SPAST — 1433 ClinVar variants

All ClinVar germline SPAST variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 423 flagged for review →

377 Pathogenic · 68 Pathogenic/Likely pathogenic · 142 Likely pathogenic · 87 Conflicting · 55 Benign · 20 Benign/Likely benign · 228 Likely benign · 456 Uncertain significance

Full SPAST gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 423

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors vs ClinVar 7

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 54

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 3

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 284

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 284

Predictors split 75

The independent predictors disagree with each other — read with care.

All SPAST variants

Pathogenic 377

Showing the top 300 by review status; the full set is in the sitemap.

Pathogenic/Likely pathogenic 68

  • c.1004+1G>C Multiple submitters SPAST-related disorder
  • c.1099-2A>C Multiple submitters hereditary spastic paraplegia 4
  • c.1173+1G>A Multiple submitters hereditary spastic paraplegia 4
  • c.1245+4A>G Multiple submitters hereditary spastic paraplegia 4
  • c.1398_1413+1dup Multiple submitters hereditary spastic paraplegia 4
  • c.1413+1_1413+2del Multiple submitters hereditary spastic paraplegia 4
  • c.1413+3_1413+6del Multiple submitters SPAST-related disorder
  • c.1413+5G>A Multiple submitters SPAST-related disorder
  • c.1413+6T>C Multiple submitters
  • c.1414-2A>T Multiple submitters hereditary spastic paraplegia
  • c.1493+2_1493+5del Multiple submitters hereditary spastic paraplegia
  • c.1537-11A>G Multiple submitters hereditary spastic paraplegia 4
  • c.1616+1G>A Multiple submitters hereditary spastic paraplegia 4
  • c.1688-1G>A Multiple submitters SPAST-related disorder
  • c.1728+2T>G Multiple submitters SPAST-related disorder
  • c.871-1G>A Multiple submitters hereditary spastic paraplegia
  • c.871-1G>C Multiple submitters hereditary spastic paraplegia 4
  • p.Ala409Thr Multiple submitters hereditary spastic paraplegia 4 ⚠
  • p.Ala495Val Multiple submitters hereditary spastic paraplegia 4
  • p.Arg450Gly Multiple submitters hereditary spastic paraplegia 4
  • p.Arg450Lys Multiple submitters hereditary spastic paraplegia 4
  • p.Arg479fs Multiple submitters hereditary spastic paraplegia 4
  • p.Arg498Gly Multiple submitters hereditary spastic paraplegia 4
  • p.Arg498Ser Multiple submitters hereditary spastic paraplegia 4
  • p.Arg499Cys Multiple submitters hereditary spastic paraplegia 4
  • p.Arg499His Multiple submitters SPAST-related disorder
  • p.Arg503Trp Multiple submitters hereditary spastic paraplegia
  • p.Arg562Gln Multiple submitters SPAST-related disorder
  • p.Asn319fs Multiple submitters hereditary spastic paraplegia 4
  • p.Asp555Gly Multiple submitters hereditary spastic paraplegia 4
  • p.Gln347Pro Multiple submitters hereditary spastic paraplegia 4
  • p.Glu112Ter Multiple submitters hereditary spastic paraplegia 4
  • p.Glu356Lys Multiple submitters Inborn genetic diseases
  • p.Glu464Ala Multiple submitters hereditary spastic paraplegia 4
  • p.Glu512Asp Multiple submitters hereditary spastic paraplegia ⚠
  • p.Gly377Glu Multiple submitters hereditary spastic paraplegia 4
  • p.Gly526fs Multiple submitters hereditary spastic paraplegia 4
  • p.Gly546Arg Multiple submitters SPAST-related disorder
  • p.Gly559Arg Multiple submitters hereditary spastic paraplegia 4 ⚠
  • p.Gly559Asp Multiple submitters SPAST-related disorder
  • p.Ile328fs Multiple submitters hereditary spastic paraplegia 4
  • p.Ile592fs Multiple submitters SPAST-related disorder
  • p.Ile592Lys Multiple submitters hereditary spastic paraplegia 4
  • p.Leu371Arg Multiple submitters hereditary spastic paraplegia 4
  • p.Leu371Pro Multiple submitters hereditary spastic paraplegia 4
  • p.Leu426Phe Multiple submitters SPAST-related disorder
  • p.Lys121Ter Multiple submitters hereditary spastic paraplegia
  • p.Lys290= Multiple submitters hereditary spastic paraplegia 4
  • p.Met390Ile Multiple submitters hereditary spastic paraplegia 4 ⚠
  • p.Phe368Ser Multiple submitters SPAST-related disorder
  • p.Phe403fs Multiple submitters SPAST-related disorder
  • p.Phe404del Multiple submitters hereditary spastic paraplegia 4
  • p.Phe404fs Multiple submitters hereditary spastic paraplegia 4
  • p.Pro384Arg Multiple submitters hereditary spastic paraplegia
  • p.Pro489Leu Multiple submitters Spastic paraparesis
  • p.Pro509Ser Multiple submitters hereditary spastic paraplegia 4
  • p.Ser101Ter Multiple submitters hereditary spastic paraplegia 4
  • p.Ser302fs Multiple submitters hereditary spastic paraplegia 4
  • p.Ser399Leu Multiple submitters SPAST-related disorder
  • p.Ser407Asn Multiple submitters hereditary spastic paraplegia 4
  • p.Ser413Ter Multiple submitters SPAST-related disorder
  • p.Ser545Leu Multiple submitters hereditary spastic paraplegia 4
  • p.Ter617Glu Multiple submitters hereditary spastic paraplegia 4
  • p.Thr305fs Multiple submitters
  • p.Thr369= Multiple submitters hereditary spastic paraplegia 4
  • p.Thr486Ile Multiple submitters hereditary spastic paraplegia 4
  • p.Thr614Ile Multiple submitters hereditary spastic paraplegia
  • p.Tyr55_Pro56insTer Multiple submitters hereditary spastic paraplegia 4

