SPG7 — 1178 ClinVar variants

All ClinVar germline SPG7 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 447 flagged for review →

61 Pathogenic · 46 Pathogenic/Likely pathogenic · 67 Likely pathogenic · 89 Conflicting · 56 Benign · 21 Benign/Likely benign · 343 Likely benign · 495 Uncertain significance

Full SPG7 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 447

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 4

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

Predictors agree, ClinVar conflicts 38

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

Predictors lean, ClinVar uncertain 306

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 306

Predictors split 99

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

All SPG7 variants

Pathogenic 61

  • c.1450-1_1457del Multiple submitters SPG7-related disorder
  • c.1937-2A>G Multiple submitters hereditary spastic paraplegia 7
  • c.1939del Multiple submitters hereditary spastic paraplegia 7
  • c.988-1G>A Multiple submitters hereditary spastic paraplegia
  • p.Ala312fs Multiple submitters hereditary spastic paraplegia 7
  • p.Ala572Val Multiple submitters Inborn genetic diseases
  • p.Arg213Ter Multiple submitters hereditary spastic paraplegia
  • p.Arg227Ter Multiple submitters optic atrophy
  • p.Arg247Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Arg398Ter Multiple submitters SPG7-related disorder
  • p.Arg457Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Asn288Ter Multiple submitters SPG7-related disorder
  • p.Asn739fs Multiple submitters hereditary spastic paraplegia 7
  • p.Gln507Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Gln568fs Multiple submitters hereditary spastic paraplegia 7
  • p.Leu158fs Multiple submitters hereditary spastic paraplegia 7
  • p.Leu706fs Multiple submitters SPG7-related disorder
  • p.Lys238fs Multiple submitters hereditary spastic paraplegia 7
  • p.Lys593Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Met260fs Multiple submitters hereditary spastic paraplegia 7
  • p.Met699fs Multiple submitters SPG7-related disorder
  • p.Pro350fs Multiple submitters hereditary spastic paraplegia 7
  • p.Thr261fs Multiple submitters hereditary spastic paraplegia 7
  • p.Val258fs Multiple submitters hereditary spastic paraplegia 7
  • p.Val540fs Multiple submitters hereditary spastic paraplegia
  • c.1150_1150+1insCTAC Single submitter hereditary spastic paraplegia 7
  • c.1151-1G>C Single submitter hereditary spastic paraplegia 7
  • c.1553-?_1779+?del Single submitter hereditary spastic paraplegia 7
  • c.1664-1G>A Single submitter
  • c.2182-1009C>T Single submitter hereditary spastic paraplegia 7
  • c.286+853A>G Single submitter hereditary spastic paraplegia 7
  • c.861+1G>T Single submitter hereditary spastic paraplegia 7
  • p.Ala510Leu Single submitter hereditary spastic paraplegia 7
  • p.Arg139fs Single submitter
  • p.Asn730fs Single submitter
  • p.Asp723fs Single submitter hereditary spastic paraplegia 7
  • p.Gln435Ter Single submitter hereditary spastic paraplegia 7
  • p.Gln491Ter Single submitter hereditary spastic paraplegia 7
  • p.Glu112Ter Single submitter
  • p.Glu535Ter Single submitter hereditary spastic paraplegia 7
  • p.Gly14fs Single submitter hereditary spastic paraplegia 7
  • p.Gly199fs Single submitter hereditary spastic paraplegia 7
  • p.Gly375fs Single submitter hereditary spastic paraplegia 7
  • p.Ile738fs Single submitter hereditary spastic paraplegia 7
  • p.Leu393fs Single submitter hereditary spastic paraplegia 7
  • p.Leu493fs Single submitter hereditary spastic paraplegia 7
  • p.Leu512Pro Single submitter hereditary spastic paraplegia 7
  • p.Leu732Pro Single submitter hereditary spastic paraplegia 7
  • p.Lys238Ter Single submitter hereditary spastic paraplegia 7
  • p.Lys355Ter Single submitter
  • p.Lys569fs Single submitter hereditary spastic paraplegia 7
  • p.Phe287fs Single submitter hereditary spastic paraplegia 7
  • p.Phe623fs Single submitter
  • p.Ser116Ter Single submitter Inborn genetic diseases
  • p.Ser392fs Single submitter hereditary spastic paraplegia 7
  • p.Thr714fs Single submitter hereditary spastic paraplegia 7
  • p.Tyr245Ter Single submitter
  • p.Tyr270fs Single submitter hereditary spastic paraplegia 7
  • p.Val581del Single submitter hereditary spastic paraplegia 7
  • p.Val654fs Single submitter hereditary spastic paraplegia 7
  • c.1450-446_1779+746delinsAAAGTGCT No assertion criteria hereditary spastic paraplegia 7

