CRTAP — 674 ClinVar variants

All ClinVar germline CRTAP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 180 flagged for review →

40 Pathogenic · 8 Pathogenic/Likely pathogenic · 15 Likely pathogenic · 23 Conflicting · 49 Benign · 1 Benign/Likely benign · 241 Likely benign · 297 Uncertain significance

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

⚑ Evidence disagreements 180

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 2

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

Predictors agree, ClinVar conflicts 8

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

Predictors lean, ClinVar uncertain 112

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

Predictors split 58

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

All CRTAP variants

Pathogenic 40

  • p.Ala10fs Multiple submitters osteogenesis imperfecta type 7
  • p.Arg6_Gly7insTer Multiple submitters osteogenesis imperfecta type 7
  • p.Gln276Ter Multiple submitters osteogenesis imperfecta type 7
  • p.His59fs Multiple submitters osteogenesis imperfecta type 7
  • p.Lys274fs Multiple submitters osteogenesis imperfecta type 7
  • p.Ser135fs Multiple submitters osteogenesis imperfecta type 7
  • p.Tyr66Ter Multiple submitters osteogenesis imperfecta
  • c.1153-3C>G Single submitter osteogenesis imperfecta type 7
  • c.923-2A>G Single submitter osteogenesis imperfecta type 7
  • p.Ala167fs Single submitter osteogenesis imperfecta type 7
  • p.Ala213fs Single submitter osteogenesis imperfecta type 7
  • p.Arg136fs Single submitter osteogenesis imperfecta type 7
  • p.Asn334fs Single submitter osteogenesis imperfecta type 7
  • p.Asp53fs Single submitter osteogenesis imperfecta type 7
  • p.Cys19fs Single submitter osteogenesis imperfecta
  • p.Cys19Ter Single submitter osteogenesis imperfecta type 7
  • p.Gln124Ter Single submitter osteogenesis imperfecta type 7
  • p.Gln143Ter Single submitter osteogenesis imperfecta type 7
  • p.Gln302Ter Single submitter osteogenesis imperfecta type 7
  • p.Gln326Ter Single submitter osteogenesis imperfecta type 7
  • p.Gln333Ter Single submitter osteogenesis imperfecta type 7
  • p.Glu137Ter Single submitter osteogenesis imperfecta type 7
  • p.Glu146Ter Single submitter osteogenesis imperfecta type 7
  • p.Glu179Ter Single submitter osteogenesis imperfecta type 7
  • p.Glu40Ter Single submitter osteogenesis imperfecta type 7
  • p.Glu58Ter Single submitter osteogenesis imperfecta type 7
  • p.Gly111fs Single submitter osteogenesis imperfecta type 7
  • p.Gly99fs Single submitter osteogenesis imperfecta type 7
  • p.Leu21fs Single submitter osteogenesis imperfecta type 7
  • p.Lys149Ter Single submitter osteogenesis imperfecta type 7
  • p.Lys157Arg Single submitter osteogenesis imperfecta type 7 ⚠
  • p.Lys254fs Single submitter osteogenesis imperfecta type 7
  • p.Met1Thr Single submitter osteogenesis imperfecta type 7
  • p.Thr296_Met297insGlnTer Single submitter osteogenesis imperfecta type 7
  • p.Trp60Ter Single submitter osteogenesis imperfecta type 7
  • c.471+1G>C No assertion criteria osteogenesis imperfecta type 7
  • p.Ala8fs No assertion criteria
  • p.Glu40fs No assertion criteria osteogenesis imperfecta type 7
  • p.Phe293fs No assertion criteria osteogenesis imperfecta type 7
  • p.Tyr187Ter No assertion criteria osteogenesis imperfecta type 7

Pathogenic/Likely pathogenic 8

  • c.471+2C>A Multiple submitters osteogenesis imperfecta
  • p.Ala97fs Multiple submitters osteogenesis imperfecta type 7
  • p.Ala9fs Multiple submitters osteogenesis imperfecta type 7
  • p.Arg107fs Multiple submitters osteogenesis imperfecta type 7
  • p.Arg212Ter Multiple submitters osteogenesis imperfecta type 7
  • p.Leu244fs Multiple submitters osteogenesis imperfecta type 7
  • p.Tyr148Ter Multiple submitters osteogenesis imperfecta type 7
  • p.Tyr340Ter Multiple submitters osteogenesis imperfecta type 7

