ATL1 — 653 ClinVar variants

All ClinVar germline ATL1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 295 flagged for review →

37 Pathogenic · 12 Pathogenic/Likely pathogenic · 40 Likely pathogenic · 50 Conflicting · 46 Benign · 13 Benign/Likely benign · 164 Likely benign · 291 Uncertain significance

Full ATL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 295

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.

ATL1 p.Arg415Trp Pathogenic/Likely pathogenic Multiple submitters
Inborn genetic diseases
ATL1 p.His258Arg Pathogenic Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Val253Ile Pathogenic/Likely pathogenic Multiple submitters
hereditary spastic paraplegia
ATL1 p.His258Leu Pathogenic Single submitter
hereditary spastic paraplegia 3A

Predictors agree, ClinVar conflicts 27

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

ATL1 p.Ala161Ser Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ala449Asp Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg415Gln Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg495Gln Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn104Ser Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn436Asp Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn9Lys Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Glu308Lys Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu66Gln Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Gly409Asp Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.His247Arg Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.His256Asp Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile333Val Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Leu192Phe Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Leu192Val Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu387Ser Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Met347Thr Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Pro208Ser Conflicting Single submitter
ATL1-related disorder
ATL1 p.Pro342Ala Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser160Pro Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser179Tyr Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser259Phe Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Tyr196Cys Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Tyr459Cys Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Val253Phe Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Val360Met Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Phe413Val Conflicting No assertion criteria
hereditary spastic paraplegia 3A

Predictors lean, ClinVar uncertain 163

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 163

ATL1 p.Ala200Thr Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Ala61Val Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Arg323Gln Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Arg55Gln Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Asn263Ser Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Asp230Asn Uncertain significance Multiple submitters
neuropathy, hereditary sensory, type 1D
ATL1 p.Gln180His Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Glu16Gln Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Glu224Lys Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.His256Asn Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.His534Gln Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Ile39Val Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Ile430Leu Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Ile441Ser Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Ile507Val Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Leu190Phe Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Leu357Ser Uncertain significance Multiple submitters
ATL1-related disorder
ATL1 p.Leu503Pro Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Leu524Phe Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Lys234Arg Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Lys369Gln Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Lys370Arg Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Met558Lys Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Met87Ile Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Phe130Leu Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Phe452Ser Uncertain significance Multiple submitters
neuropathy, hereditary sensory, type 1D
ATL1 p.Ser167Gly Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Ser438Arg Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Ser519Asn Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Tyr103Cys Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Tyr227Cys Uncertain significance Multiple submitters
ATL1 p.Tyr432Cys Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Tyr525Cys Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Tyr538Asn Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Tyr90His Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Val405Met Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Val454Leu Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Val70Leu Uncertain significance Multiple submitters
ATL1 p.Ala331Ser Uncertain significance Single submitter
ATL1 p.Ala354Val Uncertain significance Single submitter
ATL1 p.Ala361Pro Uncertain significance Single submitter
ATL1 p.Ala511Val Uncertain significance Single submitter
ATL1 p.Ala523Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ala69Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ala73Val Uncertain significance Single submitter
ATL1-related disorder
ATL1 p.Arg158Ile Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg446Cys Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg446Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg446His Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg501Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg501Pro Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn181Lys Uncertain significance Single submitter
ATL1 p.Asn252Lys Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn281Lys Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Asn355Thr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn4Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn9Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asp102His Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Asp159Glu Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Asp471Glu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asp508Ala Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asp7Asn Uncertain significance Single submitter
ATL1 p.Asp85Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Cys322Ser Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Gln183Glu Uncertain significance Single submitter
ATL1 p.Gln188His Uncertain significance Single submitter
ATL1 p.Gln210Lys Uncertain significance Single submitter
ATL1 p.Gln420Pro Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gln94His Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu16Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu195Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu195Lys Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu25Asp Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Glu288Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu308Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly101Arg Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Gly114Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly115Val Uncertain significance Single submitter
ATL1 p.Gly12Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly13Ala Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly13Glu Uncertain significance Single submitter
ATL1 p.Gly244Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly324Cys Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Gly338Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly410Ala Uncertain significance Single submitter
ATL1 p.Gly482Val Uncertain significance Single submitter
ATL1 p.Gly504Glu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly518Ala Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.His247Gln Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.His258Pro Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.His391Gln Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.His44Gln Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.His539Pro Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Ile125Met Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile125Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile320Thr Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Ile335Phe Uncertain significance Single submitter
Spastic paraplegia
ATL1 p.Ile430Thr Uncertain significance Single submitter
ATL1 p.Ile441Met Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile457Thr Uncertain significance Single submitter
ATL1 p.Ile457Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile473Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile486Thr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile56Thr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu192Ile Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu341Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu382Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu421Phe Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu57Phe Uncertain significance Single submitter
neuropathy, hereditary sensory, type 1D
ATL1 p.Lys287Arg Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys407Asn Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys546Arg Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys546Asn Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys555Glu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Met408Leu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Met479Leu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Met558Arg Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Met558Ile Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Met558Thr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Met91Ile Uncertain significance Single submitter
ATL1 p.Met91Leu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Phe282Cys Uncertain significance Single submitter
ATL1 p.Phe381Tyr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Phe413Ile Uncertain significance Single submitter
ATL1 p.Pro344Thr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Pro380Thr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Pro545Leu Uncertain significance Single submitter
neuropathy, hereditary sensory, type 1D
ATL1 p.Ser155Pro Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser346Phe Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser423Arg Uncertain significance Single submitter
ATL1 p.Ser423Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser475Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser519Thr Uncertain significance Single submitter
ATL1 p.Ser547Ala Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser547Leu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Thr147Ser Uncertain significance Single submitter
ATL1 p.Thr168Arg Uncertain significance Single submitter
ATL1 p.Thr278Ile Uncertain significance Single submitter
neuropathy, hereditary sensory, type 1D
ATL1 p.Thr366Ile Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Thr389Asn Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Thr487Ile Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Thr490Ile Uncertain significance Single submitter
ATL1 p.Thr544Ile Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Trp112Arg Uncertain significance Single submitter
ATL1 p.Trp303Arg Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Tyr19Asn Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Tyr19His Uncertain significance Single submitter
ATL1 p.Tyr332Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Tyr336His Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Tyr525His Uncertain significance Single submitter
hereditary spastic paraplegia 3A