Pathogenic/Likely pathogenic 46

  • c.1324+2T>G Multiple submitters hereditary spastic paraplegia 7
  • c.1552+1G>T Multiple submitters SPG7-related disorder
  • c.1553-2_1553-1del Multiple submitters hereditary spastic paraplegia 7
  • c.1553-2A>G Multiple submitters hereditary spastic paraplegia 7
  • c.1779+1G>T Multiple submitters hereditary spastic paraplegia 7
  • c.2104-2A>G Multiple submitters hereditary spastic paraplegia 7
  • c.376+1G>T Multiple submitters SPG7-related disorder
  • c.759-2A>G Multiple submitters hereditary spastic paraplegia 7
  • c.861+1G>C Multiple submitters hereditary spastic paraplegia 7
  • c.976_987+3del Multiple submitters hereditary spastic paraplegia 7
  • p.Ala359Pro Multiple submitters hereditary spastic paraplegia 7
  • p.Ala510Val Multiple submitters Mitochondrial DNA maintenance disorder
  • p.Ala647Glu Multiple submitters hereditary spastic paraplegia 7
  • p.Arg139Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Arg391fs Multiple submitters hereditary spastic paraplegia 7
  • p.Arg470Ter Multiple submitters SPG7-related disorder
  • p.Gln483Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Gln568Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Gln621Ter Multiple submitters spastic ataxia
  • p.Gln82Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Glu112fs Multiple submitters SPG7-related disorder
  • p.Glu126Gln Multiple submitters hereditary spastic paraplegia 7 ⚠
  • p.Glu320Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Glu396Ter Multiple submitters hereditary spastic paraplegia 7
  • p.Gly349Ser Multiple submitters SPG7-related disorder
  • p.Gly352fs Multiple submitters hereditary spastic paraplegia 7
  • p.Gly577Ser Multiple submitters hereditary spastic paraplegia 7
  • p.Gly666Arg Multiple submitters SPG7-related disorder
  • p.Gly672Arg Multiple submitters hereditary chronic pancreatitis
  • p.His701Pro Multiple submitters hereditary spastic paraplegia 7
  • p.Ile743Thr Multiple submitters SPG7-related disorder
  • p.Leu543fs Multiple submitters SPG7-related disorder
  • p.Leu67_Leu68insTer Multiple submitters hereditary spastic paraplegia 7
  • p.Leu695Pro Multiple submitters hereditary spastic paraplegia 7
  • p.Leu78Ter Multiple submitters SPG7-related disorder
  • p.Lys558Ter Multiple submitters SPG7-related disorder
  • p.Lys559Ter Multiple submitters SPG7-related disorder
  • p.Met1Lys Multiple submitters hereditary spastic paraplegia 7
  • p.Met757fs Multiple submitters hereditary spastic paraplegia 7
  • p.Phe250fs Multiple submitters SPG7-related disorder
  • p.Phe691fs Multiple submitters hereditary spastic paraplegia 7
  • p.Pro750Leu Multiple submitters SPG7-related disorder
  • p.Thr98fs Multiple submitters hereditary spastic paraplegia 7
  • p.Trp583Cys Multiple submitters hereditary spastic paraplegia 7
  • p.Trp92fs Multiple submitters hereditary spastic paraplegia 7
  • p.Val321fs Multiple submitters SPG7-related disorder

