280
LRPPRC 8 42 189 24 29 0 0 0 0 0 1 279
SLC19A3 29 5 163 57 41 0 0 0 0 0 0 279
MCOLN1 49 33 85 139 14 0 0 0 0 0 0 278
SKI 14 7 162 86 22 0 0 0 0 0 0 278
MT-ND5 14 4 113 48 104 0 0 0 1 0 0 277
ALG13 3 1 156 84 34 0 0 0 0 0 0 275
BBS12 55 31 134 69 29 0 0 0 0 0 0 275
HBA-LCR, NPRL3 38 14 150 58 16 0 0 0 0 0 0 275
HSD17B4 35 51 89 108 22 0 0 0 0 0 1 275
INPP5E 26 7 172 56 33 0 0 0 0 0 0 275
ACOX1 16 8 154 81 32 0 0 0 0 0 0 274
TRAPPC11 12 7 174 66 19 0 0 0 0 0 0 274
DYRK1A 58 24 96 74 24 0 0 0 0 0 0 270
ABCA1 16 1 161 33 60 0 0 0 0 0 0 269
GFPT1 19 8 173 43 32 0 0 0 0 0 0 269
SLC26A2 35 30 121 66 32 0 0 0 0 0 0 269
HCN1 15 3 140 93 18 0 0 0 0 0 0 267
SLC6A8 41 6 65 101 54 0 0 0 0 0 9 267
SLC12A6 15 33 169 22 33 0 0 0 0 0 1 266
KIF7 18 4 162 58 42 0 0 0 0 0 0 262
SLC6A1 29 25 116 66 29 0 0 0 0 0 1 261
GABRG2 32 17 144 66 15 0 0 0 0 0 0 260
NGLY1 34 10 163 48 8 0 0 0 0 0 0 260
ASTN2, TRIM32 17 5 190 47 9 0 0 0 0 0 0 259
CACNA2D2 6 6 161 78 8 0 0 0 0 0 0 259
PRICKLE1 6 4 186 52 13 0 0 0 0 0 0 256
GABRA1 12 18 162 51 20 0 0 0 4 0 0 254
MT-CYB 4 1 123 36 94 0 0 0 0 0 0 253
OFD1 143 13 50 19 29 0 0 0 0 0 0 251
SOS1 23 13 159 41 20 0 0 0 0 0 2 250
PRF1 31 17 157 40 30 0 0 0 0 0 0 249
STXBP2 14 1 157 67 25 0 0 0 0 0 0 247
PEX5 10 0 173 52 20 0 0 0 0 0 0 245
GAMT 32 13 129 77 7 0 0 0 0 0 4 244
FOXG1 59 31 65 81 17 0 0 0 0 0 1 243
OPA3 6 4 122 31 79 0 0 0 0 0 1 243
POLH, POLR1C 14 3 172 20 41 0 0 0 0 0 0 243
LOC101927870, RELN 5 4 167 56 21 0 0 0 0 0 0 242
VCAN 12 1 80 77 75 0 0 0 0 0 0 242
KCNB1 19 28 101 71 32 0 0 0 0 0 0 241
MT-ATP6 15 5 85 47 92 0 0 0 0 0 1 241
ERCC6 27 56 125 22 25 0 0 0 0 0 0 240
ADAR 18 11 151 60 10 0 0 0 0 0 0 239
CTSD 7 2 153 75 19 0 0 0 0 0 0 239
EP300 59 28 71 45 44 0 0 0 0 0 3 237
POLR3A 46 27 120 24 40 0 0 0 0 0 0 236
SLC13A5 14 14 149 57 7 0 0 0 0 0 0 234
ADSL 28 12 165 32 8 0 0 0 0 0 0 233
HRAS, LRRC56 17 12 135 71 7 0 0 0 0 0 0 233
SLC25A22 10 3 164 53 21 0 0 0 0 0 0 232
PTPN11 69 40 100 22 20 0 0 0 0 0 6 231
PEX10 29 21 115 81 16 0 0 0 0 0 0 230
BBS1, ZDHHC24 42 32 110 56 14 0 0 0 0 0 1 229
GRIN1 19 19 85 88 25 0 0 0 0 0 1 229
HEXB 55 55 84 51 13 0 0 0 0 0 1 229
CNTN2 2 2 145 62 19 0 0 0 0 0 0 228
CCBE1 6 0 155 21 47 0 0 0 0 0 5 227
PSEN1 51 21 112 24 27 0 0 0 0 0 0 226
SMAD4 7 0 154 15 49 0 0 0 0 0 1 223
CLN8 20 46 115 66 6 0 0 0 0 0 1 222
SATB2 48 16 67 73 20 0 0 0 0 0 0 222
DAG1 11 1 156 44 12 0 0 0 0 0 0 221