AGXT — 957 ClinVar variants

All ClinVar germline AGXT variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 212 flagged for review →

159 Pathogenic · 52 Pathogenic/Likely pathogenic · 102 Likely pathogenic · 38 Conflicting · 47 Benign · 12 Benign/Likely benign · 357 Likely benign · 190 Uncertain significance

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

⚑ Evidence disagreements 212

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 20

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

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 67

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

Predictors split 114

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

All AGXT variants

Pathogenic 159

  • c.166-1_172dup Multiple submitters primary hyperoxaluria type 1
  • c.358+1G>A Multiple submitters primary hyperoxaluria type 1
  • c.359-1_382del Multiple submitters primary hyperoxaluria type 1
  • c.525-1G>A Multiple submitters primary hyperoxaluria type 1
  • c.595+1G>T Multiple submitters primary hyperoxaluria type 1
  • c.596-2A>G Multiple submitters primary hyperoxaluria type 1
  • c.679_680+2del Multiple submitters primary hyperoxaluria type 1
  • c.776+1G>A Multiple submitters primary hyperoxaluria type 1
  • c.777-1G>C Multiple submitters primary hyperoxaluria
  • c.846+1G>T Multiple submitters primary hyperoxaluria
  • p.Arg111Ter Multiple submitters primary hyperoxaluria
  • p.Arg122Ter Multiple submitters primary hyperoxaluria type 1
  • p.Arg333Ter Multiple submitters primary hyperoxaluria type 1
  • p.Arg36Cys Multiple submitters primary hyperoxaluria type 1 ⚠
  • p.Asp201Glu Multiple submitters primary hyperoxaluria type 1
  • p.Asp243fs Multiple submitters primary hyperoxaluria type 1
  • p.Gln110fs Multiple submitters primary hyperoxaluria type 1
  • p.Gln208Ter Multiple submitters primary hyperoxaluria
  • p.Gly161Ser Multiple submitters primary hyperoxaluria ⚠
  • p.Gly190Arg Multiple submitters primary hyperoxaluria type 1
  • p.Gly47Arg Multiple submitters primary hyperoxaluria type 1 ⚠
  • p.Gly63Arg Multiple submitters primary hyperoxaluria
  • p.Gly82Arg Multiple submitters primary hyperoxaluria type 1
  • p.Gly82Glu Multiple submitters primary hyperoxaluria
  • p.Ile244Thr Multiple submitters primary hyperoxaluria ⚠
  • p.Leu151fs Multiple submitters primary hyperoxaluria
  • p.Leu193fs Multiple submitters primary hyperoxaluria
  • p.Lys245fs Multiple submitters primary hyperoxaluria type 1
  • p.Met1Asn Multiple submitters primary hyperoxaluria type 1
  • p.Phe152Ile Multiple submitters primary hyperoxaluria
  • p.Ser187Phe Multiple submitters primary hyperoxaluria
  • p.Ser205Leu Multiple submitters primary hyperoxaluria ⚠
  • p.Ser218Leu Multiple submitters primary hyperoxaluria type 1
  • p.Thr191fs Multiple submitters primary hyperoxaluria
  • p.Trp332Ter Multiple submitters primary hyperoxaluria type 1
  • p.Val324fs Multiple submitters primary hyperoxaluria type 1
  • p.Val326fs Multiple submitters primary hyperoxaluria
  • c.1_524del Single submitter primary hyperoxaluria type 1
  • c.1_595del Single submitter primary hyperoxaluria type 1
  • c.1072_1079del Single submitter primary hyperoxaluria type 1
  • c.358+1G>T Single submitter primary hyperoxaluria type 1
  • c.358+2T>G Single submitter primary hyperoxaluria type 1
  • c.525-2A>G Single submitter
  • c.595+1G>C Single submitter primary hyperoxaluria type 1