Likely pathogenic 67

  • c.1936+2T>A Multiple submitters hereditary spastic paraplegia 7
  • c.2103+2_2103+20del Multiple submitters hereditary spastic paraplegia 7
  • c.286+1G>T Multiple submitters hereditary spastic paraplegia 7
  • p.Gly666Val Multiple submitters hereditary spastic paraplegia 7
  • p.Met667fs Multiple submitters hereditary spastic paraplegia 7
  • p.Met667Ile Multiple submitters hereditary spastic paraplegia 7
  • c.1449+1_1779+1del Single submitter hereditary spastic paraplegia 7
  • c.1664-89_1671del Single submitter hereditary spastic paraplegia 7
  • c.183+1_1449+1del Single submitter hereditary spastic paraplegia 7
  • c.1937-2A>T Single submitter hereditary spastic paraplegia 7
  • c.2104-1G>C Single submitter hereditary spastic paraplegia 7
  • c.2104-2A>C Single submitter SPG7-related disorder
  • c.2181+1G>T Single submitter hereditary spastic paraplegia 7
  • c.2181+2dup Single submitter hereditary spastic paraplegia 7
  • c.2181+5G>A Single submitter hereditary spastic paraplegia 7
  • c.2182-1011A>G Single submitter hereditary spastic paraplegia 7
  • c.287-1G>C Single submitter
  • c.376+2T>A Single submitter hereditary spastic paraplegia 7
  • c.377-2A>G Single submitter hereditary spastic paraplegia 7
  • c.987+2T>C Single submitter hereditary spastic paraplegia 7
  • c.988-42_1046del Single submitter hereditary spastic paraplegia 7
  • p.Ala262fs Single submitter hereditary spastic paraplegia 7
  • p.Ala359fs Single submitter hereditary spastic paraplegia 7
  • p.Arg485fs Single submitter hereditary spastic paraplegia 7
  • p.Asn218fs Single submitter hereditary spastic paraplegia 7
  • p.Asn739Ter Single submitter hereditary spastic paraplegia 7
  • p.Asp650Tyr Single submitter hereditary spastic paraplegia
  • p.Gln289Ter Single submitter
  • p.Gln500Ter Single submitter hereditary spastic paraplegia 7
  • p.Gln664del Single submitter intellectual disability
  • p.Gln697Ter Single submitter hereditary spastic paraplegia 7
  • p.Glu179Ter Single submitter hereditary spastic paraplegia 7
  • p.Glu232fs Single submitter hereditary spastic paraplegia 7
  • p.Glu409fs Single submitter
  • p.Glu484fs Single submitter hereditary spastic paraplegia 7
  • p.Glu566Ter Single submitter hereditary spastic paraplegia 7
  • p.Glu586Ter Single submitter hereditary spastic paraplegia 7
  • p.Gly349fs Single submitter hereditary spastic paraplegia 7
  • p.Gly354Ala Single submitter hereditary spastic paraplegia 7
  • p.His752Asp Single submitter ⚠
  • p.Leu347fs Single submitter hereditary spastic paraplegia 7
  • p.Leu437Pro Single submitter hereditary spastic paraplegia 7
  • p.Leu722fs Single submitter hereditary spastic paraplegia 7
  • p.Leu733fs Single submitter hereditary spastic paraplegia 7
  • p.Lys318fs Single submitter hereditary spastic paraplegia 7
  • p.Lys559fs Single submitter hereditary spastic paraplegia 7
  • p.Lys663Ter Single submitter
  • p.Met1Thr Single submitter hereditary spastic paraplegia 7
  • p.Phe284fs Single submitter hereditary spastic paraplegia 7
  • p.Phe284Ser Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Phe324Ser Single submitter hereditary spastic paraplegia 7
  • p.Pro27fs Single submitter hereditary spastic paraplegia 7
  • p.Pro468Ala Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Ser692Thr Single submitter hereditary spastic paraplegia 7
  • p.Thr420Ile Single submitter ⚠
  • p.Trp269Ter Single submitter
  • p.Tyr100fs Single submitter hereditary spastic paraplegia 7
  • p.Tyr138fs Single submitter hereditary spastic paraplegia 7
  • p.Tyr195Ter Single submitter
  • p.Tyr547Ter Single submitter hereditary spastic paraplegia 7
  • p.Val311del Single submitter hereditary spastic paraplegia 7
  • p.Val311Glu Single submitter hereditary spastic paraplegia 7
  • p.Val368fs Single submitter hereditary spastic paraplegia 7
  • c.1450_1459del No assertion criteria hereditary spastic paraplegia 7
  • p.Arg688Ter No assertion criteria SPG7-related disorder
  • p.His574fs No assertion criteria hereditary spastic paraplegia 7
  • p.Val89fs No assertion criteria SPG7-related disorder

