PTS — 286 ClinVar variants

All ClinVar germline PTS variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 72 flagged for review →

30 Pathogenic · 21 Pathogenic/Likely pathogenic · 33 Likely pathogenic · 17 Conflicting · 12 Benign · 2 Benign/Likely benign · 119 Likely benign · 52 Uncertain significance

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

⚑ Evidence disagreements 72

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 7

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

Predictors lean, ClinVar uncertain 21

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

Predictors split 24

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

All PTS variants

Pathogenic 30

  • c.186+1G>A Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.186+1G>T Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.84-3C>G Multiple submitters PTS-related disorder
  • p.Asn52Ser Multiple submitters PTS-related disorder
  • p.Asn72Lys Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Asp96Asn Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Phe40fs Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Pro87Leu Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Pro87Ser Multiple submitters hyperphenylalaninemia due to tetrahydrobiopterin deficiency ⚠
  • p.Thr106Met Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Thr67Met Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val132fs Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.163+696_163+750del Single submitter BH4-deficient hyperphenylalaninemia A
  • c.164-7T>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.187-2A>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-2A>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+2T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Asn36fs Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Asp64Ter Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Glu108Ter Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Lys29Ter Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Pro98fs Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Thr67Lys Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Tyr128Ter Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Tyr133Ter Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Tyr53Ter Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Tyr79fs Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Tyr99Cys Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val124Leu Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val121fs No assertion criteria Hyperphenylalaninemia, bh4-deficient, a, due to partial pts deficiency

Pathogenic/Likely pathogenic 21

  • c.315-1G>A Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.315-2A>G Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.84-291A>G Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Ala111Thr Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asp136Val Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Glu134Lys Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Glu134Ter Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Glu81= Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.His49Arg Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Ile114Met Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Ile63Val Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Leu127Phe Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Lys129Glu Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Lys91Arg Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Met80Val Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Pro123Ser Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Ser32Gly Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Tyr99Ter Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Val56Met Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val57del Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Val59fs Multiple submitters BH4-deficient hyperphenylalaninemia A

Likely pathogenic 33

  • c.187-2A>G Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.243_243+1dup Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.84-1G>A Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.84-2A>G Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Asn117Lys Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asp136Gly Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asp94Gly Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Gln86Ter Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Glu82Gly Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val70fs Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.163+1G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.164-4_165del Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+1G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+2T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-1G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+1G>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.315-2A>C Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Ala111Ser Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asn47Asp Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Gln119Ter Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Glu81Ala Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Ile139Asn Single submitter
  • p.Leu88fs Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Lys78fs Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Met80Thr Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val124Ala Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val126_Leu127insTer Single submitter BH4-deficient hyperphenylalaninemia A
  • c.164-2A>G No assertion criteria BH4-deficient hyperphenylalaninemia A
  • c.315-1G>C No assertion criteria BH4-deficient hyperphenylalaninemia A
  • c.(?_-1 No assertion criteria metabolic disease
  • p.Asn36Lys No assertion criteria GTP cyclohydrolase I deficiency with hyperphenylalaninemia
  • p.Leu76fs No assertion criteria BH4-deficient hyperphenylalaninemia A
  • p.Tyr113fs No assertion criteria BH4-deficient hyperphenylalaninemia A

Conflicting classifications of pathogenicity 17

  • c.164-716A>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.*60T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Ala83Glu Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asn44= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Asp116Gly Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Glu35Gly Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Gly41Arg Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Ile114Val Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Leu127Val Single submitter Inborn genetic diseases ⚠
  • p.Lys120Asn Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Lys91Glu Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Pro65= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Ser32Asn Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Tyr113Cys Single submitter Inborn genetic diseases ⚠
  • p.Val103Ala Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val104= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Val70Asp Single submitter BH4-deficient hyperphenylalaninemia A ⚠

Benign 12

Benign/Likely benign 2

  • c.315-3T>C Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.315-8dup Multiple submitters BH4-deficient hyperphenylalaninemia A