  • c.595+2T>G Single submitter primary hyperoxaluria type 1
  • c.596-1G>A Single submitter primary hyperoxaluria type 1
  • c.680+1G>T Single submitter primary hyperoxaluria type 1
  • c.680+480_776+69delinsTGAGA Single submitter primary hyperoxaluria type 1
  • c.776+1G>C Single submitter primary hyperoxaluria type 1
  • c.776+2T>G Single submitter primary hyperoxaluria type 1
  • c.777-1G>T Single submitter primary hyperoxaluria type 1
  • c.846+1G>A Single submitter primary hyperoxaluria type 1
  • p.Ala277fs Single submitter primary hyperoxaluria type 1
  • p.Asn286fs Single submitter
  • p.Asp254fs Single submitter
  • p.Asp374His Single submitter primary hyperoxaluria type 1 ⚠
  • p.Cys173Ter Single submitter primary hyperoxaluria
  • p.Gln145Ter Single submitter primary hyperoxaluria type 1
  • p.Gln198Pro Single submitter primary hyperoxaluria type 1 ⚠
  • p.Gln23Ter Single submitter
  • p.Gln256fs Single submitter primary hyperoxaluria type 1
  • p.Gln303Ter Single submitter primary hyperoxaluria type 1
  • p.Gln385Ter Single submitter
  • p.Gln44Ter Single submitter primary hyperoxaluria type 1
  • p.Gln65Ter Single submitter primary hyperoxaluria type 1
  • p.Glu117fs Single submitter primary hyperoxaluria type 1
  • p.Glu157fs Single submitter primary hyperoxaluria type 1
  • p.Glu157Ter Single submitter primary hyperoxaluria type 1
  • p.Glu281Ter Single submitter
  • p.Glu378fs Single submitter
  • p.Glu59Ter Single submitter
  • p.Glu95Lys Single submitter primary hyperoxaluria type 1
  • p.Gly116Trp Single submitter primary hyperoxaluria type 1
  • p.Gly329fs Single submitter
  • p.Gly82fs Single submitter primary hyperoxaluria type 1
  • p.Ile220Phe Single submitter primary hyperoxaluria type 1 ⚠
  • p.Ile244Asn Single submitter primary hyperoxaluria type 1 ⚠
  • p.Leu14fs Single submitter primary hyperoxaluria type 1
  • p.Leu153Ter Single submitter primary hyperoxaluria type 1
  • p.Leu278fs Single submitter
  • p.Leu74fs Single submitter
  • p.Lys12fs Single submitter
  • p.Lys177Ter Single submitter
  • p.Lys209fs Single submitter
  • p.Lys225Ter Single submitter
  • p.Lys228fs Single submitter primary hyperoxaluria type 1
  • p.Pro10fs Single submitter primary hyperoxaluria type 1
  • p.Pro215fs Single submitter primary hyperoxaluria type 1
  • p.Ser158fs Single submitter
  • p.Ser158Ter Single submitter primary hyperoxaluria type 1
  • p.Ser184Ter Single submitter primary hyperoxaluria type 1
  • p.Ser187_Leu188insVal Single submitter primary hyperoxaluria type 1
  • p.Ser223fs Single submitter
  • p.Ser239del Single submitter primary hyperoxaluria type 1
  • p.Ser275fs Single submitter
  • p.Thr75fs Single submitter primary hyperoxaluria type 1
  • p.Trp108Ter Single submitter primary hyperoxaluria type 1
  • p.Trp251Ter Single submitter primary hyperoxaluria type 1
  • p.Tyr134Ter Single submitter primary hyperoxaluria type 1
  • p.Tyr231Ter Single submitter primary hyperoxaluria type 1
  • p.Tyr297Ter Single submitter primary hyperoxaluria type 1
  • p.Tyr66Ter Single submitter primary hyperoxaluria type 1
  • p.Val266fs Single submitter
  • p.Val321fs Single submitter
  • c.1071+1G>A No assertion criteria primary hyperoxaluria type 1
  • c.1072-2A>G No assertion criteria primary hyperoxaluria type 1
  • c.166-1G>A No assertion criteria primary hyperoxaluria type 1
  • c.424-2A>G No assertion criteria primary hyperoxaluria type 1