Likely pathogenic 142

Conflicting classifications of pathogenicity 87

Benign 55

Benign/Likely benign 20

  • c.1173+17A>C Multiple submitters hereditary spastic paraplegia 4
  • c.1493+18G>T Multiple submitters hereditary spastic paraplegia 4
  • c.1493+6G>A Multiple submitters hereditary spastic paraplegia 4
  • c.1494-3del Multiple submitters hereditary spastic paraplegia 4
  • c.1494-3dup Multiple submitters hereditary spastic paraplegia 4
  • c.1728+16A>G Multiple submitters hereditary spastic paraplegia 4
  • c.415+12G>A Multiple submitters hereditary spastic paraplegia 4
  • c.683-9C>T Multiple submitters hereditary spastic paraplegia 4
  • c.*256A>G Multiple submitters hereditary spastic paraplegia 4
  • c.*51A>G Multiple submitters hereditary spastic paraplegia 4
  • p.Arg23Lys Multiple submitters hereditary spastic paraplegia
  • p.Arg309His Multiple submitters hereditary spastic paraplegia 4
  • p.Arg581Gln Multiple submitters hereditary spastic paraplegia 4
  • p.Gln531= Multiple submitters hereditary spastic paraplegia 4
  • p.His289Tyr Multiple submitters hereditary spastic paraplegia 4
  • p.Ile359= Multiple submitters hereditary spastic paraplegia 4
  • p.Pro293= Multiple submitters hereditary spastic paraplegia 4
  • p.Pro97Thr Multiple submitters hereditary spastic paraplegia 4
  • p.Ser276= Multiple submitters hereditary spastic paraplegia 4
  • p.Val162Ile Multiple submitters hereditary spastic paraplegia

