ClinVar Miner

Variants studied for Hereditary spastic paraplegia

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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 not provided total
144 116 1199 383 251 7 1 1 2091

Gene and significance breakdown #

Total genes and gene combinations: 105
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign affects association not provided total
SPG11 37 21 71 17 15 0 0 0 157
SACS 10 7 88 36 13 0 0 0 153
USP8 0 0 61 38 20 0 0 0 119
ZFYVE26 6 4 59 29 21 0 0 0 119
AP5Z1 2 4 72 12 13 0 0 0 103
KIF1A 4 4 54 18 11 0 0 0 91
SPAST 26 22 24 3 2 0 0 0 77
TECPR2 1 2 51 12 8 0 0 0 74
SETX 0 0 47 18 6 0 0 0 71
SPG7 15 6 30 8 7 0 0 0 66
KIF1C 0 1 39 6 9 0 0 0 53
PNPLA6 1 2 30 10 7 0 0 0 50
KIF5A 3 5 21 11 6 0 0 1 45
ALS2 0 0 32 6 3 0 0 0 41
POLG 5 3 21 6 6 0 0 0 41
WASHC5 0 1 27 6 4 0 0 0 38
CYP7B1 6 8 12 3 2 0 0 0 31
AP4E1 0 0 22 7 1 0 0 0 30
PGAP1 0 0 21 5 4 0 0 0 30
USP50, USP8 0 0 17 7 5 0 0 0 29
ALDH18A1 0 1 17 5 5 0 0 0 28
DDHD1 1 0 20 4 3 0 0 0 28
CYP2U1 1 2 19 3 2 0 0 0 27
GBA2 2 1 17 3 4 0 0 0 27
L1CAM 0 0 11 12 4 0 0 0 27
AP4M1 1 0 20 1 4 0 0 0 26
DDHD2 1 2 14 8 1 0 0 0 26
AP4B1 0 1 14 4 5 0 0 0 24
BSCL2, HNRNPUL2-BSCL2 1 0 20 2 1 0 0 0 24
FA2H 1 2 11 3 7 0 0 0 24
ENTPD1 0 0 18 2 1 0 0 0 21
HSPD1 0 0 8 6 7 0 0 0 21
SPG21 2 2 15 0 1 0 0 0 20
TWNK 0 0 16 3 1 0 0 0 20
ATL1 3 4 2 7 3 0 0 0 19
GJC2 0 0 11 6 2 0 0 0 19
REEP1 5 5 6 2 1 0 0 0 19
SPART 0 0 15 2 1 0 0 0 18
POLG, POLGARF 0 0 9 5 3 0 0 0 17
RTN2 0 0 7 6 4 0 0 0 17
VPS37A 0 0 10 4 2 0 0 0 16
MILR1, POLG2 0 0 8 4 2 0 0 0 14
C19orf12 2 0 6 1 2 0 0 0 11
ERLIN2 3 1 6 0 2 0 0 0 11
MTRFR 0 0 7 3 1 0 0 0 11
SLC33A1 0 0 5 5 1 0 0 0 11
ERLIN1 0 1 7 2 0 0 0 0 10
SLC16A2 0 1 4 4 1 0 0 0 10
NIPA1 1 0 5 1 1 0 0 0 8
KIF1C, LOC126862473 0 0 4 1 2 0 0 0 7
LOC130056709, NIPA1 0 0 3 4 1 0 0 0 7
AP4S1 0 0 3 3 0 0 0 0 6
LOC130059818, SPG7 0 0 4 0 2 0 0 0 6
CNNM2, NT5C2 0 0 3 1 1 0 0 0 5
LOC126860498, WASHC5 0 0 2 2 1 0 0 0 5
PLP1, RAB9B 1 0 3 0 1 0 0 0 5
FANCI, POLG 0 0 1 0 3 0 0 0 4
KIF1A, LOC126806583 0 0 2 2 0 0 0 0 4
NT5C2 0 0 4 0 0 0 0 0 4
AP5B1 0 0 3 0 0 0 0 0 3
CPT1C 0 0 3 0 0 0 0 0 3
KIF1C, LOC126862472 0 0 2 1 0 0 0 0 3
LOC130009366, SACS 0 0 3 0 0 0 0 0 3
MAG 0 0 3 0 0 0 0 0 3
MCOLN1, PNPLA6 0 0 0 0 3 0 0 0 3
AP4B1, DCLRE1B, LOC129931235 0 0 2 0 0 0 0 0 2
AP5Z1, LOC129997861 0 0 0 1 1 0 0 0 2
ARSI 0 0 2 0 0 0 0 0 2
BICD2 0 0 2 0 0 0 0 0 2
CYP2U1, LOC129992929 0 0 1 0 1 0 0 0 2
FA2H, LOC130059394 0 0 2 0 0 0 0 0 2
LOC130064702, RTN2 0 0 2 0 0 0 0 0 2
SPTAN1 2 0 0 0 0 0 0 0 2
ADAM28, ADAM7 0 0 0 0 0 1 0 0 1
ADGRB2 0 0 1 0 0 0 0 0 1
AMPD2 0 0 1 0 0 0 0 0 1
AMPD2, LOC126805822 0 0 1 0 0 0 0 0 1
AP5Z1, LOC129997864 0 0 1 0 0 0 0 0 1
AP5Z1, MIR4656 0 0 1 0 0 0 0 0 1
ARHGAP9, MARS1 0 0 1 0 0 0 0 0 1
ARMC9, B3GNT7, LINC00471, LOC108348027, LOC114004369, LOC121009629, LOC121725122, LOC121725123, LOC122861306, LOC122861307, LOC122861308, LOC122861309, LOC122861310, LOC126806551, LOC129389008, LOC129389009, LOC129935822, LOC129935823, LOC129935824, LOC129935825, LOC129935826, LOC129935827, LOC129935828, LOC129935829, LOC129935830, LOC129935831, LOC129935832, LOC129935833, LOC129935834, LOC129935835, LOC129935836, LOC129935837, LOC129935838, LOC129935839, LOC129935840, LOC129935841, MIR4777, NCL, NMUR1, SNORA75, SNORD20, SNORD82, TEX44 0 0 1 0 0 0 0 0 1
