PAPSS2 — 409 ClinVar variants

All ClinVar germline PAPSS2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 138 flagged for review →

29 Pathogenic · 3 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 5 Conflicting · 41 Benign · 16 Benign/Likely benign · 139 Likely benign · 167 Uncertain significance

Full PAPSS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 138

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 2

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

Predictors lean, ClinVar uncertain 104

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

Predictors split 32

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

All PAPSS2 variants

Pathogenic 29

  • p.Arg334Ter Multiple submitters autosomal recessive brachyolmia
  • p.Arg41Ter Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.His360fs Multiple submitters PAPSS2-related disorder
  • p.Tyr492Ter Multiple submitters Inborn genetic diseases
  • c.1721+2T>C Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.520+1G>A Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.639+1G>T Single submitter
  • p.Arg129His Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Arg556Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Gln377Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Glu10Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Glu242Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Glu473Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Leu333Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Leu425fs Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Phe228fs Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Ser480Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Thr353fs Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Trp351Ter Single submitter
  • p.Trp462fs Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Tyr164Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Tyr439Ter Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Val106fs Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Ala113fs No assertion criteria spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Arg437fs No assertion criteria spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Ile221fs No assertion criteria spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Lys161fs No assertion criteria spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Thr48Arg No assertion criteria spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Val206fs No assertion criteria spondyloepimetaphyseal dysplasia, PAPSS2 type

Pathogenic/Likely pathogenic 3

  • c.640-1G>C Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Arg238Ter Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Tyr74Ter Multiple submitters brachyolmia

Likely pathogenic 9

Conflicting classifications of pathogenicity 5

  • c.381+2T>G Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Asp389= Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Gly270Asp Single submitter Inborn genetic diseases ⚠
  • p.Leu531Pro Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Thr610fs Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type

Benign 41

Benign/Likely benign 16

  • c.145+14AT[10] Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.145+14AT[6] Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.145+14AT[8] Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.381+21_381+24dup Multiple submitters
  • c.381+23_381+24dup Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.381+24del Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.381+24dup Multiple submitters
  • c.753+4A>C Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Asp159= Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Glu10Lys Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.His204= Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Leu287= Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Leu89= Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Phe125= Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Val296Met Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.381+21_381+24del No assertion criteria