Predictors split 101

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

ATL1 p.Ala229Gly Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Ala444Ser Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Ala445Val Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Arg55Trp Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Asn318Ile Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Asp437Asn Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Asp516Asn Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Cys477Ser Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Gln420Arg Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Gly137Cys Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Ile425Thr Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Ile472Val Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Leu300Met Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Lys295Arg Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Ser59Leu Uncertain significance Multiple submitters
hereditary spastic paraplegia 3A
ATL1 p.Trp11Cys Uncertain significance Multiple submitters
Inborn genetic diseases
ATL1 p.Ala141Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ala505Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ala69Ser Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Arg403Gln Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg416Cys Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Arg416His Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Arg501Gln Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Arg535Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn104Ile Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Asn252His Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asn252Tyr Uncertain significance Single submitter
ATL1 p.Asn316Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asp378Glu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asp386Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asp42Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Asp43Asn Uncertain significance Single submitter
ATL1 p.Asp49Glu Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Asp64Glu Uncertain significance Single submitter
ATL1 p.Asp98Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gln154Arg Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gln251Lys Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gln419Leu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu117Gln Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu237Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu237Lys Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu237Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu248Lys Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu24Gln Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu292Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu292Lys Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu397Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu397Gln Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu411Ala Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Glu60Ala Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu60Gln Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Glu66Lys Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly324Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly377Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Gly518Arg Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.His343Asp Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile170Thr Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Ile257Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile312Thr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile315Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile425Leu Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Ile425Met Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile472Ser Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ile473Thr Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu131Phe Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu157Phe Likely pathogenic Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Leu58Val Uncertain significance Single submitter
ATL1 p.Lys138Glu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys139Arg Uncertain significance Single submitter
ATL1 p.Lys139Asn Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys234Ile Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys238Arg Uncertain significance Single submitter
ATL1 p.Lys255Glu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys298Arg Uncertain significance Single submitter
ATL1 p.Lys319Gln Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Lys379Thr Uncertain significance Single submitter
Inborn genetic diseases
ATL1 p.Lys406Gln Likely pathogenic Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Lys555Asn Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Met201Thr Uncertain significance Single submitter
ATL1 p.Met91Val Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Pro106Arg Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Pro135Leu Uncertain significance Single submitter
ATL1 p.Ser153Thr Likely pathogenic Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser15Leu Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Ser259Tyr Pathogenic Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser306Arg Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser306Gly Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Ser45Ala Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Thr108Ala Conflicting Single submitter
Inborn genetic diseases
ATL1 p.Thr351Ala Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Thr550Ile Likely benign Single submitter
ATL1 p.Trp21Arg Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Val100Ala Uncertain significance Single submitter
ATL1 p.Val253Leu Conflicting Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Val326Met Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Val37Leu Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Val40Phe Pathogenic Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Val453Ala Uncertain significance Single submitter
hereditary spastic paraplegia 3A
ATL1 p.Val460Met Uncertain significance Single submitter
ATL1 p.Val464Met Uncertain significance Single submitter
ATL1 p.Gln154Glu Uncertain significance No assertion criteria
hereditary spastic paraplegia 3A

All ATL1 variants

Pathogenic 37

p.Arg501Ter Multiple submitters ATL1-related spastic paraplegia, recessive
p.His258Arg Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Met408Thr Multiple submitters hereditary spastic paraplegia 3A
p.Thr156Ile Multiple submitters hereditary spastic paraplegia 3A
c.523-2A>C Single submitter
p.Ala350Thr Single submitter hereditary spastic paraplegia 3A
p.Arg118Gln Single submitter hereditary spastic paraplegia 3A
p.Arg118Ter Single submitter
p.Arg239Leu Single submitter hereditary spastic paraplegia 3A
p.Arg403fs Single submitter hereditary spastic paraplegia 3A
p.Asn355Lys Single submitter Penetrating foot ulcers
p.Asn440Thr Single submitter hereditary spastic paraplegia 3A
p.Gln174fs Single submitter hereditary spastic paraplegia 3A
p.Gln191Arg Single submitter hereditary spastic paraplegia 3A
p.Glu195Ala Single submitter hereditary spastic paraplegia 3A
p.His189Asp Single submitter hereditary spastic paraplegia 3A
p.His258Leu Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu157Ser Single submitter hereditary spastic paraplegia 3A
p.Leu192His Single submitter hereditary spastic paraplegia 3A
p.Leu250Pro Single submitter hereditary spastic paraplegia 3A
p.Lys330Ter Single submitter hereditary spastic paraplegia 3A
p.Met408Val Single submitter hereditary spastic paraplegia 3A
p.Pro342Ser Single submitter hereditary spastic paraplegia 3A
p.Pro344fs Single submitter hereditary spastic paraplegia 3A
p.Ser259Tyr Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser398Phe Single submitter hereditary spastic paraplegia 3A
p.Thr18_Tyr19insTer Single submitter hereditary spastic paraplegia 3A
p.Trp112Ter Single submitter hereditary spastic paraplegia 3A
p.Trp491Ter Single submitter hereditary spastic paraplegia 3A
p.Trp515Arg Single submitter hereditary spastic paraplegia 3A
p.Tyr336Ter Single submitter hereditary spastic paraplegia 3A
p.Tyr367Ter Single submitter hereditary spastic paraplegia 3A
p.Tyr496Ter Single submitter hereditary spastic paraplegia 3A
p.Val163Ala Single submitter hereditary spastic paraplegia 3A
p.Val40Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu157Trp No assertion criteria hereditary spastic paraplegia 3A
p.Leu199Gln No assertion criteria hereditary spastic paraplegia 3A