Likely benign 228

  • c.1321+9A>G Multiple submitters hereditary spastic paraplegia 4
  • c.1414-6T>C Multiple submitters hereditary spastic paraplegia 4
  • c.1536+17G>T Multiple submitters hereditary spastic paraplegia 4
  • c.1687+29G>C Multiple submitters
  • c.415+17G>T Multiple submitters hereditary spastic paraplegia 4
  • c.416-66C>A Multiple submitters
  • c.503-117A>T Multiple submitters
  • c.586+7A>G Multiple submitters hereditary spastic paraplegia 4
  • c.870+122A>G Multiple submitters
  • c.871-12G>A Multiple submitters hereditary spastic paraplegia 4
  • c.-41C>T Multiple submitters hereditary spastic paraplegia 4
  • p.Ala95= Multiple submitters hereditary spastic paraplegia 4
  • p.Asp548= Multiple submitters hereditary spastic paraplegia 4
  • p.Gln473Lys Multiple submitters Inborn genetic diseases ⚠
  • p.Glu454= Multiple submitters hereditary spastic paraplegia 4
  • p.Gly385= Multiple submitters hereditary spastic paraplegia 4
  • p.Gly5= Multiple submitters hereditary spastic paraplegia 4
  • p.Leu314= Multiple submitters hereditary spastic paraplegia 4
  • p.Leu363= Multiple submitters hereditary spastic paraplegia 4
  • p.Leu57= Multiple submitters hereditary spastic paraplegia 4
  • p.Leu74= Multiple submitters hereditary spastic paraplegia 4
  • p.Pro22Ala Multiple submitters Inborn genetic diseases
  • p.Ser13= Multiple submitters hereditary spastic paraplegia 4
  • p.Ser322Asn Multiple submitters hereditary spastic paraplegia 4
  • p.Tyr544= Multiple submitters hereditary spastic paraplegia 4
  • c.1004+16T>C Single submitter hereditary spastic paraplegia 4
  • c.1004+17A>G Single submitter hereditary spastic paraplegia 4
  • c.1005-128C>T Single submitter
  • c.1005-16A>C Single submitter hereditary spastic paraplegia 4
  • c.1098+19C>A Single submitter hereditary spastic paraplegia
  • c.1098+19C>G Single submitter
  • c.1099-12T>C Single submitter hereditary spastic paraplegia 4
  • c.1099-20C>A Single submitter hereditary spastic paraplegia 4
  • c.1099-20C>G Single submitter hereditary spastic paraplegia 4
  • c.1099-4T>G Single submitter hereditary spastic paraplegia 4
  • c.1099-5148T>G Single submitter
  • c.1173+12C>G Single submitter hereditary spastic paraplegia 4
  • c.1173+20T>C Single submitter hereditary spastic paraplegia 4
  • c.1173+283dup Single submitter
  • c.1173+7G>T Single submitter hereditary spastic paraplegia 4
  • c.1173+9T>C Single submitter hereditary spastic paraplegia 4
  • c.1174-15T>C Single submitter hereditary spastic paraplegia 4
  • c.1174-16C>T Single submitter hereditary spastic paraplegia 4
  • c.1174-19G>T Single submitter hereditary spastic paraplegia 4
  • c.1174-208G>A Single submitter
  • c.1174-5T>C Single submitter hereditary spastic paraplegia 4
  • c.1245+10_1245+11del Single submitter hereditary spastic paraplegia 4
  • c.1245+12G>A Single submitter hereditary spastic paraplegia 4
  • c.1245+19A>G Single submitter hereditary spastic paraplegia 4
  • c.1246-21_1246-14del Single submitter hereditary spastic paraplegia 4
  • c.1321+13T>C Single submitter hereditary spastic paraplegia 4
  • c.1321+19A>C Single submitter hereditary spastic paraplegia 4
  • c.1321+20C>T Single submitter hereditary spastic paraplegia 4
  • c.1321+8C>T Single submitter
  • c.1322-11A>G Single submitter hereditary spastic paraplegia 4
  • c.1322-13G>A Single submitter hereditary spastic paraplegia 4