Likely pathogenic 15

  • c.1068+1G>T Single submitter osteogenesis imperfecta type 7
  • c.472-1021C>G Single submitter CRTAP-related disorder
  • c.473_621+1del Single submitter
  • c.794-1G>C Single submitter osteogenesis imperfecta type 7
  • c.794-2A>G Single submitter osteogenesis imperfecta type 7
  • p.Ala20fs Single submitter osteogenesis imperfecta type 7
  • p.Ala318fs Single submitter osteogenesis imperfecta type 7
  • p.Asp349Gly Single submitter osteogenesis imperfecta type 7 ⚠
  • p.Gln27fs Single submitter osteogenesis imperfecta type 7
  • p.Glu230Ter Single submitter osteogenesis imperfecta type 7
  • p.Lys157Ter Single submitter osteogenesis imperfecta type 7
  • p.Phe142fs Single submitter osteogenesis imperfecta type 7
  • p.Tyr298Ter Single submitter
  • p.Tyr340fs Single submitter osteogenesis imperfecta type 7
  • c.471+2C>G No assertion criteria osteogenesis imperfecta type 7

Conflicting classifications of pathogenicity 23

  • c.1068+11T>C Single submitter osteogenesis imperfecta type 7
  • c.1153-8T>C Single submitter osteogenesis imperfecta type 7
  • c.471+2C>T Single submitter osteogenesis imperfecta type 7
  • c.471+4A>G Single submitter osteogenesis imperfecta type 7
  • c.-101G>C Single submitter osteogenesis imperfecta type 7
  • c.-35C>T Single submitter osteogenesis imperfecta type 7
  • p.Asn218= Single submitter osteogenesis imperfecta type 7
  • p.Asp310= Single submitter osteogenesis imperfecta type 7
  • p.Gln152His Single submitter osteogenesis imperfecta type 7 ⚠
  • p.Gly219Ser Single submitter osteogenesis imperfecta type 7 ⚠
  • p.Leu126= Single submitter osteogenesis imperfecta type 7
  • p.Leu151Pro Single submitter osteogenesis imperfecta type 7 ⚠
  • p.Leu151Val Single submitter osteogenesis imperfecta ⚠
  • p.Leu244= Single submitter osteogenesis imperfecta
  • p.Leu335= Single submitter osteogenesis imperfecta type 7
  • p.Leu347Phe Single submitter osteogenesis imperfecta ⚠
  • p.Lys149Arg Single submitter osteogenesis imperfecta type 7 ⚠
  • p.Lys254Arg Single submitter osteogenesis imperfecta type 7 ⚠
  • p.Pro176= Single submitter osteogenesis imperfecta type 7
  • p.Pro234= Single submitter osteogenesis imperfecta
  • p.Pro94= Single submitter osteogenesis imperfecta
  • p.Ser56Asn Single submitter osteogenesis imperfecta type 7 ⚠
  • p.Val268Ile Single submitter osteogenesis imperfecta type 7 ⚠

