LITAF — 300 ClinVar variants

All ClinVar germline LITAF variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 109 flagged for review →

5 Pathogenic · 1 Pathogenic/Likely pathogenic · 2 Likely pathogenic · 20 Conflicting · 50 Benign · 9 Benign/Likely benign · 66 Likely benign · 147 Uncertain significance

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

⚑ Evidence disagreements 109

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 agree, ClinVar conflicts 11

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

Predictors lean, ClinVar uncertain 76

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 22

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

All LITAF variants

Pathogenic 5

  • p.Ala111Gly Multiple submitters Charcot-Marie-Tooth disease
  • p.Gly112Ser Multiple submitters LITAF-related disorders ⚠
  • p.Pro135Thr Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Trp116Gly Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Leu122Val No assertion criteria Charcot-Marie-Tooth disease type 1C ⚠

Pathogenic/Likely pathogenic 1

  • p.Thr115Asn Multiple submitters Charcot-Marie-Tooth disease type 1C

Likely pathogenic 2

  • p.Pro135Ala Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Thr78Ser Single submitter Tip-toe gait

Conflicting classifications of pathogenicity 20

Benign 50

Benign/Likely benign 9

  • c.377+13C>G Multiple submitters Charcot-Marie-Tooth disease type 1C
  • c.377+3G>A Multiple submitters Charcot-Marie-Tooth disease
  • c.*99C>T Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Ala111= Multiple submitters Inborn genetic diseases
  • p.Ala9= Multiple submitters Inborn genetic diseases
  • p.Asn110= Multiple submitters Charcot-Marie-Tooth disease
  • p.Cys119= Multiple submitters Charcot-Marie-Tooth disease
  • p.Pro36= Multiple submitters Inborn genetic diseases
  • p.Ser2= Multiple submitters Inborn genetic diseases

Likely benign 66

  • c.220+65T>C Multiple submitters
  • c.221-16C>T Multiple submitters Charcot-Marie-Tooth disease
  • c.377+1867T>G Multiple submitters
  • p.Ala129= Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Asp143= Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Cys123= Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Leu161= Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Met94Val Multiple submitters Inborn genetic diseases
  • p.Pro17= Multiple submitters Inborn genetic diseases
  • p.Pro34= Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Ser15= Multiple submitters Inborn genetic diseases
  • p.Ser18= Multiple submitters Inborn genetic diseases
  • p.Thr11Ile Multiple submitters Inborn genetic diseases
  • p.Thr45= Multiple submitters Inborn genetic diseases
  • p.Thr49= Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Thr75= Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Tyr80= Multiple submitters Inborn genetic diseases
  • p.Val81Met Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • c.220+12del Single submitter Charcot-Marie-Tooth disease type 1C
  • c.221-147A>C Single submitter
  • c.377+10C>T Single submitter Charcot-Marie-Tooth disease type 1C
  • c.377+11C>T Single submitter Charcot-Marie-Tooth disease type 1C
  • c.377+1594A>G Single submitter
  • c.377+15C>T Single submitter Charcot-Marie-Tooth disease type 1C
  • c.377+1716C>T Single submitter
  • c.377+1747G>A Single submitter
  • c.377+1792G>A Single submitter
  • c.377+17C>G Single submitter
  • c.377+1801A>C Single submitter
  • c.377+261C>T Single submitter
  • c.377+297A>G Single submitter
  • c.378-1794G>C Single submitter
  • c.378-194G>A Single submitter
  • c.378-22GT[2] Single submitter Charcot-Marie-Tooth disease type 1C
  • c.378-27G>A Single submitter
  • c.-5-16T>G Single submitter
  • c.-5-183C>G Single submitter
  • c.-5-196T>A Single submitter
  • c.-6+681dup Single submitter
  • c.*1853A>G Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Ala113= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Ala140= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Ala66= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Arg90= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Cys127= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Cys137= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Cys95= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Gly156= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Ile103= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Leu117= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Leu122= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Leu124= Single submitter
  • p.Leu154= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Phe133= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Pro13= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Pro4= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Pro43= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Pro73Ser Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Ser14= Single submitter
  • p.Ser60Leu Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Tyr109= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Tyr32= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Tyr33= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Val79= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Val81= Single submitter Charcot-Marie-Tooth disease type 1C
  • c.378-17TC[6] No assertion criteria LITAF-related disorder