Pathogenic/Likely pathogenic 12

p.Arg217Gln Multiple submitters hereditary spastic paraplegia 3A
p.Arg239Cys Multiple submitters hereditary spastic paraplegia
p.Arg415Trp Multiple submitters Inborn genetic diseases ⚠
p.Arg495Trp Multiple submitters Inborn genetic diseases
p.Asn436del Multiple submitters hereditary spastic paraplegia
p.Gly409Cys Multiple submitters hereditary spastic paraplegia 3A
p.Gly410Arg Multiple submitters hereditary spastic paraplegia 3A
p.Lys407del Multiple submitters hereditary spastic paraplegia 3A
p.Lys407Met Multiple submitters Inborn genetic diseases
p.Phe402Leu Multiple submitters hereditary spastic paraplegia 3A
p.Thr156Pro Multiple submitters hereditary spastic paraplegia 3A
p.Val253Ile Multiple submitters hereditary spastic paraplegia ⚠

Likely pathogenic 40

p.Arg239His Multiple submitters Spastic paraplegia
p.Arg403Pro Multiple submitters hereditary spastic paraplegia 3A
c.35-1G>A Single submitter hereditary spastic paraplegia 3A
c.417+1G>T Single submitter
p.Ala161Val Single submitter hereditary spastic paraplegia 3A
p.Ala277Pro Single submitter hereditary spastic paraplegia 3A
p.Ala350Ser Single submitter hereditary spastic paraplegia 3A
p.Ala352Glu Single submitter
p.Arg198Gly Single submitter hereditary spastic paraplegia 3A
p.Arg198Ser Single submitter hereditary spastic paraplegia 3A
p.Asn356Lys Single submitter hereditary spastic paraplegia 3A
p.Asn436Lys Single submitter
p.Gln188Arg Single submitter
p.Gln509Pro Single submitter hereditary spastic paraplegia 3A
p.Glu314Ter Single submitter hereditary spastic paraplegia 3A
p.Glu340Lys Single submitter Neurodevelopmental delay
p.Glu353Lys Single submitter hereditary spastic paraplegia 3A
p.Glu373= Single submitter hereditary spastic paraplegia 3A
p.Gly409Ser Single submitter congenital nervous system disorder
p.Gly504fs Single submitter hereditary spastic paraplegia 3A
p.His247Pro Single submitter
p.Ile315Ser Single submitter
p.Ile333Lys Single submitter hereditary spastic paraplegia 3A
p.Leu157Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu341del Single submitter hereditary spastic paraplegia 3A
p.Lys345Glu Single submitter hereditary spastic paraplegia 3A
p.Lys406Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys406Glu Single submitter hereditary spastic paraplegia 3A
p.Met347Ile Single submitter hereditary spastic paraplegia 3A
p.Met371fs Single submitter neuropathy, hereditary sensory, type 1D
p.Phe413Leu Single submitter hereditary spastic paraplegia 3A
p.Pro342Leu Single submitter hereditary spastic paraplegia 3A
p.Pro344His Single submitter Neurodevelopmental delay
p.Ser153Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser398Tyr Single submitter hereditary spastic paraplegia 3A
p.Ser414Arg Single submitter
p.Trp219Ter Single submitter hereditary spastic paraplegia
p.Tyr417Asn Single submitter
p.Val405Gly Single submitter hereditary spastic paraplegia 3A
c.522+1G>T No assertion criteria hereditary spastic paraplegia 3A

Conflicting classifications of pathogenicity 50

c.1120-15C>T Single submitter hereditary spastic paraplegia 3A
c.631-7T>A Single submitter hereditary spastic paraplegia 3A
c.990+20A>G Single submitter hereditary spastic paraplegia 3A
c.990+4T>A Single submitter Inborn genetic diseases
p.Ala161Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Ala449Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Ala505_Val506insTer Single submitter hereditary spastic paraplegia 3A
p.Ala541= Single submitter Inborn genetic diseases
p.Arg415Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg416Cys Single submitter Inborn genetic diseases ⚠
p.Arg416His Single submitter Inborn genetic diseases ⚠
p.Arg495Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn104Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn252= Single submitter hereditary spastic paraplegia 3A
p.Asn436Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn9Lys Single submitter Inborn genetic diseases ⚠
p.Gln154Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.Gln251Lys Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu24Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu308Lys Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu66Gln Single submitter Inborn genetic diseases ⚠
p.Gly409Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.His247Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.His256Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile333Val Single submitter Inborn genetic diseases ⚠
p.Leu192Phe Single submitter Inborn genetic diseases ⚠
p.Leu192Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu387Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu470= Single submitter hereditary spastic paraplegia 3A
p.Lys400= Single submitter Inborn genetic diseases
p.Met347Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Phe261fs Single submitter hereditary spastic paraplegia 3A
p.Pro208Ser Single submitter ATL1-related disorder ⚠
p.Pro342Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Pro384= Single submitter hereditary spastic paraplegia 3A
p.Ser15Leu Single submitter Inborn genetic diseases ⚠
p.Ser160Pro Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser179Tyr Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser259Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Thr108Ala Single submitter Inborn genetic diseases ⚠
p.Thr351Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Tyr196Cys Single submitter Inborn genetic diseases ⚠
p.Tyr459Cys Single submitter hereditary spastic paraplegia 3A ⚠
p.Val100= Single submitter Inborn genetic diseases
p.Val253Leu Single submitter hereditary spastic paraplegia 3A ⚠
p.Val253Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Val360Met Single submitter Inborn genetic diseases ⚠
p.Ile507fs No assertion criteria hereditary spastic paraplegia 3A
p.Phe413Val No assertion criteria hereditary spastic paraplegia 3A ⚠
p.Val326fs No assertion criteria Charcot-Marie-Tooth disease

