AGPS — 744 ClinVar variants

All ClinVar germline AGPS variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 112 flagged for review →

7 Pathogenic · 1 Pathogenic/Likely pathogenic · 22 Likely pathogenic · 16 Conflicting · 70 Benign · 7 Benign/Likely benign · 422 Likely benign · 199 Uncertain significance

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

⚑ Evidence disagreements 112

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 lean, ClinVar uncertain 68

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

Predictors split 44

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

All AGPS variants

Pathogenic 7

  • c.638-1G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Arg515Ter Single submitter
  • p.Gly556fs Single submitter
  • p.Phe184fs Single submitter
  • p.Tyr580fs Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Leu469Pro No assertion criteria rhizomelic chondrodysplasia punctata type 3
  • p.Thr568Met No assertion criteria rhizomelic chondrodysplasia punctata type 3

Pathogenic/Likely pathogenic 1

  • p.Arg182Ter Multiple submitters rhizomelic chondrodysplasia punctata type 3

Likely pathogenic 22

  • p.Thr309Ile Multiple submitters rhizomelic chondrodysplasia punctata type 3
  • c.1233+1G>A Single submitter
  • c.1286delG Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.1546-84_1591dup Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.1608-1G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.557_562+5del Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.562+1G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.637+2T>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.710-2A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Arg204Ter Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Arg419His Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Asn272fs Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Glu199Ter Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Glu306fs Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Glu346fs Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Glu520fs Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Ile194fs Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Lys169Ter Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Lys553fs Single submitter rhizomelic chondrodysplasia punctata
  • p.Ser101fs Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Trp96Ter Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Tyr513fs Single submitter rhizomelic chondrodysplasia punctata type 3

Conflicting classifications of pathogenicity 16

  • c.1475+12A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.637+13C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.638-7T>C Single submitter
  • p.Ala7Val Single submitter ⚠
  • p.Arg50Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg50Trp Single submitter rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Asp445= Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Cys297= Single submitter
  • p.Leu507= Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Lys555= Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Phe636= Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Pro460= Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Thr145= Single submitter
  • p.Val183= Single submitter
  • p.Val402Ile Single submitter Inborn genetic diseases ⚠
  • p.Val523= Single submitter rhizomelic chondrodysplasia punctata type 3

Benign 70

Benign/Likely benign 7

  • c.1233+13AT[7] Multiple submitters rhizomelic chondrodysplasia punctata type 3
  • c.1233+14T>A Multiple submitters rhizomelic chondrodysplasia punctata type 3
  • c.1698-14T>C Multiple submitters rhizomelic chondrodysplasia punctata type 3
  • c.*5023C>A Multiple submitters rhizomelic chondrodysplasia punctata type 3
  • p.Gly12Asp Multiple submitters rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Pro415= Multiple submitters rhizomelic chondrodysplasia punctata type 3
  • p.Val384= Multiple submitters rhizomelic chondrodysplasia punctata type 3