Uncertain significance 147

  • c.220+4C>T Multiple submitters Inborn genetic diseases
  • p.Ala129Val Multiple submitters Inborn genetic diseases ⚠
  • p.Ala140Thr Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ala153Thr Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ala153Val Multiple submitters Inborn genetic diseases ⚠
  • p.Arg160His Multiple submitters Charcot-Marie-Tooth disease ⚠
  • p.Arg90His Multiple submitters Charcot-Marie-Tooth disease ⚠
  • p.Asn30Tyr Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Asn70Ser Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Asp143Glu Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Cys137Tyr Multiple submitters Inborn genetic diseases ⚠
  • p.Gly42Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Leu124Pro Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Met94Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Pro34Thr Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro67Ser Multiple submitters Charcot-Marie-Tooth disease ⚠
  • p.Pro84Leu Multiple submitters Charcot-Marie-Tooth disease type 1C
  • p.Pro91Arg Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ser2Leu Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Thr78Met Multiple submitters Inborn genetic diseases
  • p.Tyr80Cys Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • p.Val29Ile Multiple submitters Charcot-Marie-Tooth disease type 1C ⚠
  • c.377+9G>C Single submitter
  • c.378-3C>T Single submitter Charcot-Marie-Tooth disease type 1C
  • c.-6+513G>C Single submitter Charcot-Marie-Tooth disease type 1C
  • c.-6+539G>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.-6+618C>G Single submitter Charcot-Marie-Tooth disease type 1C
  • c.-6+657C>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1054A>C Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1170A>G Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1217A>C Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1364A>C Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1386G>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1399C>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1422A>G Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1436T>G Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1557C>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*185T>C Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*1879A>G Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*192C>T Single submitter
  • c.*193G>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*234C>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*294A>T Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*33G>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*500A>G Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*52T>A Single submitter
  • c.*563A>C Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*598G>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*723A>G Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*882G>A Single submitter Charcot-Marie-Tooth disease type 1C
  • c.*949A>G Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Ala10Ser Single submitter ⚠
  • p.Ala111Val Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Ala113Val Single submitter Inborn genetic diseases ⚠
  • p.Ala129Thr Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ala16Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ala19Val Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ala28Thr Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ala38Thr Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ala66Val Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ala9Glu Single submitter ⚠
  • p.Asn100Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn110_Ala111insAsn Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Asn150Lys Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Asn150Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Asn72Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Asp139His Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Asp143Tyr Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Cys123Trp Single submitter Inborn genetic diseases ⚠
  • p.Cys123Tyr Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Cys127Tyr Single submitter ⚠
  • p.Cys131Tyr Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Cys137Arg Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Cys137Gly Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Cys95Arg Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Cys95Tyr Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Gln142Glu Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Gln142Ter Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Gln77Arg Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Gly112Ala Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Gly112Asp Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Gly120Arg Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Gly130Ala Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Gly130Ser Single submitter ⚠
  • p.Gly50Val Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Gly53Ala Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Gly55= Single submitter Charcot-Marie-Tooth disease type 1C
  • p.His83Gln Single submitter ⚠
  • p.His83Tyr Single submitter Inborn genetic diseases ⚠
  • p.Ile128Val Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ile85Val Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Leu114Val Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Leu125Pro Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Leu155= Single submitter
  • p.Leu161Phe Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Met1Ile Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Met56fs Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Phe136Leu Single submitter ⚠
  • p.Phe136Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro135Leu Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro17Gln Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro34Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro39Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro41Ser Single submitter ⚠
  • p.Pro58Leu Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro58Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro59Arg Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro69Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro6Leu Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro84Ala Single submitter ⚠
  • p.Pro91Leu Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Pro91Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Ser118Pro Single submitter ⚠
  • p.Ser121Ile Single submitter
  • p.Thr115Ile Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Thr157Ser Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Thr26Ile Single submitter
  • p.Thr45fs Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Thr45Met Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Thr75Ala Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Thr78Ala Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Trp116Cys Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Tyr158Cys Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Tyr33Phe Single submitter ⚠
  • p.Tyr61Cys Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Tyr7Cys Single submitter ⚠
  • p.Val104Leu Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Val138Leu Single submitter
  • p.Val144Leu Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Val144Met Single submitter Charcot-Marie-Tooth disease ⚠
  • p.Val48Ala Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Val76Leu Single submitter Charcot-Marie-Tooth disease type 1C
  • p.Val79Ala Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • p.Val81Leu Single submitter Charcot-Marie-Tooth disease type 1C ⚠
  • c.377+1760_377+1763inv No assertion criteria Charcot-Marie-Tooth disease type 1
  • c.378-48C>A No assertion criteria Charcot-Marie-Tooth disease
  • c.*116C>A No assertion criteria distal hereditary motor neuropathy
  • c.*138G>C No assertion criteria distal hereditary motor neuropathy
  • c.*24C>A No assertion criteria Charcot-Marie-Tooth disease
  • c.*48C>T No assertion criteria Charcot-Marie-Tooth disease
  • p.Ala140Pro No assertion criteria Charcot-Marie-Tooth disease ⚠
  • p.Gly112fs No assertion criteria distal hereditary motor neuropathy
  • p.Ile74= No assertion criteria
  • p.Lys101fs No assertion criteria Charcot-Marie-Tooth disease type 1
  • p.Pro135Arg No assertion criteria Charcot-Marie-Tooth disease ⚠
  • p.Pro135Ser No assertion criteria Charcot-Marie-Tooth disease ⚠
  • p.Val29Gly No assertion criteria Charcot-Marie-Tooth disease ⚠