Likely benign 139

Uncertain significance 167

  • p.Ala22Val Multiple submitters Inborn genetic diseases ⚠
  • p.Ala336Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Ala409Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Ala563Thr Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg101Cys Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg133Leu Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg273Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg273Trp Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Arg314Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg392His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg431Cys Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg463Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg463Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg505Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg556Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Asn17Asp Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Asp369Tyr Multiple submitters Inborn genetic diseases ⚠
  • p.Gln13Glu Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Glu472Lys Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Glu497Lys Multiple submitters Inborn genetic diseases ⚠
  • p.Glu592Ala Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Glu594Lys Multiple submitters Inborn genetic diseases ⚠
  • p.Glu617del Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Gly114Ala Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Gly438Asp Multiple submitters Inborn genetic diseases
  • p.Gly451Ser Multiple submitters Inborn genetic diseases ⚠
  • p.His536Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Ile303Val Multiple submitters Inborn genetic diseases ⚠
  • p.Lys403Glu Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Lys529Asn Multiple submitters Inborn genetic diseases ⚠
  • p.Lys588Thr Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Met365Val Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro603Ser Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ser68Pro Multiple submitters Inborn genetic diseases ⚠
  • p.Trp452Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Trp462Arg Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Tyr560Cys Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Tyr65His Multiple submitters Inborn genetic diseases ⚠
  • p.Val237Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Val307Ile Multiple submitters spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Val372Ala Multiple submitters Inborn genetic diseases ⚠
  • p.Val372Phe Multiple submitters ⚠
  • c.1491+3G>A Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.1492-3T>C Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.1721+5G>A Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.1722-3C>T Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.1722-9del Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.27+6C>T Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.381+1_381+2insGAAAA Single submitter Fetal anomalies with a likely genetic cause
  • c.381+3A>G Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.381+3A>T Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.381+4A>G Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.865+4T>C Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.866-1G>A Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • c.880+3A>G Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Ala139Val Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ala336Val Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ala468Thr Single submitter Inborn genetic diseases ⚠
  • p.Arg133Cys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg328Trp Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg346Cys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Arg349Cys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg349His Single submitter Inborn genetic diseases ⚠
  • p.Arg416Cys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg416His Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Arg432Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg437Gly Single submitter Inborn genetic diseases ⚠
  • p.Arg585Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg591Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg82His Single submitter Inborn genetic diseases ⚠
  • p.Asn11His Single submitter ⚠
  • p.Asn561Lys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Asn595Asp Single submitter Inborn genetic diseases ⚠
  • p.Asp112Glu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Asp179Asn Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Asp386Gly Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Asp429Gly Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Asp455Glu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Asp568Glu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Asp611fs Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Cys355Arg Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Cys355Ser Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Gln12Arg Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Gln12His Single submitter Inborn genetic diseases ⚠
  • p.Gln499His Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Glu137Lys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Glu183Lys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Glu262Lys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Glu473Gln Single submitter Inborn genetic diseases ⚠
  • p.Glu592Lys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Glu64Lys Single submitter Inborn genetic diseases
  • p.Gly295Ser Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Gly317Val Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Gly327Glu Single submitter Inborn genetic diseases ⚠
  • p.Gly368Trp Single submitter Inborn genetic diseases ⚠
  • p.Gly373Asp Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Gly374Glu Single submitter Inborn genetic diseases ⚠
  • p.Gly537Val Single submitter Inborn genetic diseases ⚠
  • p.His358Gln Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.His360Leu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.His420Arg Single submitter Inborn genetic diseases ⚠
  • p.His441Leu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ile135Met Single submitter Inborn genetic diseases ⚠
  • p.Ile172Thr Single submitter ⚠
  • p.Ile178Leu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ile297Met Single submitter Inborn genetic diseases ⚠
  • p.Ile297Val Single submitter Inborn genetic diseases ⚠
  • p.Ile482Val Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ile514Thr Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ile581Leu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ile581Val Single submitter Inborn genetic diseases
  • p.Leu209Ile Single submitter Inborn genetic diseases ⚠
  • p.Leu234Pro Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Leu305Arg Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Leu323Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu376Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu398Arg Single submitter Inborn genetic diseases ⚠
  • p.Leu460Pro Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Leu471Phe Single submitter Inborn genetic diseases
  • p.Leu89Val Single submitter Inborn genetic diseases ⚠
  • p.Met272Leu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Met363Val Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Met365Ile Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Met506Val Single submitter Inborn genetic diseases ⚠
  • p.Met601Thr Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Phe144del Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Phe147Ser Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Phe228Ser Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Phe580Cys Single submitter Inborn genetic diseases ⚠
  • p.Phe600Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro151Ser Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro230Arg Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro442Ala Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro442Arg Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro442Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro448Ser Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro487Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro519Thr Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro523Leu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Pro525Ala Single submitter Inborn genetic diseases ⚠
  • p.Pro534Leu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Pro545His Single submitter Inborn genetic diseases
  • p.Pro572Thr Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro596Ser Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Pro597fs Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Pro72Ala Single submitter Inborn genetic diseases
  • p.Pro93Arg Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ser319Gly Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Ser542Gly Single submitter Inborn genetic diseases ⚠
  • p.Ser92Tyr Single submitter Inborn genetic diseases ⚠
  • p.Thr119Ser Single submitter Inborn genetic diseases ⚠
  • p.Thr176Ile Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Thr535Ser Single submitter Inborn genetic diseases ⚠
  • p.Thr548Asn Single submitter Inborn genetic diseases ⚠
  • p.Thr610Arg Single submitter Inborn genetic diseases ⚠
  • p.Tyr20Cys Single submitter Inborn genetic diseases ⚠
  • p.Tyr339Cys Single submitter Inborn genetic diseases ⚠
  • p.Tyr570Cys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Tyr65Cys Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠
  • p.Val160Ile Single submitter Inborn genetic diseases ⚠
  • p.Val203Ala Single submitter Inborn genetic diseases ⚠
  • p.Val206Ile Single submitter Inborn genetic diseases ⚠
  • p.Val45Met Single submitter ⚠
  • p.Val475Phe Single submitter Inborn genetic diseases ⚠
  • p.Val483del Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type
  • p.Val540Ile Single submitter Inborn genetic diseases ⚠
  • p.Val550Leu Single submitter spondyloepimetaphyseal dysplasia, PAPSS2 type ⚠