Benign 46

c.1048-168G>T Multiple submitters
c.1048-58G>A Multiple submitters
c.1119+136_1119+137insAT Multiple submitters neuropathy, hereditary sensory, type 1D
c.1119+149T>G Multiple submitters hereditary spastic paraplegia 3A
c.1551+249T>C Multiple submitters
c.1552-24_1552-20del Multiple submitters neuropathy, hereditary sensory, type 1D
c.1552-68_1552-67insATA Multiple submitters neuropathy, hereditary sensory, type 1D
c.1567-77C>A Multiple submitters
c.34+110G>C Multiple submitters
c.35-14G>A Multiple submitters neuropathy, hereditary sensory, type 1D
c.35-74G>C Multiple submitters
c.418-19G>T Multiple submitters hereditary spastic paraplegia 3A
c.522+154G>A Multiple submitters
c.523-112A>G Multiple submitters
c.574-57TC[11] Multiple submitters hereditary spastic paraplegia 3A
c.630+105G>A Multiple submitters neuropathy, hereditary sensory, type 1D
c.630+7G>A Multiple submitters neuropathy, hereditary sensory, type 1D
c.863-54A>G Multiple submitters hereditary spastic paraplegia 3A
c.-140+108C>T Multiple submitters
c.-140+55A>T Multiple submitters
c.-140+60G>A Multiple submitters
p.Glu117= Multiple submitters neuropathy, hereditary sensory, type 1D
p.Phe235= Multiple submitters hereditary spastic paraplegia 3A
p.Pro28= Multiple submitters hereditary spastic paraplegia 3A
p.Pro545= Multiple submitters neuropathy, hereditary sensory, type 1D
c.1119+150A>G Single submitter
c.1552-103_1552-102insTTCTT Single submitter
c.1552-176C>T Single submitter
c.418-175T>C Single submitter
c.573+24dup Single submitter hereditary spastic paraplegia 3A
c.574-132G>A Single submitter
c.574-5del Single submitter hereditary spastic paraplegia 3A
c.630+264del Single submitter
c.862+220C>T Single submitter
c.862+286C>T Single submitter
c.990+245G>A Single submitter
c.991-13dup Single submitter hereditary spastic paraplegia 3A
c.991-3del Single submitter hereditary spastic paraplegia 3A
c.*212T>A Single submitter hereditary spastic paraplegia 3A
c.*392C>A Single submitter hereditary spastic paraplegia 3A
c.*450A>G Single submitter hereditary spastic paraplegia 3A
c.*475G>A Single submitter hereditary spastic paraplegia 3A
c.*621G>A Single submitter hereditary spastic paraplegia 3A
p.His443= Single submitter hereditary spastic paraplegia 3A
p.Ile486= Single submitter hereditary spastic paraplegia 3A
p.Lys30= Single submitter hereditary spastic paraplegia 3A

Benign/Likely benign 13

c.417+3A>G Multiple submitters hereditary spastic paraplegia
c.991-3dup Multiple submitters neuropathy, hereditary sensory, type 1D
c.991-6T>G Multiple submitters hereditary spastic paraplegia 3A
c.*305T>C Multiple submitters hereditary spastic paraplegia 3A
p.Asp102Glu Multiple submitters Inborn genetic diseases
p.Asp136= Multiple submitters hereditary spastic paraplegia
p.Gly231= Multiple submitters hereditary spastic paraplegia 3A
p.Gly410= Multiple submitters Inborn genetic diseases
p.His391= Multiple submitters Inborn genetic diseases
p.Lys207= Multiple submitters Inborn genetic diseases
p.Pro307= Multiple submitters neuropathy, hereditary sensory, type 1D
p.Ser10= Multiple submitters Inborn genetic diseases
p.Tyr223= Multiple submitters hereditary spastic paraplegia

