PRPS1 — 350 ClinVar variants

All ClinVar germline PRPS1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 102 flagged for review →

18 Pathogenic · 6 Pathogenic/Likely pathogenic · 25 Likely pathogenic · 9 Conflicting · 15 Benign · 16 Benign/Likely benign · 138 Likely benign · 123 Uncertain significance

Full PRPS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 102

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 1

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

Predictors agree, ClinVar conflicts 6

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

Predictors lean, ClinVar uncertain 80

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

All PRPS1 variants

Pathogenic 18

  • p.Ser169Leu Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • c.307-2A>G Single submitter Inborn genetic diseases
  • p.Ala113Ser Single submitter hearing loss, X-linked 1
  • p.Ala190_Leu191insTer Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Trp154Ter Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val208fs Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val309Phe Single submitter Charcot-Marie-Tooth disease X-linked recessive 5
  • p.Ala190Val No assertion criteria phosphoribosylpyrophosphate synthetase superactivity
  • p.Asp52His No assertion criteria phosphoribosylpyrophosphate synthetase superactivity
  • p.Asp65Asn No assertion criteria hearing loss, X-linked 1
  • p.Gln133Pro No assertion criteria Arts syndrome
  • p.Gln277Pro No assertion criteria Arts syndrome
  • p.Glu43Asp No assertion criteria Charcot-Marie-Tooth disease X-linked recessive 5
  • p.His193Gln No assertion criteria phosphoribosylpyrophosphate synthetase superactivity
  • p.Ile290Thr No assertion criteria hearing loss, X-linked 1
  • p.Leu129Ile No assertion criteria phosphoribosylpyrophosphate synthetase superactivity
  • p.Ser16Pro No assertion criteria Charcot-Marie-Tooth disease X-linked recessive 5
  • p.Val142Leu No assertion criteria Arts syndrome

Pathogenic/Likely pathogenic 6

  • p.Arg196Trp Multiple submitters PRPS1-related disorder
  • p.Arg214Trp Multiple submitters PRPS1-related disorder
  • p.Arg84Trp Multiple submitters PRPS1-related disorder
  • p.Met115Thr Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Met115Val Multiple submitters Charcot-Marie-Tooth disease X-linked recessive 5
  • p.Gly306Arg No assertion criteria PRPS1-related disorder

Likely pathogenic 25

  • p.Asn114Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Ile107Val Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • c.122+1G>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ala121Gly Single submitter PRPS1-related disorder
  • p.Ala121Thr Single submitter
  • p.Asp183His Single submitter Arts syndrome
  • p.Asp52Ala Single submitter phosphoribosylpyrophosphate synthetase superactivity
  • p.Cys165Arg Single submitter
  • p.Glu43Lys Single submitter Arts syndrome
  • p.Glu46Lys Single submitter PRPS1-related disorder
  • p.Gly120Val Single submitter phosphoribosylpyrophosphate synthetase superactivity
  • p.Gly9Arg Single submitter
  • p.Ile192Asn Single submitter hearing loss, X-linked 1
  • p.Ile72Ser Single submitter PRPS1-related disorder
  • p.Ile72Thr Single submitter PRPS1-related disorder
  • p.Leu145Val Single submitter phosphoribosylpyrophosphate synthetase superactivity
  • p.Leu25Pro Single submitter
  • p.Lys280Glu Single submitter hearing loss, X-linked 1
  • p.Pro276Ala Single submitter hearing loss, X-linked 1
  • p.Pro276Leu Single submitter PRPS1-related disorder
  • p.Ser36Gly Single submitter PRPS1-related disorder
  • p.Thr126Ile Single submitter phosphoribosylpyrophosphate synthetase superactivity
  • p.Arg214Pro No assertion criteria inherited retinal dystrophy
  • p.Pro276Ser No assertion criteria Charcot-Marie-Tooth disease X-linked recessive 5
  • p.Ser16Phe No assertion criteria inherited retinal dystrophy

Conflicting classifications of pathogenicity 9

Benign 15

Benign/Likely benign 16

  • c.123-16dup Multiple submitters Arts syndrome
  • c.406-20G>C Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • c.531-15C>T Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • c.705-11T>C Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • c.705-16C>T Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • c.705-6C>T Multiple submitters Nephrolithiasis/nephrocalcinosis
  • c.864+10A>G Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Arg96= Multiple submitters Charcot-Marie-Tooth disease X-linked recessive 5
  • p.Asp220= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Glu148= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Gly240= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Ile159= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Ile4= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Leu191= Multiple submitters Nephrolithiasis/nephrocalcinosis
  • p.Lys286= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Ser314= Multiple submitters Nephrolithiasis/nephrocalcinosis

Likely benign 138

  • c.864+61G>A Multiple submitters
  • p.Ala105= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Ala20= Multiple submitters Nephrolithiasis/nephrocalcinosis
  • p.Ala257= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Asn263= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Gly45= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Gly59= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Ile140= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Ile290= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Ile292= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Lys153= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Ser254= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Tyr94= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • p.Val316= Multiple submitters Charcot-Marie-Tooth Neuropathy X
  • c.122+10A>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.122+11A>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.122+11A>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.122+13T>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.122+15G>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.122+16G>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.122+17G>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.122+18A>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.122+254C>T Single submitter
  • c.122+9C>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.123-11C>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.123-36A>G Single submitter
  • c.123-4G>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.123-6T>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.306+17A>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.306+7G>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.307-14T>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.307-6A>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.307-8C>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.405+13G>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.405+14C>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.405+7G>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.406-13C>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.406-14G>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.406-15A>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.406-17C>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.406-4A>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.406-9T>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.530+10A>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.530+11A>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.530+14_530+17dup Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.530+15A>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.530+18A>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.530+19T>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.530+19T>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.531-11_531-10del Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.531-18A>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.531-19A>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.531-21T>C Single submitter
  • c.531-262C>T Single submitter
  • c.531-9G>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.704+8T>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.705-5T>A Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.705-7C>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.864+18G>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.864+7A>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.864+9G>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.865-14T>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.865-17C>T Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.865-19T>C Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.865-19T>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.865-20T>G Single submitter Charcot-Marie-Tooth Neuropathy X
  • c.-45AGC[3] Single submitter
  • p.Ala119= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ala131= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ala147= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ala150= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ala239= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ala76= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ala87= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ala95= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Arg204= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Arg243= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Arg84= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asn164= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asn200= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asn262= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asn37= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asp122= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asp21= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asp210= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asp213= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Asp224= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Cys165= Single submitter
  • p.Cys60= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Cys77= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Cys91= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Gln13= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Gln57= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Glu157= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Glu26= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Glu278= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Glu39= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Gly173= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Gly227= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Gly251= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Gly61= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Gly9= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.His231= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.His315= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ile290Val Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ile300= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu111= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu116= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu145= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu15= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu152= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu185= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu23= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu27= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Leu312= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Lys18= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Lys198= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Lys280= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Lys29= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Lys33= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Phe189= Single submitter
  • p.Phe253= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Pro149= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ser160= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ser8= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Ser83= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Thr126= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Thr225= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Thr32= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Thr40= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val112= Single submitter Nephrolithiasis/nephrocalcinosis
  • p.Val208= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val244= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val269= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val270= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val289= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val56= Single submitter Charcot-Marie-Tooth Neuropathy X
  • p.Val88= Single submitter Charcot-Marie-Tooth Neuropathy X

Uncertain significance 123