  • c.1322-18T>C Single submitter hereditary spastic paraplegia 4
  • c.1322-19A>C Single submitter hereditary spastic paraplegia 4
  • c.1322-4C>T Single submitter hereditary spastic paraplegia 4
  • c.1322-7C>T Single submitter hereditary spastic paraplegia 4
  • c.1413+10_1413+13del Single submitter hereditary spastic paraplegia 4
  • c.1413+10G>A Single submitter hereditary spastic paraplegia 4
  • c.1413+19A>G Single submitter hereditary spastic paraplegia 4
  • c.1414-15A>G Single submitter hereditary spastic paraplegia 4
  • c.1414-4G>C Single submitter
  • c.1493+18G>A Single submitter hereditary spastic paraplegia 4
  • c.1493+8G>A Single submitter hereditary spastic paraplegia 4
  • c.1493+9A>C Single submitter hereditary spastic paraplegia 4
  • c.1494-15G>A Single submitter hereditary spastic paraplegia 4
  • c.1494-7T>C Single submitter hereditary spastic paraplegia 4
  • c.1494-9T>C Single submitter hereditary spastic paraplegia 4
  • c.1536+17G>C Single submitter hereditary spastic paraplegia 4
  • c.1536+266A>G Single submitter
  • c.1616+18G>A Single submitter hereditary spastic paraplegia 4
  • c.1616+19G>C Single submitter hereditary spastic paraplegia 4
  • c.1616+220T>C Single submitter
  • c.1617-15C>T Single submitter hereditary spastic paraplegia 4
  • c.1617-253G>A Single submitter
  • c.1687+10C>A Single submitter hereditary spastic paraplegia 4
  • c.1687+8T>C Single submitter hereditary spastic paraplegia 4
  • c.1688-18G>A Single submitter hereditary spastic paraplegia 4
  • c.1728+12T>C Single submitter hereditary spastic paraplegia 4
  • c.1728+14_1728+15insTC Single submitter hereditary spastic paraplegia 4
  • c.1728+16A>C Single submitter hereditary spastic paraplegia 4
  • c.1728+18_1728+19insGCAG Single submitter hereditary spastic paraplegia 4
  • c.1728+19A>G Single submitter hereditary spastic paraplegia 4
  • c.1728+73TG[6] Single submitter
  • c.415+10G>A Single submitter
  • c.415+12G>C Single submitter hereditary spastic paraplegia 4
  • c.415+17G>C Single submitter hereditary spastic paraplegia 4
  • c.416-153C>T Single submitter
  • c.416-16A>T Single submitter hereditary spastic paraplegia 4
  • c.416-17_416-15del Single submitter hereditary spastic paraplegia 4
  • c.416-240A>G Single submitter
  • c.416-31C>G Single submitter
  • c.502+10T>C Single submitter hereditary spastic paraplegia 4
  • c.502+284ATT[11] Single submitter
  • c.502+8T>C Single submitter hereditary spastic paraplegia 4
  • c.502+9del Single submitter hereditary spastic paraplegia 4
  • c.502+9G>A Single submitter hereditary spastic paraplegia 4
  • c.503-19A>G Single submitter hereditary spastic paraplegia 4
  • c.586+14T>C Single submitter hereditary spastic paraplegia 4
  • c.587-14T>G Single submitter hereditary spastic paraplegia 4
  • c.587-17C>T Single submitter hereditary spastic paraplegia 4
  • c.587-4A>G Single submitter hereditary spastic paraplegia 4
  • c.682+20C>T Single submitter hereditary spastic paraplegia 4
  • c.683-12T>C Single submitter hereditary spastic paraplegia 4
  • c.683-13T>C Single submitter hereditary spastic paraplegia 4
  • c.683-16A>G Single submitter hereditary spastic paraplegia 4
  • c.870+10del Single submitter
  • c.870+60A>C Single submitter
  • c.871-12G>T Single submitter hereditary spastic paraplegia 4
  • c.*1156T>C Single submitter hereditary spastic paraplegia 4
  • c.*11T>C Single submitter
  • c.*244_*247del Single submitter
  • c.*372TTGT[2] Single submitter