Likely benign 164

c.1047+12T>C Multiple submitters hereditary spastic paraplegia 3A
c.1120-47A>C Multiple submitters
c.1551+11C>G Multiple submitters hereditary spastic paraplegia 3A
c.1551+158T>C Multiple submitters
c.1551+241A>G Multiple submitters
c.1567-78A>G Multiple submitters
c.34+16G>A Multiple submitters hereditary spastic paraplegia 3A
c.523-13T>C Multiple submitters hereditary spastic paraplegia 3A
c.574-24G>C Multiple submitters
c.574-6T>C Multiple submitters Inborn genetic diseases
c.990+11C>T Multiple submitters hereditary spastic paraplegia 3A
p.Ala229= Multiple submitters Inborn genetic diseases
p.Arg323= Multiple submitters hereditary spastic paraplegia 3A
p.Cys260= Multiple submitters Inborn genetic diseases
p.Ser15= Multiple submitters hereditary spastic paraplegia 3A
p.Ser211= Multiple submitters hereditary spastic paraplegia 3A
p.Ser547= Multiple submitters Inborn genetic diseases
p.Ter559= Multiple submitters hereditary spastic paraplegia 3A
c.1047+10A>G Single submitter hereditary spastic paraplegia 3A
c.1047+17_1047+19del Single submitter hereditary spastic paraplegia 3A
c.1047+18G>A Single submitter hereditary spastic paraplegia 3A
c.1048-16T>C Single submitter hereditary spastic paraplegia 3A
c.1048-20A>G Single submitter hereditary spastic paraplegia 3A
c.1048-6C>T Single submitter hereditary spastic paraplegia 3A
c.1048-7T>C Single submitter hereditary spastic paraplegia 3A
c.1119+19A>G Single submitter hereditary spastic paraplegia 3A
c.1119+7G>A Single submitter hereditary spastic paraplegia 3A
c.1120-10T>C Single submitter hereditary spastic paraplegia 3A
c.1120-11_1120-8del Single submitter hereditary spastic paraplegia 3A
c.1120-13C>G Single submitter hereditary spastic paraplegia 3A
c.1551+10C>T Single submitter hereditary spastic paraplegia 3A
c.1551+41T>C Single submitter
c.1551+9A>G Single submitter hereditary spastic paraplegia 3A
c.1566+10A>T Single submitter hereditary spastic paraplegia 3A
c.1566+10dup Single submitter hereditary spastic paraplegia 3A
c.1566+49_1566+51del Single submitter
c.1567-12del Single submitter hereditary spastic paraplegia 3A
c.1567-13G>A Single submitter hereditary spastic paraplegia 3A
c.1567-18T>C Single submitter hereditary spastic paraplegia 3A
c.1567-195dup Single submitter
c.282+15C>G Single submitter hereditary spastic paraplegia 3A
c.282+15C>T Single submitter hereditary spastic paraplegia 3A
c.282+18T>G Single submitter hereditary spastic paraplegia 3A
c.283-16C>G Single submitter hereditary spastic paraplegia 3A
c.283-17A>G Single submitter hereditary spastic paraplegia 3A
c.283-20del Single submitter hereditary spastic paraplegia 3A
c.283-20T>C Single submitter hereditary spastic paraplegia 3A
c.283-56G>A Single submitter
c.283-8T>C Single submitter hereditary spastic paraplegia 3A
c.34+109del Single submitter
c.34+10A>G Single submitter hereditary spastic paraplegia 3A
c.34+16G>C Single submitter hereditary spastic paraplegia 3A
c.34+16G>T Single submitter hereditary spastic paraplegia 3A
c.35-10T>C Single submitter hereditary spastic paraplegia 3A
c.35-11C>A Single submitter hereditary spastic paraplegia 3A
c.35-15T>C Single submitter hereditary spastic paraplegia 3A
c.35-16C>T Single submitter hereditary spastic paraplegia 3A
c.35-20G>T Single submitter hereditary spastic paraplegia 3A
c.35-8T>C Single submitter hereditary spastic paraplegia 3A
c.417+19A>G Single submitter hereditary spastic paraplegia 3A
c.417+23_417+27del Single submitter hereditary spastic paraplegia 3A
c.417+4T>A Single submitter
c.418-14C>G Single submitter hereditary spastic paraplegia 3A
c.418-19G>A Single submitter hereditary spastic paraplegia 3A
c.418-8G>T Single submitter
c.522+10A>G Single submitter hereditary spastic paraplegia 3A
c.522+15C>T Single submitter hereditary spastic paraplegia 3A
c.522+19T>C Single submitter hereditary spastic paraplegia 3A
c.522+19T>G Single submitter hereditary spastic paraplegia 3A
c.522+25_522+27del Single submitter hereditary spastic paraplegia 3A
c.573+14T>C Single submitter hereditary spastic paraplegia 3A
c.574-14A>G Single submitter hereditary spastic paraplegia 3A
c.574-19T>C Single submitter hereditary spastic paraplegia 3A
c.574-20G>A Single submitter hereditary spastic paraplegia 3A
c.630+13T>C Single submitter hereditary spastic paraplegia 3A
c.630+15A>T Single submitter hereditary spastic paraplegia 3A
c.630+20T>C Single submitter hereditary spastic paraplegia 3A
c.630+9G>A Single submitter hereditary spastic paraplegia 3A
c.631-166G>A Single submitter
c.631-20C>G Single submitter hereditary spastic paraplegia 3A
c.631-7T>G Single submitter hereditary spastic paraplegia 3A
c.631-9_631-7del Single submitter hereditary spastic paraplegia 3A