  • c.680+5G>C No assertion criteria primary hyperoxaluria type 1
  • c.846+646_942+139del No assertion criteria primary hyperoxaluria type 1
  • c.943-1G>A No assertion criteria primary hyperoxaluria type 1
  • p.Ala186_Ser187delinsAspArg No assertion criteria primary hyperoxaluria type 1
  • p.Ala210Pro No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Ala304fs No assertion criteria primary hyperoxaluria type 1
  • p.Ala368Thr No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Ala383Asp No assertion criteria primary hyperoxaluria type 1
  • p.Ala85Asp No assertion criteria primary hyperoxaluria type 1
  • p.Asn249fs No assertion criteria primary hyperoxaluria type 1
  • p.Asn72fs No assertion criteria primary hyperoxaluria type 1
  • p.Asn92fs No assertion criteria primary hyperoxaluria type 1
  • p.Asp243His No assertion criteria primary hyperoxaluria type 1
  • p.Gln137fs No assertion criteria primary hyperoxaluria type 1
  • p.Gln137Ter No assertion criteria primary hyperoxaluria type 1
  • p.Gln282Ter No assertion criteria primary hyperoxaluria type 1
  • p.Gln308Ter No assertion criteria primary hyperoxaluria type 1
  • p.Gln69Ter No assertion criteria primary hyperoxaluria type 1
  • p.Glu117Ter No assertion criteria primary hyperoxaluria type 1
  • p.Glu141Asp No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Glu285Ter No assertion criteria primary hyperoxaluria type 1
  • p.Gly109Val No assertion criteria primary hyperoxaluria type 1
  • p.Gly170fs No assertion criteria primary hyperoxaluria type 1
  • p.Gly349Ser No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Gly42Glu No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.His124Pro No assertion criteria primary hyperoxaluria type 1
  • p.His261Gln No assertion criteria primary hyperoxaluria type 1
  • p.Ile267fs No assertion criteria primary hyperoxaluria type 1
  • p.Ile279fs No assertion criteria primary hyperoxaluria type 1
  • p.Leu150Pro No assertion criteria primary hyperoxaluria type 1
  • p.Leu153Val No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Leu25Arg No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Leu26Pro No assertion criteria primary hyperoxaluria type 1
  • p.Leu284Pro No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Leu307fs No assertion criteria primary hyperoxaluria type 1
  • p.Leu316Pro No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Met195Leu No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Met1Ile No assertion criteria primary hyperoxaluria type 1
  • p.Pro10Ser No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Pro28fs No assertion criteria primary hyperoxaluria type 1
  • p.Pro319Leu No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Ser205Ter No assertion criteria primary hyperoxaluria type 1
  • p.Ser221Pro No assertion criteria primary hyperoxaluria type 1
  • p.Ser287Thr No assertion criteria primary hyperoxaluria type 1
  • p.Ser81Ter No assertion criteria primary hyperoxaluria type 1
  • p.Thr154fs No assertion criteria primary hyperoxaluria type 1
  • p.Thr320fs No assertion criteria primary hyperoxaluria type 1
  • p.Tyr204Ter No assertion criteria primary hyperoxaluria type 1
  • p.Tyr338Ter No assertion criteria primary hyperoxaluria type 1
  • p.Val149fs No assertion criteria primary hyperoxaluria type 1
  • p.Val376fs No assertion criteria primary hyperoxaluria type 1