Likely benign 119

  • c.163+121A>G Multiple submitters
  • c.187-52G>A Multiple submitters
  • c.243+9A>G Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Tyr133= Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Val140= Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.163+133G>A Single submitter
  • c.163+14_163+15inv Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+17T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+697A>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+711T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+717T>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+720G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+729_163+730del Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+732T>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+746G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+7G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.164-10C>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.164-258C>A Single submitter
  • c.164-4A>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.164-4A>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.164-714C>T Single submitter
  • c.164-734C>T Single submitter
  • c.164-7T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+14A>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+16A>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+17T>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+18T>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+18T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+19del Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+19T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+20G>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+7G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+7G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.186+9A>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.187-10T>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.187-177A>G Single submitter
  • c.187-58C>T Single submitter
  • c.187-8T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+10T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+10T>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+11G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+13T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+15G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+30C>G Single submitter
  • c.243+7G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-13G>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-17C>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-18C>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-4C>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-4C>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-8G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-8G>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-8G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.244-9T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+10A>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+11C>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+13G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+14T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+14T>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+20G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+7G>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.314+8G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.315-17del Single submitter BH4-deficient hyperphenylalaninemia A
  • c.315-17G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.315-17G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.315-20T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.315-5T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.315-6T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.315-8T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.83+190C>A Single submitter
  • c.84-10T>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-15T>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-18T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-4T>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-5del Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-5G>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-5G>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-5G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-6G>T Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-7T>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.84-8T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Ala101= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Ala111= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Ala74= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Ala83= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Asn109= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Asn36= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Asn44Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn47= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Asp64= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Asp96= Single submitter
  • p.Gly41= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Gly48= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.His49= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.His60= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Leu39= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Leu76= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Leu93= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Lys131= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Lys77= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Lys91= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Phe100= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Phe40= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Pro123= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Pro87= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Thr106= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Thr135= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Thr58= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Tyr53= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Tyr79= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Val103= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Val124= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Val130= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Val56= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Val59= Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Val97= Single submitter BH4-deficient hyperphenylalaninemia A
  • c.163+753C>T No assertion criteria PTS-related disorder
  • c.164-718C>T No assertion criteria PTS-related disorder
  • c.84-3C>T No assertion criteria

Uncertain significance 52

  • c.164-672C>T Multiple submitters BH4-deficient hyperphenylalaninemia A
  • c.84-323A>T Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Asn44Asp Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • p.Glu62= Multiple submitters BH4-deficient hyperphenylalaninemia A
  • p.Gly50Arg Multiple submitters BH4-deficient hyperphenylalaninemia A ⚠
  • c.164-37dup Single submitter BH4-deficient hyperphenylalaninemia A
  • c.243+4A>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.*148C>A Single submitter BH4-deficient hyperphenylalaninemia A
  • c.*16T>C Single submitter BH4-deficient hyperphenylalaninemia A
  • c.*213A>G Single submitter BH4-deficient hyperphenylalaninemia A
  • c.*58G>C Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Ala101Val Single submitter ⚠
  • p.Ala66Thr Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asn117Asp Single submitter ⚠
  • p.Asn138His Single submitter ⚠
  • p.Asn36Asp Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asn92His Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asp33Val Single submitter ⚠
  • p.Asp94Glu Single submitter ⚠
  • p.Asp94Tyr Single submitter ⚠
  • p.Gln119Arg Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Glu35Asp Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Gly50Glu Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.His51Tyr Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.His60Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu122Ile Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Lys143Asn Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Lys29Ile Single submitter BH4-deficient hyperphenylalaninemia A
  • p.Met69Val Single submitter ⚠
  • p.Met71Thr Single submitter ⚠
  • p.Met71Val Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Phe100Val Single submitter ⚠
  • p.Phe40Leu Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Pro46Thr Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Pro65Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro65Ser Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Pro65Thr Single submitter Inborn genetic diseases ⚠
  • p.Pro98Gln Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Pro98Ser Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Tyr53Ser Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val126Asp Single submitter BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val132Leu Single submitter Inborn genetic diseases
  • p.Asn109Ser No assertion criteria BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asn92Asp No assertion criteria BH4-deficient hyperphenylalaninemia A ⚠
  • p.Asp136Asn No assertion criteria BH4-deficient hyperphenylalaninemia A ⚠
  • p.Glu134Asp No assertion criteria BH4-deficient hyperphenylalaninemia A ⚠
  • p.Glu145Lys No assertion criteria BH4-deficient hyperphenylalaninemia A ⚠
  • p.Leu31Ile No assertion criteria GTP cyclohydrolase I deficiency with hyperphenylalaninemia ⚠
  • p.Met80Ile No assertion criteria PTS-related disorder
  • p.Ter146Tyr No assertion criteria BH4-deficient hyperphenylalaninemia A
  • p.Val132Ala No assertion criteria BH4-deficient hyperphenylalaninemia A ⚠
  • p.Val97Met No assertion criteria BH4-deficient hyperphenylalaninemia A ⚠