ClinVar Miner

Variants studied for Spastic paraplegia

Coded as:
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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 total
870 240 2733 6136 940 10910

Gene and significance breakdown #

Total genes and gene combinations: 80
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign total
SACS 354 18 236 2351 225 3184
ZFYVE26 192 40 506 1380 76 2193
KIF5A 24 10 392 531 43 1000
L1CAM 51 17 106 504 266 944
CYP7B1 58 7 149 191 15 419
AP4E1 5 10 182 144 25 366
KDM5C 17 8 84 154 77 340
B4GALNT1 12 4 102 89 19 226
GBA2 16 4 96 90 15 221
GJC2 10 2 127 60 9 208
CYP2U1 14 5 98 78 8 202
HSPD1 0 0 86 85 18 189
SLC16A2 22 2 71 55 30 180
FA2H 18 3 60 72 17 170
RTN2 5 1 72 62 22 162
SLC33A1 2 0 63 52 9 126
ARSI 0 0 70 25 16 111
ERLIN2 7 4 49 38 12 110
ZFYVE27 0 0 40 23 19 82
LOC130009366, SACS 6 2 2 63 4 77
TAPBPL, VAMP1 6 1 31 35 3 76
AP4S1 11 13 22 27 5 73
FA2H, LOC130059394 10 0 19 12 2 43
AP4B1 0 30 0 0 0 30
AP4M1 1 24 0 0 0 25
HPDL 0 25 0 0 0 25
SPAST 3 1 14 0 0 18
CYP7B1, LOC130000507 0 0 7 9 0 16
KIF1A 3 1 5 0 0 9
CYP2U1, LOC129992929 1 0 5 1 1 8
ABHD16A 0 0 6 0 0 6
KDM5C, LOC130068308 0 0 3 1 2 6
FA2H, LOC130059393 1 0 1 3 0 5
REEP1 1 1 3 0 0 5
BICD2 1 0 2 0 0 3
ATL1 1 1 0 0 0 2
CPT1C 0 0 2 0 0 2
HPDL, LOC129930439 0 2 0 0 0 2
LINC00362, LOC130009362, LOC130009363, LOC130009364, LOC130009365, LOC130009366, LOC130009367, LOC130009368, LOC130009369, LOC132090179, SACS, SGCG 1 0 1 0 0 2
RDH11, RDH12, ZFYVE26 1 0 1 0 0 2
RNF170 2 0 0 0 0 2
SACS, SGCG 2 0 0 0 0 2
SPG11 1 1 0 0 0 2
WASHC5 0 0 1 0 1 2
ABCD1, ARHGAP4, ATP2B3, ATP6AP1, AVPR2, BCAP31, BGN, BRCC3, CCNQ, CLIC2, CMC4, CTAG1A, CTAG1B, CTAG2, DKC1, DNASE1L1, DUSP9, EMD, F8, F8A1, F8A2, F8A3, FAM3A, FAM50A, FLNA, FUNDC2, G6PD, GAB3, GDI1, H2AB1, H2AB2, H2AB3, HAUS7, HCFC1, IDH3G, IKBKG, IRAK1, L1CAM, LAGE3, MAGEA1, MECP2, MPP1, MTCP1, NAA10, NSDHL, OPN1LW, OPN1MW, OPN1MW2, PDZD4, PLXNA3, PLXNB3, PNCK, PNMA3, PNMA5, PNMA6A, PNMA6E, RAB39B, RENBP, RPL10, SLC10A3, SLC6A8, SMIM9, SRPK3, SSR4, TAFAZZIN, TEX28, TKTL1, TMEM187, TMLHE, TREX2, UBL4A, VBP1, ZFP92, ZNF185, ZNF275 1 0 0 0 0 1
ABCD1, ARHGAP4, ATP6AP1, AVPR2, BCAP31, CTAG1A, CTAG1B, CTAG2, DKC1, DNASE1L1, EMD, FAM3A, FAM50A, FLNA, G6PD, GAB3, GDI1, HCFC1, IDH3G, IKBKG, IRAK1, L1CAM, LAGE3, MECP2, NAA10, OPN1LW, OPN1MW, OPN1MW2, PDZD4, PLXNA3, PLXNB3, RENBP, RPL10, SLC10A3, SLC6A8, SRPK3, SSR4, TAFAZZIN, TEX28, TKTL1, TMEM187, UBL4A 1 0 0 0 0 1
ABCD1, ARHGAP4, AVPR2, BCAP31, HCFC1, IDH3G, IRAK1, L1CAM, NAA10, PDZD4, PLXNB3, RENBP, SLC6A8, SRPK3, SSR4, TMEM187 0 0 1 0 0 1
ADAM9, ADGRA2, ADRB3, ASH2L, BAG4, BRF2, DDHD2, EIF4EBP1, ERLIN2, FGFR1, GOT1L1, HTRA4, LETM2, LINC03042, LSM1, NSD3, PLEKHA2, PLPBP, PLPP5, RAB11FIP1, STAR, TACC1, TM2D2 0 0 1 0 0 1
AGAP2, APOF, ARHGAP9, ARHGEF25, ATP5F1B, B4GALNT1, BAZ2A, CDK4, CYP27B1, DCTN2, DDIT3, DTX3, EEF1AKMT3, GLI1, GLS2, GPR182, HSD17B6, IL23A, INHBC, INHBE, KIF5A, LRP1, MARCHF9, MARS1, MBD6, METTL1, MIP, MIR616, MYO1A, NAB2, NACA, NDUFA4L2, NEMP1, NXPH4, OS9, PAN2, PIP4K2C, PRIM1, PTGES3, R3HDM2, RBMS2, RDH16, SDR9C7, SHMT2, SPRYD4, STAC3, STAT2, STAT6, TAC3, TIMELESS, TSFM, TSPAN31, ZBTB39 0 0 1 0 0 1