Conflicting classifications of pathogenicity 89

  • c.1151-8C>T Single submitter hereditary spastic paraplegia
  • c.1324+10C>T Single submitter hereditary spastic paraplegia
  • c.1324+4224C>T Single submitter
  • c.1325-6C>T Single submitter Inborn genetic diseases
  • c.1552+2dup Single submitter hereditary spastic paraplegia 7
  • c.1664-11C>A Single submitter hereditary spastic paraplegia 7
  • c.184-4T>C Single submitter hereditary spastic paraplegia 7
  • c.2181+19G>A Single submitter hereditary spastic paraplegia 7
  • c.2182-881A>G Single submitter
  • c.618+14C>T Single submitter hereditary spastic paraplegia 7
  • c.618+8A>G Single submitter hereditary spastic paraplegia 7
  • c.619-7C>A Single submitter hereditary spastic paraplegia 7
  • c.759-11_759-8del Single submitter hereditary spastic paraplegia 7
  • c.759-6C>T Single submitter hereditary spastic paraplegia 7
  • c.861+2dup Single submitter hereditary spastic paraplegia 7
  • c.861+5G>A Single submitter hereditary spastic paraplegia 7
  • c.861+6T>C Single submitter hereditary spastic paraplegia 7
  • c.861+8C>G Single submitter hereditary spastic paraplegia 7
  • c.987+5A>C Single submitter hereditary spastic paraplegia 7
  • c.988-7C>T Single submitter hereditary spastic paraplegia 7
  • p.Ala293Val Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Ala345Pro Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Ala412= Single submitter hereditary spastic paraplegia 7
  • p.Ala453= Single submitter hereditary spastic paraplegia 7
  • p.Ala529Val Single submitter ⚠
  • p.Ala637Thr Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Ala647Ser Single submitter hereditary spastic paraplegia ⚠
  • p.Ala647Val Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Ala658Thr Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Ala759Thr Single submitter hereditary spastic paraplegia ⚠
  • p.Arg213Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg273His Single submitter spastic ataxia ⚠
  • p.Arg470Gln Single submitter SPG7-related disorder ⚠
  • p.Arg486Gln Single submitter hereditary spastic paraplegia ⚠
  • p.Arg551= Single submitter hereditary spastic paraplegia
  • p.Arg656Pro Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Arg688Trp Single submitter Inborn genetic diseases ⚠
  • p.Asn102= Single submitter hereditary spastic paraplegia 7
  • p.Asn641= Single submitter hereditary spastic paraplegia 7
  • p.Asn721Asp Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Asp135Asn Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Asp411Asn Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Asp650Asn Single submitter leukoencephalopathy with vanishing white matter 1 ⚠
  • p.Gln82Glu Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Glu702Lys Single submitter SPG7-related disorder ⚠
  • p.Glu790= Single submitter hereditary spastic paraplegia 7
  • p.Gly26Cys Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Gly344= Single submitter hereditary spastic paraplegia
  • p.Gly344Asp Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Gly349Val Single submitter SPG7-related disorder ⚠
  • p.Gly352Ser Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Gly423Ser Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Gly577Ala Single submitter hereditary spastic paraplegia ⚠
  • p.Gly577Asp Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Gly632Arg Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Gly74Arg Single submitter hereditary spastic paraplegia
  • p.Gly774= Single submitter hereditary spastic paraplegia 7
  • p.His172= Single submitter hereditary spastic paraplegia
  • p.His474Tyr Single submitter hereditary spastic paraplegia 7 ⚠
  • p.His537Gln Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Ile219Thr Single submitter hereditary spastic paraplegia 7
  • p.Ile657= Single submitter hereditary spastic paraplegia 7
  • p.Ile758= Single submitter hereditary spastic paraplegia 7
  • p.Ile764Val Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Leu175Pro Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Leu233= Single submitter hereditary spastic paraplegia 7
  • p.Leu255= Single submitter hereditary spastic paraplegia 7
  • p.Leu67= Single submitter hereditary spastic paraplegia
  • p.Leu695= Single submitter hereditary spastic paraplegia 7
  • p.Leu695Val Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Leu78Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu84= Single submitter hereditary spastic paraplegia 7
  • p.Lys113Arg Single submitter Inborn genetic diseases ⚠
  • p.Lys221= Single submitter hereditary spastic paraplegia 7
  • p.Lys416= Single submitter hereditary spastic paraplegia 7
  • p.Met152Val Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Phe676Leu Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Pro350Thr Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Pro749Leu Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Pro791= Single submitter hereditary spastic paraplegia 7
  • p.Ser576= Single submitter hereditary spastic paraplegia
  • p.Ser576Trp Single submitter SPG7-related disorder ⚠
  • p.Ser635Leu Single submitter hereditary spastic paraplegia 7
  • p.Ser645Thr Single submitter inherited retinal dystrophy ⚠
  • p.Thr419= Single submitter hereditary spastic paraplegia 7
  • p.Thr588Met Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Thr644Ile Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Val183Ile Single submitter hereditary spastic paraplegia 7 ⚠
  • p.Val390Ala Single submitter hereditary spastic paraplegia 7 ⚠

Benign 56

Benign/Likely benign 21

Likely benign 343

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

Uncertain significance 495

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