Benign 49

Benign/Likely benign 1

  • c.622-16T>C Multiple submitters osteogenesis imperfecta type 7

Likely benign 241

  • c.471+7C>T Multiple submitters osteogenesis imperfecta type 7
  • c.621+98T>C Multiple submitters
  • c.793+16A>G Multiple submitters osteogenesis imperfecta type 7
  • c.793+17T>A Multiple submitters osteogenesis imperfecta type 7
  • c.794-14_794-13del Multiple submitters osteogenesis imperfecta type 7
  • c.*2474T>G Multiple submitters osteogenesis imperfecta type 7
  • c.*288C>T Multiple submitters osteogenesis imperfecta type 7
  • c.*7G>A Multiple submitters
  • p.Ala166= Multiple submitters osteogenesis imperfecta type 7
  • p.Ala318= Multiple submitters osteogenesis imperfecta type 7
  • p.Arg212= Multiple submitters osteogenesis imperfecta type 7
  • p.Arg6= Multiple submitters osteogenesis imperfecta type 7
  • p.Asp177= Multiple submitters osteogenesis imperfecta type 7
  • p.Leu139= Multiple submitters osteogenesis imperfecta type 7
  • p.Leu394= Multiple submitters osteogenesis imperfecta type 7
  • p.Leu41= Multiple submitters osteogenesis imperfecta type 7
  • p.Lys376= Multiple submitters osteogenesis imperfecta type 7
  • p.Phe83= Multiple submitters osteogenesis imperfecta type 7
  • p.Thr203= Multiple submitters osteogenesis imperfecta type 7
  • c.1068+13C>T Single submitter osteogenesis imperfecta type 7
  • c.1068+14A>C Single submitter osteogenesis imperfecta type 7
  • c.1068+14A>T Single submitter osteogenesis imperfecta type 7
  • c.1068+15C>T Single submitter osteogenesis imperfecta type 7
  • c.1068+161T>C Single submitter
  • c.1068+17A>G Single submitter osteogenesis imperfecta type 7
  • c.1068+18C>T Single submitter osteogenesis imperfecta type 7
  • c.1069-10G>T Single submitter osteogenesis imperfecta type 7
  • c.1069-12G>T Single submitter osteogenesis imperfecta type 7
  • c.1069-202A>G Single submitter
  • c.1069-5A>G Single submitter osteogenesis imperfecta type 7
  • c.1069-8_1069-5del Single submitter osteogenesis imperfecta type 7
  • c.1152+10del Single submitter osteogenesis imperfecta type 7
  • c.1152+12T>A Single submitter osteogenesis imperfecta type 7
  • c.1153-9C>G Single submitter osteogenesis imperfecta type 7
  • c.471+11C>T Single submitter osteogenesis imperfecta type 7
  • c.471+127G>T Single submitter
  • c.471+12T>G Single submitter osteogenesis imperfecta type 7
  • c.471+13C>T Single submitter osteogenesis imperfecta type 7
  • c.471+14G>A Single submitter osteogenesis imperfecta type 7
  • c.471+14G>T Single submitter osteogenesis imperfecta type 7
  • c.471+16C>T Single submitter osteogenesis imperfecta type 7
  • c.471+17C>A Single submitter osteogenesis imperfecta type 7
  • c.471+18C>A Single submitter osteogenesis imperfecta type 7
  • c.471+18C>G Single submitter osteogenesis imperfecta type 7
  • c.471+18C>T Single submitter osteogenesis imperfecta type 7
  • c.471+19G>T Single submitter osteogenesis imperfecta type 7
  • c.471+254C>T Single submitter
  • c.471+8C>T Single submitter osteogenesis imperfecta type 7
  • c.471+9G>C Single submitter osteogenesis imperfecta type 7
  • c.471+9G>T Single submitter osteogenesis imperfecta type 7
  • c.472-1010G>A Single submitter
  • c.472-1021C>T Single submitter osteogenesis imperfecta type 7
  • c.472-1033A>C Single submitter
  • c.472-10G>T Single submitter osteogenesis imperfecta type 7
  • c.472-12T>G Single submitter osteogenesis imperfecta type 7
  • c.472-13T>C Single submitter osteogenesis imperfecta type 7
  • c.472-17G>A Single submitter osteogenesis imperfecta type 7
  • c.472-257G>A Single submitter
  • c.472-4T>G Single submitter osteogenesis imperfecta type 7