ANKRD18B, AQP3, ARHGEF39, ARID3C, ATOSB, CA9, CCDC107, CCIN, CCL19, CCL21, CCL27, CD72, CIMIP2B, CLTA, CNTFR, CREB3, DCAF12, DCTN3, DNAI1, DNAJB5, ENHO, FAM219A, FAM221B, FANCG, GALT, GBA2, GLIPR2, GNE, GRHPR, HINT2, HRCT1, IL11RA, KIF24, MELK, MSMP, MYORG, NOL6, NPR2, NUDT2, OR13J1, OR2S2, PAX5, PHF24, PIGO, PRSS3, RECK, RGP1, RMRP, RNF38, RPP25L, RUSC2, SIGMAR1, SIT1, SPAG8, SPATA31F1, SPATA31G1, SPMIP6, STOML2, TESK1, TLN1, TMEM8B, TPM2, UBAP1, UBAP2, UBE2R2, UNC13B, VCP, ZCCHC7 1 0 0 0 0 1
AP4E1, ARPP19, ATOSA, BCL2L10, CYP19A1, DMXL2, GLDN, GNB5, LEO1, LYSMD2, MAPK6, MYO5A, MYO5C, ONECUT1, SCG3, SPPL2A, TMOD2, TMOD3, TNFAIP8L3, WDR72 1 0 0 0 0 1
AP4E1, SPPL2A 0 0 1 0 0 1
AP4S1, ARHGAP5, COCH, DTD2, G2E3, GPR33, HEATR5A, HECTD1, NUBPL, PRKD1, SCFD1, STRN3 1 0 0 0 0 1
AP5Z1 0 0 1 0 0 1
ARF1, C1orf35, GJC2, GUK1, IBA57, MRPL55, OBSCN, WNT3A 1 0 0 0 0 1
ARHGEF25, B4GALNT1, DTX3, KIF5A, PIP4K2C 0 0 1 0 0 1
BCAR1, CFDP1, CTRB1, CTRB2, FA2H, GLG1, LDHD, MLKL, RFWD3, WDR59, ZFP1, ZNRF1 0 0 1 0 0 1
BIRC6, DPY30, NLRC4, SLC30A6, SPAST, TTC27, YIPF4 0 0 1 0 0 1
DCTN2, DDIT3, KIF5A, MARS1, MBD6, MIR616 0 0 1 0 0 1
EGR2 0 0 1 0 0 1
GJC2, IBA57 0 0 1 0 0 1
HPDL, LOC129930440 0 1 0 0 0 1
HSD17B10, IQSEC2, KDM5C, RIBC1, SMC1A 0 0 1 0 0 1
IRF2BPL 0 1 0 0 0 1
KDM5C, MIR6894 0 0 0 0 1 1
KDM5C, MIR6895 0 0 0 1 0 1
LINC00362, LOC130009362, LOC130009363, LOC130009364, LOC132090179, SACS, SGCG 1 0 0 0 0 1
LOC130007245, TAPBPL, VAMP1 1 0 0 0 0 1
LOC130056709, NIPA1 0 0 1 0 0 1
LOC130068443, SLC16A2 0 0 1 0 0 1
MIPEP, PCOTH, SACS, SGCG, TNFRSF19 0 0 1 0 0 1
MTM1 1 0 0 0 0 1
NIPA1 1 0 0 0 0 1
NLRC4, SLC30A6, SPAST 0 1 0 0 0 1
RDH12, ZFYVE26 0 0 1 0 0 1
SETX 0 0 1 0 0 1
SLC19A3 0 0 1 0 0 1
SPG7 0 0 1 0 0 1
VAMP1 0 0 1 0 0 1
VCP 1 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 15
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign total
Invitae 853 129 2684 6136 940 10742
Yale Center for Mendelian Genomics, Yale University 2 101 0 0 0 103
Paris Brain Institute, Inserm - ICM 6 0 43 0 0 49
NIHR Bioresource Rare Diseases, University of Cambridge 4 4 0 0 0 8
Institute of Human Genetics, University of Wuerzburg 1 1 5 0 0 7
Care4Rare-SOLVE, CHEO 0 0 6 0 0 6
Baylor Genetics 0 1 1 0 0 2
Centre for Mendelian Genomics, University Medical Centre Ljubljana 2 0 0 0 0 2
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre 0 1 0 0 0 1
Blueprint Genetics 1 0 0 0 0 1
Dept. of Medical Genetics, Telemark Hospital Trust, Telemark Hospital Trust 0 1 0 0 0 1
Laboratoire de Genetique Moleculaire, Centre Hospitalier Universitaire de Bordeaux 0 0 1 0 0 1
Institute of Bioinformatics 1 0 0 0 0 1
Department of Hematologic Diagnostics and Genetics, Jagiellonian University Hospital in Krakow 0 1 0 0 0 1
Human Genetics Bochum, Ruhr University Bochum 0 1 0 0 0 1

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