c.723+10A>C Single submitter hereditary spastic paraplegia 3A
c.723+273_723+277del Single submitter
c.723+7T>G Single submitter hereditary spastic paraplegia 3A
c.862+15A>G Single submitter hereditary spastic paraplegia 3A
c.863-12T>C Single submitter hereditary spastic paraplegia 3A
c.990+14T>C Single submitter hereditary spastic paraplegia 3A
c.990+19G>C Single submitter hereditary spastic paraplegia 3A
c.990+281del Single submitter
c.990+287T>C Single submitter
c.990+9C>G Single submitter hereditary spastic paraplegia 3A
c.991-12_991-11del Single submitter hereditary spastic paraplegia 3A
c.991-12C>G Single submitter hereditary spastic paraplegia 3A
c.991-16T>C Single submitter hereditary spastic paraplegia 3A
c.991-19T>A Single submitter hereditary spastic paraplegia 3A
c.*87C>G Single submitter
p.Ala161= Single submitter hereditary spastic paraplegia 3A
p.Ala233= Single submitter hereditary spastic paraplegia 3A
p.Ala358= Single submitter hereditary spastic paraplegia 3A
p.Ala359= Single submitter hereditary spastic paraplegia 3A
p.Ala444= Single submitter hereditary spastic paraplegia 3A
p.Ala449= Single submitter hereditary spastic paraplegia 3A
p.Arg118= Single submitter hereditary spastic paraplegia 3A
p.Arg415= Single submitter hereditary spastic paraplegia 3A
p.Arg446= Single submitter hereditary spastic paraplegia 3A
p.Arg495= Single submitter hereditary spastic paraplegia 3A
p.Arg8= Single submitter hereditary spastic paraplegia 3A
p.Asn177= Single submitter hereditary spastic paraplegia 3A
p.Asn245= Single submitter hereditary spastic paraplegia 3A
p.Asn436= Single submitter hereditary spastic paraplegia 3A
p.Asn478= Single submitter hereditary spastic paraplegia 3A
p.Asp218= Single submitter hereditary spastic paraplegia 3A
p.Asp291= Single submitter hereditary spastic paraplegia 3A
p.Asp386= Single submitter hereditary spastic paraplegia 3A
p.Asp42= Single submitter hereditary spastic paraplegia 3A
p.Asp426= Single submitter
p.Asp437= Single submitter hereditary spastic paraplegia 3A
p.Asp64= Single submitter hereditary spastic paraplegia 3A
p.Gln148= Single submitter hereditary spastic paraplegia 3A
p.Glu184= Single submitter hereditary spastic paraplegia 3A
p.Glu20= Single submitter hereditary spastic paraplegia 3A
p.Glu422= Single submitter hereditary spastic paraplegia 3A
p.Gly284= Single submitter hereditary spastic paraplegia 3A
p.Gly404= Single submitter
p.Gly504= Single submitter hereditary spastic paraplegia 3A
p.Leu190= Single submitter hereditary spastic paraplegia 3A
p.Leu192= Single submitter hereditary spastic paraplegia 3A
p.Leu212= Single submitter hereditary spastic paraplegia 3A
p.Leu38= Single submitter hereditary spastic paraplegia 3A
p.Leu401= Single submitter hereditary spastic paraplegia 3A
p.Leu476= Single submitter hereditary spastic paraplegia 3A
p.Leu483= Single submitter hereditary spastic paraplegia 3A
p.Leu514= Single submitter hereditary spastic paraplegia 3A
p.Leu537= Single submitter hereditary spastic paraplegia 3A
p.Leu83= Single submitter hereditary spastic paraplegia 3A
p.Lys334= Single submitter hereditary spastic paraplegia 3A
p.Lys345= Single submitter hereditary spastic paraplegia 3A
p.Lys379= Single submitter hereditary spastic paraplegia 3A
p.Phe293= Single submitter hereditary spastic paraplegia 3A
p.Pro106= Single submitter hereditary spastic paraplegia 3A
p.Ser116= Single submitter hereditary spastic paraplegia 3A
p.Ser309= Single submitter hereditary spastic paraplegia 3A
p.Ser45= Single submitter hereditary spastic paraplegia 3A
p.Ser59= Single submitter hereditary spastic paraplegia 3A
p.Thr150= Single submitter hereditary spastic paraplegia 3A
p.Thr162= Single submitter
p.Thr18= Single submitter hereditary spastic paraplegia 3A
p.Thr194= Single submitter hereditary spastic paraplegia 3A
p.Thr447= Single submitter hereditary spastic paraplegia 3A
p.Thr458= Single submitter hereditary spastic paraplegia 3A
p.Thr484= Single submitter hereditary spastic paraplegia 3A
p.Thr550= Single submitter hereditary spastic paraplegia 3A
p.Thr550Ile Single submitter ⚠
p.Tyr332= Single submitter hereditary spastic paraplegia 3A
p.Tyr432= Single submitter hereditary spastic paraplegia 3A
p.Tyr459= Single submitter hereditary spastic paraplegia 3A
p.Val142= Single submitter hereditary spastic paraplegia 3A
p.Val37= Single submitter hereditary spastic paraplegia 3A
p.Val399= Single submitter hereditary spastic paraplegia 3A
p.Val464= Single submitter hereditary spastic paraplegia 3A
p.Val506= Single submitter hereditary spastic paraplegia 3A
p.Val67Ala Single submitter hereditary spastic paraplegia 3A
p.Val70= Single submitter hereditary spastic paraplegia 3A