Pathogenic/Likely pathogenic 52

  • c.423+1G>A Multiple submitters primary hyperoxaluria type 1
  • c.525-2A>T Multiple submitters primary hyperoxaluria type 1
  • c.680+1G>A Multiple submitters primary hyperoxaluria
  • c.680+2T>A Multiple submitters primary hyperoxaluria type 1
  • c.847-1G>C Multiple submitters primary hyperoxaluria
  • c.847-3C>G Multiple submitters primary hyperoxaluria type 1
  • c.942+1G>A Multiple submitters primary hyperoxaluria type 1
  • c.942+1G>T Multiple submitters primary hyperoxaluria type 1
  • c.943-1G>T Multiple submitters primary hyperoxaluria type 1
  • p.Ala112Asp Multiple submitters primary hyperoxaluria
  • p.Ala325fs Multiple submitters primary hyperoxaluria type 1
  • p.Ala40fs Multiple submitters primary hyperoxaluria
  • p.Ala85fs Multiple submitters primary hyperoxaluria type 1
  • p.Arg111Gln Multiple submitters primary hyperoxaluria type 1 ⚠
  • p.Arg233Cys Multiple submitters primary hyperoxaluria ⚠
  • p.Arg233His Multiple submitters primary hyperoxaluria type 1 ⚠
  • p.Arg360Gln Multiple submitters primary hyperoxaluria type 1
  • p.Arg360Trp Multiple submitters primary hyperoxaluria type 1
  • p.Arg36His Multiple submitters primary hyperoxaluria ⚠
  • p.Asn72Ile Multiple submitters primary hyperoxaluria type 1
  • p.Cys173_His174delinsTrpAsn Multiple submitters primary hyperoxaluria type 1
  • p.Cys178Tyr Multiple submitters primary hyperoxaluria type 1
  • p.Cys253Arg Multiple submitters primary hyperoxaluria type 1
  • p.Cys387Ter Multiple submitters primary hyperoxaluria type 1
  • p.Gln145fs Multiple submitters primary hyperoxaluria type 1
  • p.Gln164Ter Multiple submitters primary hyperoxaluria type 1
  • p.Gly116Arg Multiple submitters primary hyperoxaluria type 1
  • p.Gly156Arg Multiple submitters primary hyperoxaluria type 1
  • p.Gly161Cys Multiple submitters primary hyperoxaluria type 1
  • p.Gly170Arg Multiple submitters primary hyperoxaluria ⚠
  • p.Gly216Arg Multiple submitters primary hyperoxaluria type 1
  • p.Gly350Asp Multiple submitters primary hyperoxaluria type 1
  • p.Gly41Arg Multiple submitters primary hyperoxaluria type 1 ⚠
  • p.Gly41Val Multiple submitters primary hyperoxaluria type 1 ⚠
  • p.Leu101Pro Multiple submitters primary hyperoxaluria type 1
  • p.Leu269Pro Multiple submitters primary hyperoxaluria
  • p.Leu43fs Multiple submitters primary hyperoxaluria
  • p.Lys225fs Multiple submitters primary hyperoxaluria type 1
  • p.Met195Arg Multiple submitters primary hyperoxaluria type 1
  • p.Met1Thr Multiple submitters primary hyperoxaluria
  • p.Pro11Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Pro125fs Multiple submitters primary hyperoxaluria type 1
  • p.Ser158Leu Multiple submitters primary hyperoxaluria type 1
  • p.Ser205Pro Multiple submitters primary hyperoxaluria type 1
  • p.Ser81Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Trp108Arg Multiple submitters primary hyperoxaluria type 1
  • p.Trp246Ter Multiple submitters primary hyperoxaluria type 1
  • p.Trp332fs Multiple submitters primary hyperoxaluria type 1
  • p.Tyr270fs Multiple submitters primary hyperoxaluria type 1
  • p.Val336Asp Multiple submitters primary hyperoxaluria type 1
  • p.Gly199Ser No assertion criteria primary hyperoxaluria type 1 ⚠
  • p.Val77fs No assertion criteria primary hyperoxaluria type 1

Likely pathogenic 102

Conflicting classifications of pathogenicity 38

Benign 47

Benign/Likely benign 12

  • c.166-14C>T Multiple submitters primary hyperoxaluria type 1
  • c.942+12C>G Multiple submitters primary hyperoxaluria type 1
  • c.-23G>A Multiple submitters primary hyperoxaluria type 1
  • p.Ala186Val Multiple submitters primary hyperoxaluria type 1
  • p.Ala280Val Multiple submitters primary hyperoxaluria type 1 ⚠
  • p.Ala295Thr Multiple submitters primary hyperoxaluria type 1 ⚠
  • p.Arg197Gln Multiple submitters primary hyperoxaluria type 1
  • p.Ile244= Multiple submitters primary hyperoxaluria type 1
  • p.Ile340Met Multiple submitters primary hyperoxaluria type 1
  • p.Met49Leu Multiple submitters primary hyperoxaluria type 1
  • p.Thr235= Multiple submitters primary hyperoxaluria type 1
  • p.Thr9Asn Multiple submitters primary hyperoxaluria type 1

Likely benign 357

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

Uncertain significance 190