  • c.472-7C>A Single submitter osteogenesis imperfecta type 7
  • c.621+10G>A Single submitter osteogenesis imperfecta type 7
  • c.621+15T>G Single submitter osteogenesis imperfecta type 7
  • c.621+17A>G Single submitter osteogenesis imperfecta type 7
  • c.621+188G>A Single submitter
  • c.621+314C>G Single submitter
  • c.621+7T>G Single submitter osteogenesis imperfecta type 7
  • c.621+8T>C Single submitter osteogenesis imperfecta type 7
  • c.622-11A>G Single submitter osteogenesis imperfecta type 7
  • c.622-15C>A Single submitter osteogenesis imperfecta type 7
  • c.622-18C>T Single submitter osteogenesis imperfecta type 7
  • c.622-280T>C Single submitter
  • c.622-7C>A Single submitter osteogenesis imperfecta type 7
  • c.622-81G>A Single submitter
  • c.622-9G>A Single submitter osteogenesis imperfecta type 7
  • c.793+11G>A Single submitter osteogenesis imperfecta type 7
  • c.793+12G>C Single submitter osteogenesis imperfecta type 7
  • c.793+17T>C Single submitter osteogenesis imperfecta type 7
  • c.793+19G>A Single submitter osteogenesis imperfecta type 7
  • c.793+7G>A Single submitter osteogenesis imperfecta type 7
  • c.794-12G>T Single submitter osteogenesis imperfecta type 7
  • c.794-14A>G Single submitter osteogenesis imperfecta type 7
  • c.794-16A>G Single submitter osteogenesis imperfecta type 7
  • c.794-18T>G Single submitter osteogenesis imperfecta type 7
  • c.794-19T>C Single submitter osteogenesis imperfecta type 7
  • c.794-240A>G Single submitter
  • c.922+12T>C Single submitter osteogenesis imperfecta type 7
  • c.922+14del Single submitter osteogenesis imperfecta type 7
  • c.922+15G>A Single submitter osteogenesis imperfecta type 7
  • c.922+17G>A Single submitter osteogenesis imperfecta type 7
  • c.922+18A>G Single submitter osteogenesis imperfecta type 7
  • c.922+8A>G Single submitter osteogenesis imperfecta type 7
  • c.923-10C>T Single submitter osteogenesis imperfecta type 7
  • c.923-14C>T Single submitter osteogenesis imperfecta type 7
  • c.923-171G>A Single submitter
  • c.923-18T>G Single submitter osteogenesis imperfecta type 7
  • c.923-19C>T Single submitter osteogenesis imperfecta type 7
  • c.923-4C>G Single submitter osteogenesis imperfecta type 7
  • c.-39C>G Single submitter
  • c.-45T>G Single submitter
  • c.*1041C>T Single submitter osteogenesis imperfecta type 7
  • c.*1124C>A Single submitter osteogenesis imperfecta type 7
  • c.*1861A>G Single submitter osteogenesis imperfecta type 7
  • c.*2524G>A Single submitter osteogenesis imperfecta type 7
  • c.*2876C>T Single submitter osteogenesis imperfecta type 7
  • c.*2943A>G Single submitter osteogenesis imperfecta type 7
  • c.*31C>T Single submitter osteogenesis imperfecta type 7
  • c.*3454C>T Single submitter osteogenesis imperfecta type 7
  • c.*3950G>A Single submitter osteogenesis imperfecta type 7
  • c.*4017G>A Single submitter osteogenesis imperfecta type 7
  • c.*4129T>C Single submitter osteogenesis imperfecta type 7
  • c.*4705G>T Single submitter osteogenesis imperfecta type 7
  • p.Ala101= Single submitter osteogenesis imperfecta type 7
  • p.Ala116= Single submitter osteogenesis imperfecta type 7
  • p.Ala13= Single submitter osteogenesis imperfecta type 7
  • p.Ala140= Single submitter osteogenesis imperfecta type 7
  • p.Ala164= Single submitter osteogenesis imperfecta type 7
  • p.Ala194= Single submitter osteogenesis imperfecta type 7
  • p.Ala216= Single submitter osteogenesis imperfecta type 7
  • p.Ala315= Single submitter osteogenesis imperfecta type 7
  • p.Ala47= Single submitter osteogenesis imperfecta type 7
  • p.Ala61= Single submitter osteogenesis imperfecta type 7
  • p.Ala8= Single submitter osteogenesis imperfecta type 7