  • p.Ala102= Single submitter hereditary spastic paraplegia 4
  • p.Ala104= Single submitter hereditary spastic paraplegia 4
  • p.Ala104_Pro105insSerAla Single submitter hereditary spastic paraplegia 4
  • p.Ala104Pro Single submitter Inborn genetic diseases
  • p.Ala106= Single submitter
  • p.Ala113= Single submitter hereditary spastic paraplegia 4
  • p.Ala123= Single submitter hereditary spastic paraplegia 4
  • p.Ala130= Single submitter hereditary spastic paraplegia 4
  • p.Ala285Thr Single submitter hereditary spastic paraplegia 4
  • p.Ala30= Single submitter hereditary spastic paraplegia 4
  • p.Ala30Val Single submitter hereditary spastic paraplegia 4
  • p.Ala32= Single submitter hereditary spastic paraplegia 4
  • p.Ala345= Single submitter hereditary spastic paraplegia 4
  • p.Ala35= Single submitter
  • p.Ala373= Single submitter hereditary spastic paraplegia 4
  • p.Ala375= Single submitter hereditary spastic paraplegia 4
  • p.Ala39= Single submitter hereditary spastic paraplegia 4
  • p.Ala408= Single submitter hereditary spastic paraplegia 4
  • p.Ala538= Single submitter hereditary spastic paraplegia 4
  • p.Ala603= Single submitter hereditary spastic paraplegia 4
  • p.Arg176= Single submitter hereditary spastic paraplegia 4
  • p.Arg221Cys Single submitter hereditary spastic paraplegia 4
  • p.Arg318= Single submitter
  • p.Arg364= Single submitter hereditary spastic paraplegia 4
  • p.Arg459= Single submitter hereditary spastic paraplegia 4
  • p.Arg81= Single submitter hereditary spastic paraplegia 4
  • p.Asn405= Single submitter hereditary spastic paraplegia 4
  • p.Asn487= Single submitter hereditary spastic paraplegia 4
  • p.Asp134= Single submitter hereditary spastic paraplegia 4
  • p.Asp210= Single submitter hereditary spastic paraplegia 4
  • p.Asp214= Single submitter hereditary spastic paraplegia 4
  • p.Asp444= Single submitter hereditary spastic paraplegia 4
  • p.Asp584= Single submitter hereditary spastic paraplegia 4
  • p.Asp613= Single submitter hereditary spastic paraplegia 4
  • p.Gln141= Single submitter hereditary spastic paraplegia 4
  • p.Gln599= Single submitter hereditary spastic paraplegia 4
  • p.Glu125= Single submitter hereditary spastic paraplegia 4
  • p.Glu43= Single submitter hereditary spastic paraplegia 4
  • p.Gly256= Single submitter hereditary spastic paraplegia 4
  • p.Gly262= Single submitter hereditary spastic paraplegia 4
  • p.Gly346= Single submitter hereditary spastic paraplegia 4
  • p.Gly37= Single submitter hereditary spastic paraplegia 4
  • p.Gly8= Single submitter hereditary spastic paraplegia 4
  • p.His120= Single submitter hereditary spastic paraplegia 4
  • p.His241= Single submitter hereditary spastic paraplegia 4
  • p.His264= Single submitter hereditary spastic paraplegia 4
  • p.His455= Single submitter hereditary spastic paraplegia 4
  • p.Ile127= Single submitter hereditary spastic paraplegia 4
  • p.Ile357= Single submitter hereditary spastic paraplegia 4
  • p.Leu131= Single submitter hereditary spastic paraplegia 4
  • p.Leu202= Single submitter hereditary spastic paraplegia 4
  • p.Leu272= Single submitter
  • p.Leu29= Single submitter hereditary spastic paraplegia 4
  • p.Leu466= Single submitter
  • p.Leu552= Single submitter hereditary spastic paraplegia 4
  • p.Leu63= Single submitter hereditary spastic paraplegia 4
  • p.Leu71= Single submitter hereditary spastic paraplegia 4