CCT5 0 0 1 0 0 0 0 0 1
CEP63, KY 1 0 0 0 0 0 0 0 1
CYP7B1, LOC130000507 0 0 1 0 0 0 0 0 1
DNAJC16 0 0 0 0 0 1 0 0 1
FLRT1, MACROD1 0 0 1 0 0 0 0 0 1
GAD1 0 0 1 0 0 0 0 0 1
IFNA1, IFNA13, IFNA2, IFNA5, IFNA6, IFNA8, KLHL9, LOC130001592, LOC130001593, LOC130001594, LOC130001595, LOC130001596, LOC130001597, MIR31HG 0 0 1 0 0 0 0 0 1
JAK3 0 0 0 0 0 1 0 0 1
KIF26A 0 0 0 0 0 0 1 0 1
LOC126860782, SETX 0 0 0 1 0 0 0 0 1
LOC129935332, PGAP1 0 0 1 0 0 0 0 0 1
LOC130056519, TECPR2 0 0 1 0 0 0 0 0 1
LOC130063377, PNPLA6 0 0 1 0 0 0 0 0 1
MIR6766, POLG 0 0 0 1 0 0 0 0 1
MYT1 0 0 0 0 0 1 0 0 1
NRG1 0 0 0 0 0 1 0 0 1
PLEKHG5 0 1 0 0 0 0 0 0 1
PTPN23 0 1 0 0 0 0 0 0 1
RETREG1 0 0 1 0 0 0 0 0 1
SH3TC2 0 1 0 0 0 0 0 0 1
SLC1A5 0 0 0 0 0 1 0 0 1
TUBB 0 0 0 0 0 1 0 0 1
WDR48 0 0 1 0 0 0 0 0 1
ZFR 0 0 1 0 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 24
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign affects association not provided total
Genome Diagnostics Laboratory, The Hospital for Sick Children 95 81 1069 337 226 0 0 0 1808
Labcorp Genetics (formerly Invitae), Labcorp 0 0 78 45 25 0 0 0 148
Unit for Genetic & Epidemiological Research on Neurological Disorders, Instituto de Investigação e Inovação em Saúde 18 5 47 0 0 0 0 0 70
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 32 21 0 0 0 0 0 0 53
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 8 2 0 0 0 0 0 0 10
Yunnan Provincial Key Laboratory of Clinical Virology, Institution of Basic and Clinical Medicine of Yunnan Province, The First People's Hospital of Yunnan Province 1 0 0 0 0 7 0 0 8
Molecular Genetics, Royal Melbourne Hospital 0 1 2 1 0 0 0 0 4
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 3 0 0 0 0 0 3
Paris Brain Institute, Inserm - ICM 3 0 0 0 0 0 0 0 3
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 2 0 0 0 0 0 0 0 2
Inherited Neuropathy Consortium 0 2 0 0 0 0 0 0 2
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 2 0 0 0 0 0 2
Clinical Genetics Laboratory, Skane University Hospital Lund 0 1 1 0 0 0 0 0 2
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 1 0 0 0 0 0 0 1
Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen 0 1 0 0 0 0 0 0 1
Neuromuscular disorders lab, University of Helsinki 1 0 0 0 0 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 0 0 0 0 0 1 0 1
The Morris Kahn Laboratory of Human Genetics, Ben-Gurion University of the Negev 1 0 0 0 0 0 0 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 0 1 0 0 0 0 0 1
New Leaf Center 0 1 0 0 0 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 0 1 0 0 0 0 0 1
University of Science and Technology Houari Boumediene, Laboratory of Molecular and Cellular Biology (LBCM) 0 1 0 0 0 0 0 0 1
Solve-RD Consortium 0 0 1 0 0 0 0 0 1
Genetic Medicine Clinic, University Of Washington Medical Center 0 0 0 0 0 0 0 1 1

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