  • p.Ala82= Single submitter osteogenesis imperfecta type 7
  • p.Ala9= Single submitter osteogenesis imperfecta type 7
  • p.Ala90= Single submitter osteogenesis imperfecta type 7
  • p.Ala97= Single submitter osteogenesis imperfecta type 7
  • p.Arg107= Single submitter osteogenesis imperfecta type 7
  • p.Arg121= Single submitter osteogenesis imperfecta type 7
  • p.Arg145= Single submitter osteogenesis imperfecta type 7
  • p.Arg183= Single submitter osteogenesis imperfecta type 7
  • p.Arg215= Single submitter osteogenesis imperfecta type 7
  • p.Arg223= Single submitter osteogenesis imperfecta type 7
  • p.Arg25= Single submitter osteogenesis imperfecta type 7
  • p.Arg251= Single submitter osteogenesis imperfecta type 7
  • p.Arg30= Single submitter osteogenesis imperfecta type 7
  • p.Arg38= Single submitter osteogenesis imperfecta type 7
  • p.Arg72= Single submitter osteogenesis imperfecta type 7
  • p.Arg78= Single submitter osteogenesis imperfecta type 7
  • p.Asn159= Single submitter osteogenesis imperfecta type 7
  • p.Asn160= Single submitter osteogenesis imperfecta type 7
  • p.Asn184= Single submitter osteogenesis imperfecta type 7
  • p.Asn309= Single submitter osteogenesis imperfecta type 7
  • p.Asp141= Single submitter osteogenesis imperfecta type 7
  • p.Asp325= Single submitter osteogenesis imperfecta type 7
  • p.Asp79= Single submitter osteogenesis imperfecta type 7
  • p.Cys247= Single submitter osteogenesis imperfecta type 7
  • p.Cys84= Single submitter osteogenesis imperfecta type 7
  • p.Gln124= Single submitter osteogenesis imperfecta type 7
  • p.Gln143= Single submitter osteogenesis imperfecta type 7
  • p.Gln27= Single submitter osteogenesis imperfecta type 7
  • p.Gln353= Single submitter osteogenesis imperfecta type 7
  • p.Gln93= Single submitter osteogenesis imperfecta type 7
  • p.Glu195= Single submitter osteogenesis imperfecta type 7
  • p.Glu2= Single submitter osteogenesis imperfecta type 7
  • p.Glu242= Single submitter osteogenesis imperfecta type 7
  • p.Glu248= Single submitter osteogenesis imperfecta type 7
  • p.Glu252= Single submitter osteogenesis imperfecta type 7
  • p.Glu269= Single submitter osteogenesis imperfecta type 7
  • p.Glu279= Single submitter osteogenesis imperfecta type 7
  • p.Glu399= Single submitter osteogenesis imperfecta type 7
  • p.Glu68= Single submitter osteogenesis imperfecta type 7
  • p.Gly110= Single submitter osteogenesis imperfecta type 7
  • p.Gly125= Single submitter osteogenesis imperfecta type 7
  • p.Gly219= Single submitter osteogenesis imperfecta type 7
  • p.Gly24= Single submitter osteogenesis imperfecta type 7
  • p.Gly385= Single submitter osteogenesis imperfecta type 7
  • p.Gly65= Single submitter osteogenesis imperfecta type 7
  • p.Gly7= Single submitter osteogenesis imperfecta type 7
  • p.His117= Single submitter osteogenesis imperfecta type 7
  • p.His341= Single submitter osteogenesis imperfecta type 7
  • p.His50= Single submitter osteogenesis imperfecta type 7
  • p.His74= Single submitter osteogenesis imperfecta type 7
  • p.His85= Single submitter osteogenesis imperfecta type 7
  • p.Ile165= Single submitter osteogenesis imperfecta type 7
  • p.Ile211= Single submitter osteogenesis imperfecta type 7
  • p.Ile253= Single submitter osteogenesis imperfecta type 7
  • p.Ile285= Single submitter osteogenesis imperfecta type 7
  • p.Ile69= Single submitter osteogenesis imperfecta type 7
  • p.Leu106= Single submitter osteogenesis imperfecta type 7
  • p.Leu108= Single submitter osteogenesis imperfecta type 7
  • p.Leu11= Single submitter osteogenesis imperfecta type 7
  • p.Leu113= Single submitter osteogenesis imperfecta type 7