Uncertain significance 291

c.630+3G>A Multiple submitters Inborn genetic diseases
c.630+6C>T Multiple submitters hereditary spastic paraplegia 3A
c.723+3_723+19del Multiple submitters hereditary spastic paraplegia 3A
p.Ala200Thr Multiple submitters Inborn genetic diseases ⚠
p.Ala229Gly Multiple submitters Inborn genetic diseases ⚠
p.Ala444Ser Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ala445Val Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ala61Val Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Arg323Gln Multiple submitters Inborn genetic diseases ⚠
p.Arg55Gln Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Arg55Trp Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Asn263Ser Multiple submitters Inborn genetic diseases ⚠
p.Asn318Ile Multiple submitters Inborn genetic diseases ⚠
p.Asp230Asn Multiple submitters neuropathy, hereditary sensory, type 1D ⚠
p.Asp437Asn Multiple submitters Inborn genetic diseases ⚠
p.Asp516Asn Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Cys477Ser Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Gln180His Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Gln420Arg Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Glu16Gln Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Glu224Lys Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Gly137Cys Multiple submitters Inborn genetic diseases ⚠
p.His256Asn Multiple submitters hereditary spastic paraplegia 3A ⚠
p.His534Gln Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ile39Val Multiple submitters Inborn genetic diseases ⚠
p.Ile425Thr Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ile430Leu Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ile441Ser Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ile472Val Multiple submitters Inborn genetic diseases ⚠
p.Ile507Val Multiple submitters Inborn genetic diseases ⚠
p.Leu190Phe Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Leu300Met Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Leu357Ser Multiple submitters ATL1-related disorder ⚠
p.Leu503Pro Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Leu524Phe Multiple submitters Inborn genetic diseases ⚠
p.Lys234Arg Multiple submitters Inborn genetic diseases ⚠
p.Lys295Arg Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Lys369Gln Multiple submitters Inborn genetic diseases ⚠
p.Lys370Arg Multiple submitters Inborn genetic diseases ⚠
p.Met558Lys Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Met87Ile Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Phe130Leu Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Phe452Ser Multiple submitters neuropathy, hereditary sensory, type 1D ⚠
p.Ser167Gly Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ser438Arg Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ser519Asn Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Ser59Leu Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Trp11Cys Multiple submitters Inborn genetic diseases ⚠
p.Tyr103Cys Multiple submitters Inborn genetic diseases ⚠
p.Tyr227Cys Multiple submitters ⚠
p.Tyr432Cys Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Tyr525Cys Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Tyr538Asn Multiple submitters Inborn genetic diseases ⚠
p.Tyr90His Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Val405Met Multiple submitters hereditary spastic paraplegia 3A ⚠
p.Val454Leu Multiple submitters Inborn genetic diseases ⚠
p.Val70Leu Multiple submitters ⚠
c.1047+20C>T Single submitter hereditary spastic paraplegia 3A
c.1047+4T>C Single submitter hereditary spastic paraplegia 3A
c.1120-1086T>C Single submitter
c.1566+1G>C Single submitter hereditary spastic paraplegia 3A
c.1566+2dup Single submitter hereditary spastic paraplegia 3A
c.1567-14T>C Single submitter hereditary spastic paraplegia 3A
c.282+4T>C Single submitter hereditary spastic paraplegia 3A
c.34+3G>C Single submitter hereditary spastic paraplegia 3A
c.34+4A>G Single submitter hereditary spastic paraplegia 3A
c.34+6T>G Single submitter hereditary spastic paraplegia 3A
c.35-3C>T Single submitter hereditary spastic paraplegia 3A
c.522+5G>A Single submitter hereditary spastic paraplegia 3A
c.574-3T>C Single submitter Inborn genetic diseases
c.630+6C>A Single submitter hereditary spastic paraplegia 3A
c.724-9T>G Single submitter hereditary spastic paraplegia 3A
c.862+3T>G Single submitter hereditary spastic paraplegia 3A
c.862+4T>G Single submitter hereditary spastic paraplegia 3A
c.863-3T>C Single submitter hereditary spastic paraplegia 3A
c.991-12_991-11insA Single submitter hereditary spastic paraplegia 3A
c.-139-16C>G Single submitter hereditary spastic paraplegia 3A
c.-19C>T Single submitter
c.*109A>C Single submitter hereditary spastic paraplegia 3A
c.*180A>C Single submitter hereditary spastic paraplegia 3A
c.*304C>T Single submitter hereditary spastic paraplegia 3A
c.*327A>G Single submitter hereditary spastic paraplegia 3A
c.*335C>T Single submitter hereditary spastic paraplegia 3A
c.*371T>A Single submitter hereditary spastic paraplegia 3A
c.*464C>T Single submitter hereditary spastic paraplegia 3A
c.*528A>C Single submitter hereditary spastic paraplegia 3A
c.*653T>C Single submitter hereditary spastic paraplegia 3A
p.Ala141Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Ala331Ser Single submitter ⚠
p.Ala354Val Single submitter ⚠
p.Ala361Pro Single submitter ⚠
p.Ala505Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Ala511Val Single submitter ⚠
p.Ala523Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Ala69Ser Single submitter Inborn genetic diseases ⚠
p.Ala69Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Ala73Val Single submitter ATL1-related disorder ⚠
p.Arg158Ile Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg403Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg446Cys Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg446Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg446His Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg501Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg501Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg501Pro Single submitter hereditary spastic paraplegia 3A ⚠
p.Arg535Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn104Ile Single submitter Inborn genetic diseases ⚠
p.Asn181Lys Single submitter ⚠
p.Asn252His Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn252Lys Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn252Tyr Single submitter ⚠
p.Asn281Lys Single submitter Inborn genetic diseases ⚠
p.Asn316Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn355Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn4Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Asn9Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Asp102His Single submitter Inborn genetic diseases ⚠
p.Asp159Glu Single submitter Inborn genetic diseases ⚠
p.Asp378Glu Single submitter hereditary spastic paraplegia 3A ⚠
p.Asp386Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Asp42Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Asp43Asn Single submitter ⚠
p.Asp471Glu Single submitter hereditary spastic paraplegia 3A ⚠
p.Asp49Glu Single submitter Inborn genetic diseases ⚠
p.Asp508Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Asp64Glu Single submitter ⚠
p.Asp7Asn Single submitter ⚠
p.Asp85Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Asp98Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Cys322Ser Single submitter Inborn genetic diseases ⚠
p.Gln183Glu Single submitter ⚠
p.Gln188His Single submitter ⚠
p.Gln210Lys Single submitter ⚠
p.Gln419Leu Single submitter hereditary spastic paraplegia 3A ⚠
p.Gln420Pro Single submitter hereditary spastic paraplegia 3A ⚠
p.Gln94= Single submitter hereditary spastic paraplegia 3A
p.Gln94His Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu117Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu16Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu195Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu195Lys Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu237Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu237Lys Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu237Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu248Lys Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu25Asp Single submitter Inborn genetic diseases ⚠