  • p.Leu73= Single submitter hereditary spastic paraplegia 4
  • p.Leu78= Single submitter hereditary spastic paraplegia 4
  • p.Lys151= Single submitter hereditary spastic paraplegia 4
  • p.Lys312= Single submitter hereditary spastic paraplegia 4
  • p.Lys9= Single submitter hereditary spastic paraplegia 4
  • p.Met253Ile Single submitter hereditary spastic paraplegia 4
  • p.Phe58= Single submitter
  • p.Phe585= Single submitter hereditary spastic paraplegia 4
  • p.Phe69= Single submitter hereditary spastic paraplegia 4
  • p.Phe75Leu Single submitter hereditary spastic paraplegia 4
  • p.Pro105= Single submitter hereditary spastic paraplegia 4
  • p.Pro107= Single submitter hereditary spastic paraplegia 4
  • p.Pro109= Single submitter hereditary spastic paraplegia 4
  • p.Pro109Leu Single submitter hereditary spastic paraplegia 4
  • p.Pro19= Single submitter hereditary spastic paraplegia 4
  • p.Pro203= Single submitter hereditary spastic paraplegia 4
  • p.Pro22Ser Single submitter Inborn genetic diseases
  • p.Pro25= Single submitter hereditary spastic paraplegia 4
  • p.Pro26= Single submitter hereditary spastic paraplegia 4
  • p.Pro286= Single submitter
  • p.Pro301= Single submitter hereditary spastic paraplegia 4
  • p.Pro33= Single submitter hereditary spastic paraplegia 4
  • p.Pro34= Single submitter hereditary spastic paraplegia 4
  • p.Pro34Thr Single submitter hereditary spastic paraplegia 4
  • p.Pro361= Single submitter hereditary spastic paraplegia 4
  • p.Pro383= Single submitter hereditary spastic paraplegia 4
  • p.Pro4= Single submitter hereditary spastic paraplegia 4
  • p.Pro40Leu Single submitter hereditary spastic paraplegia 4
  • p.Pro41= Single submitter hereditary spastic paraplegia 4
  • p.Pro42= Single submitter hereditary spastic paraplegia 4
  • p.Pro45= Single submitter hereditary spastic paraplegia 4
  • p.Pro489= Single submitter hereditary spastic paraplegia 4
  • p.Pro56= Single submitter hereditary spastic paraplegia 4
  • p.Ser101= Single submitter hereditary spastic paraplegia 4
  • p.Ser17Arg Single submitter hereditary spastic paraplegia 4
  • p.Ser399= Single submitter hereditary spastic paraplegia 4
  • p.Ser44= Single submitter hereditary spastic paraplegia 4
  • p.Ser547= Single submitter hereditary spastic paraplegia 4
  • p.Ser575= Single submitter hereditary spastic paraplegia 4
  • p.Ser595= Single submitter hereditary spastic paraplegia 4
  • p.Thr165Ile Single submitter hereditary spastic paraplegia 4
  • p.Thr287Ala Single submitter Inborn genetic diseases
  • p.Thr303= Single submitter hereditary spastic paraplegia 4
  • p.Thr305= Single submitter hereditary spastic paraplegia 4
  • p.Thr402= Single submitter hereditary spastic paraplegia 4
  • p.Tyr126Cys Single submitter hereditary spastic paraplegia 4
  • p.Tyr505= Single submitter hereditary spastic paraplegia 4
  • p.Tyr51= Single submitter hereditary spastic paraplegia 4
  • p.Tyr55= Single submitter hereditary spastic paraplegia 4
  • p.Val108= Single submitter hereditary spastic paraplegia 4
  • p.Val20= Single submitter hereditary spastic paraplegia 4
  • p.Val333= Single submitter
  • p.Val443= Single submitter hereditary spastic paraplegia 4
  • p.Val504= Single submitter hereditary spastic paraplegia 4
  • p.Gly111fs No assertion criteria SPAST-related disorder

Uncertain significance 456

Showing the top 300 by review status; the full set is in the sitemap.