  • p.Leu119= Single submitter osteogenesis imperfecta type 7
  • p.Leu12= Single submitter osteogenesis imperfecta type 7
  • p.Leu151= Single submitter osteogenesis imperfecta type 7
  • p.Leu172= Single submitter osteogenesis imperfecta type 7
  • p.Leu201= Single submitter osteogenesis imperfecta type 7
  • p.Leu209= Single submitter osteogenesis imperfecta type 7
  • p.Leu261= Single submitter osteogenesis imperfecta type 7
  • p.Leu271= Single submitter osteogenesis imperfecta type 7
  • p.Leu323= Single submitter osteogenesis imperfecta type 7
  • p.Leu371= Single submitter osteogenesis imperfecta type 7
  • p.Leu44= Single submitter osteogenesis imperfecta type 7
  • p.Leu52= Single submitter osteogenesis imperfecta type 7
  • p.Leu67= Single submitter osteogenesis imperfecta type 7
  • p.Leu73= Single submitter osteogenesis imperfecta type 7
  • p.Leu76= Single submitter osteogenesis imperfecta type 7
  • p.Leu77= Single submitter osteogenesis imperfecta type 7
  • p.Lys120= Single submitter osteogenesis imperfecta type 7
  • p.Lys123= Single submitter osteogenesis imperfecta type 7
  • p.Lys149= Single submitter osteogenesis imperfecta type 7
  • p.Lys54= Single submitter osteogenesis imperfecta type 7
  • p.Phe150= Single submitter osteogenesis imperfecta type 7
  • p.Phe153= Single submitter osteogenesis imperfecta type 7
  • p.Phe171= Single submitter osteogenesis imperfecta type 7
  • p.Phe240= Single submitter osteogenesis imperfecta type 7
  • p.Phe303= Single submitter osteogenesis imperfecta type 7
  • p.Phe33= Single submitter osteogenesis imperfecta type 7
  • p.Phe36= Single submitter osteogenesis imperfecta type 7
  • p.Pro104= Single submitter osteogenesis imperfecta type 7
  • p.Pro134= Single submitter osteogenesis imperfecta type 7
  • p.Pro147= Single submitter osteogenesis imperfecta type 7
  • p.Pro162= Single submitter osteogenesis imperfecta type 7
  • p.Pro289= Single submitter osteogenesis imperfecta type 7
  • p.Pro3= Single submitter osteogenesis imperfecta type 7
  • p.Pro37= Single submitter osteogenesis imperfecta type 7
  • p.Pro43= Single submitter osteogenesis imperfecta type 7
  • p.Pro92= Single submitter osteogenesis imperfecta type 7
  • p.Pro96= Single submitter osteogenesis imperfecta type 7
  • p.Ser132= Single submitter osteogenesis imperfecta type 7
  • p.Ser190= Single submitter osteogenesis imperfecta type 7
  • p.Ser208= Single submitter osteogenesis imperfecta type 7
  • p.Ser32= Single submitter osteogenesis imperfecta type 7
  • p.Ser35= Single submitter osteogenesis imperfecta type 7
  • p.Ser56= Single submitter osteogenesis imperfecta type 7
  • p.Ser63= Single submitter osteogenesis imperfecta type 7
  • p.Ser70= Single submitter osteogenesis imperfecta type 7
  • p.Thr224= Single submitter osteogenesis imperfecta type 7
  • p.Thr296= Single submitter osteogenesis imperfecta type 7
  • p.Thr365= Single submitter osteogenesis imperfecta type 7
  • p.Thr400= Single submitter osteogenesis imperfecta type 7
  • p.Tyr148= Single submitter osteogenesis imperfecta type 7
  • p.Tyr197= Single submitter osteogenesis imperfecta type 7
  • p.Tyr241= Single submitter osteogenesis imperfecta type 7
  • p.Tyr300= Single submitter osteogenesis imperfecta type 7
  • p.Tyr306= Single submitter osteogenesis imperfecta type 7
  • p.Tyr31= Single submitter osteogenesis imperfecta type 7
  • p.Val268= Single submitter osteogenesis imperfecta type 7
  • p.Val336= Single submitter osteogenesis imperfecta type 7
  • p.Val64= Single submitter osteogenesis imperfecta type 7
  • c.472-1011C>T No assertion criteria CRTAP-related disorder

Uncertain significance 297