p.Glu288Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu292Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu292Lys Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu308Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu397Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu397Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu411Ala Single submitter Inborn genetic diseases ⚠
p.Glu502fs Single submitter hereditary spastic paraplegia 3A
p.Glu551Ter Single submitter
p.Glu60Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu60Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.Glu66Lys Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly101Arg Single submitter Inborn genetic diseases ⚠
p.Gly114Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly115Val Single submitter ⚠
p.Gly12Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly13Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly13Glu Single submitter ⚠
p.Gly244Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly324Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly324Cys Single submitter Inborn genetic diseases ⚠
p.Gly338Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly377Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly410Ala Single submitter ⚠
p.Gly482Val Single submitter ⚠
p.Gly504Glu Single submitter hereditary spastic paraplegia 3A ⚠
p.Gly518Ala Single submitter Inborn genetic diseases ⚠
p.Gly518Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.His247Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.His258Pro Single submitter hereditary spastic paraplegia 3A ⚠
p.His343Asp Single submitter hereditary spastic paraplegia 3A ⚠
p.His391Gln Single submitter hereditary spastic paraplegia 3A ⚠
p.His44Gln Single submitter Inborn genetic diseases ⚠
p.His539del Single submitter Inborn genetic diseases
p.His539Pro Single submitter Inborn genetic diseases ⚠
p.Ile125Met Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile125Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile170Thr Single submitter Inborn genetic diseases ⚠
p.Ile257Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile312Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile315Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile320Thr Single submitter Inborn genetic diseases ⚠
p.Ile335Phe Single submitter Spastic paraplegia ⚠
p.Ile425Leu Single submitter Inborn genetic diseases ⚠
p.Ile425Met Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile430Thr Single submitter ⚠
p.Ile441Met Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile457Thr Single submitter ⚠
p.Ile457Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile472Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile473Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile473Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile486Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Ile56Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu131Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu178Ter Single submitter
p.Leu192Ile Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu341Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu382Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu421Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Leu57Phe Single submitter neuropathy, hereditary sensory, type 1D ⚠
p.Leu58Val Single submitter ⚠
p.Lys138Glu Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys138Ter Single submitter
p.Lys139Arg Single submitter ⚠
p.Lys139Asn Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys234Ile Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys238Arg Single submitter ⚠
p.Lys255Glu Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys287Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys298Arg Single submitter ⚠
p.Lys319Gln Single submitter Inborn genetic diseases ⚠
p.Lys379Thr Single submitter Inborn genetic diseases ⚠
p.Lys407Asn Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys546Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys546Asn Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys555Asn Single submitter hereditary spastic paraplegia 3A ⚠
p.Lys555Glu Single submitter hereditary spastic paraplegia 3A ⚠
p.Met201Thr Single submitter ⚠
p.Met408Leu Single submitter hereditary spastic paraplegia 3A ⚠
p.Met479Leu Single submitter hereditary spastic paraplegia 3A ⚠
p.Met558Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.Met558Ile Single submitter hereditary spastic paraplegia 3A ⚠
p.Met558Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Met91Ile Single submitter ⚠
p.Met91Leu Single submitter hereditary spastic paraplegia 3A ⚠
p.Met91Val Single submitter hereditary spastic paraplegia 3A ⚠
p.Phe282Cys Single submitter ⚠
p.Phe381Tyr Single submitter hereditary spastic paraplegia 3A ⚠
p.Phe413Ile Single submitter ⚠
p.Pro106Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.Pro135Leu Single submitter ⚠
p.Pro344Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Pro380Thr Single submitter hereditary spastic paraplegia 3A ⚠
p.Pro545Leu Single submitter neuropathy, hereditary sensory, type 1D ⚠
p.Ser155Pro Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser179fs Single submitter
p.Ser306Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser306Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser346Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser423Arg Single submitter ⚠
p.Ser423Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser45Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser475Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser519Thr Single submitter ⚠
p.Ser547Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Ser547Leu Single submitter hereditary spastic paraplegia 3A ⚠
p.Thr147Ser Single submitter ⚠
p.Thr168Arg Single submitter ⚠
p.Thr278Ile Single submitter neuropathy, hereditary sensory, type 1D ⚠
p.Thr366Ile Single submitter hereditary spastic paraplegia 3A ⚠
p.Thr389Asn Single submitter hereditary spastic paraplegia 3A ⚠
p.Thr487Ile Single submitter hereditary spastic paraplegia 3A ⚠
p.Thr490Ile Single submitter ⚠
p.Thr544Ile Single submitter hereditary spastic paraplegia 3A ⚠
p.Trp112Arg Single submitter ⚠
p.Trp21Arg Single submitter hereditary spastic paraplegia 3A ⚠
p.Trp303Arg Single submitter Inborn genetic diseases ⚠
p.Tyr19Asn Single submitter hereditary spastic paraplegia 3A ⚠
p.Tyr19His Single submitter ⚠
p.Tyr332Ser Single submitter hereditary spastic paraplegia 3A ⚠
p.Tyr336His Single submitter hereditary spastic paraplegia 3A ⚠
p.Tyr525His Single submitter hereditary spastic paraplegia 3A ⚠
p.Tyr538Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Val100Ala Single submitter ⚠
p.Val100Phe Single submitter hereditary spastic paraplegia 3A ⚠
p.Val142Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Val182Ile Single submitter hereditary spastic paraplegia 3A ⚠
p.Val29Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Val326Met Single submitter hereditary spastic paraplegia 3A ⚠
p.Val360Gly Single submitter hereditary spastic paraplegia 3A ⚠
p.Val37Leu Single submitter hereditary spastic paraplegia 3A ⚠
p.Val453Ala Single submitter hereditary spastic paraplegia 3A ⚠
p.Val460Glu Single submitter hereditary spastic paraplegia 3A ⚠
p.Val460Met Single submitter ⚠
p.Val464Met Single submitter ⚠
p.Val70Glu Single submitter ⚠
p.Ala350Val No assertion criteria Lingual thyroid ⚠
p.Ala492fs No assertion criteria hereditary spastic paraplegia 3A
p.Gln154Glu No assertion criteria hereditary spastic paraplegia 3A ⚠
p.Ile170Val No assertion criteria ⚠
p.Phe151Ser No assertion criteria hereditary spastic paraplegia 3A ⚠
p.Pro342Gln No assertion criteria hereditary spastic paraplegia 3A ⚠
p.Pro344Ser No assertion criteria hereditary spastic paraplegia 3A ⚠
p.Thr490fs No assertion criteria hereditary spastic paraplegia 3A