Likely benign 422

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

Uncertain significance 199

  • c.1855+6C>A Multiple submitters rhizomelic chondrodysplasia punctata type 3
  • c.*118A>G Multiple submitters rhizomelic chondrodysplasia punctata type 3
  • p.Ala22Arg Multiple submitters Inborn genetic diseases
  • p.Arg265Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Asn649Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Asp28Val Multiple submitters rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Asp32_Arg33insProGly Multiple submitters
  • p.Asp590His Multiple submitters Inborn genetic diseases ⚠
  • p.Gly9Ala Multiple submitters Inborn genetic diseases ⚠
  • p.Leu120Val Multiple submitters Inborn genetic diseases ⚠
  • p.Phe450Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Pro415Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Pro460Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Thr72Ala Multiple submitters Inborn genetic diseases ⚠
  • c.1362+3A>G Single submitter
  • c.1363-2A>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.1697+2T>C Single submitter
  • c.709+4G>C Single submitter
  • c.870+4T>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.871-16A>G Single submitter
  • c.-5_-3del Single submitter
  • c.*1073T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1105T>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1238T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1312T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1424G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1469T>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1628C>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*165T>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1744A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1838AT[12] Single submitter
  • c.*1858A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1860G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1865C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1869T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1880A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1880AT[7] Single submitter
  • c.*1882A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*1884A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*206T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2088T>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2311G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2318A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2437A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2455C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2487C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2582C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2621C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2667G>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2730G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*2833G>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3060A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3262C>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3381G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3524T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3606A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*361C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*378G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3911AGTTTT[1] Single submitter
  • c.*3931A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3953A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3971A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*3977T>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4056T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4100A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4132A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4228A>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4232A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*428C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4625C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4674A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*469A>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4780G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4788G>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4885A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4910C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*4996C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*5026C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*513T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*5155C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*5159T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*5453C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*5465C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*5506T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*5609G>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*560T>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*641T>C Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*683A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*731A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*794C>T Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*823T>A Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*921A>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • c.*947T>G Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Ala2Glu Single submitter ⚠
  • p.Ala377Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala409Ser Single submitter ⚠
  • p.Ala496Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala4Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala560Pro Single submitter rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Ala5Val Single submitter rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Ala70Thr Single submitter ⚠
  • p.Arg27Pro Single submitter Inborn genetic diseases ⚠
  • p.Arg27Trp Single submitter ⚠
  • p.Arg317Cys Single submitter ⚠
  • p.Arg39Trp Single submitter ⚠
  • p.Arg419Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg503Gly Single submitter Inborn genetic diseases ⚠
  • p.Asn151Tyr Single submitter rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Asn461Ser Single submitter ⚠
  • p.Asn56Asp Single submitter ⚠
  • p.Asn609Ser Single submitter ⚠
  • p.Asp24Val Single submitter ⚠
  • p.Asp26Val Single submitter ⚠
  • p.Asp30Val Single submitter ⚠
  • p.Asp32Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp473Gly Single submitter ⚠
  • p.Asp535Glu Single submitter Inborn genetic diseases ⚠
  • p.Cys247Phe Single submitter ⚠
  • p.Cys413Tyr Single submitter ⚠
  • p.Gln290= Single submitter rhizomelic chondrodysplasia punctata
  • p.Gln479Arg Single submitter ⚠
  • p.Gln558Pro Single submitter Inborn genetic diseases ⚠
  • p.Gln597Glu Single submitter Inborn genetic diseases ⚠
  • p.Glu170Val Single submitter Inborn genetic diseases ⚠
  • p.Glu3Lys Single submitter ⚠
  • p.Glu51Gly Single submitter Inborn genetic diseases ⚠
  • p.Glu605Asp Single submitter ⚠
  • p.Gly124Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly12Arg Single submitter ⚠
  • p.Gly238Arg Single submitter ⚠
  • p.Gly299Ser Single submitter ⚠
  • p.Gly446Arg Single submitter ⚠
  • p.Gly81Ala Single submitter Inborn genetic diseases ⚠
  • p.His142Arg Single submitter ⚠
  • p.His277Asn Single submitter Inborn genetic diseases ⚠
  • p.His430Pro Single submitter Inborn genetic diseases ⚠
  • p.Ile235Val Single submitter ⚠
  • p.Ile379Val Single submitter rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Ile381Val Single submitter ⚠
  • p.Ile418Leu Single submitter Inborn genetic diseases ⚠
  • p.Ile588Leu Single submitter Inborn genetic diseases ⚠
  • p.Ile631Val Single submitter Inborn genetic diseases ⚠
  • p.Leu150Ter Single submitter
  • p.Leu258= Single submitter rhizomelic chondrodysplasia punctata type 3
  • p.Leu447Phe Single submitter ⚠
  • p.Lys227Arg Single submitter ⚠
  • p.Lys410Arg Single submitter ⚠
  • p.Lys555Thr Single submitter Inborn genetic diseases ⚠
  • p.Lys85Glu Single submitter Inborn genetic diseases ⚠
  • p.Met201Thr Single submitter Inborn genetic diseases ⚠
  • p.Met263Leu Single submitter Inborn genetic diseases ⚠
  • p.Phe202Leu Single submitter Inborn genetic diseases ⚠
  • p.Phe443Ile Single submitter Inborn genetic diseases ⚠
  • p.Pro49Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro533Thr Single submitter rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Pro75Ala Single submitter Inborn genetic diseases ⚠
  • p.Ser153Arg Single submitter ⚠
  • p.Ser54Cys Single submitter ⚠
  • p.Ser65Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser80Leu Single submitter Inborn genetic diseases ⚠
  • p.Thr135Asn Single submitter Inborn genetic diseases ⚠
  • p.Thr135Ile Single submitter ⚠
  • p.Thr171Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr252Arg Single submitter Inborn genetic diseases ⚠
  • p.Thr283Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr549Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr82Ser Single submitter Inborn genetic diseases ⚠
  • p.Tyr296His Single submitter Inborn genetic diseases ⚠
  • p.Tyr485Cys Single submitter Inborn genetic diseases ⚠
  • p.Tyr505Asp Single submitter Inborn genetic diseases ⚠
  • p.Tyr522Cys Single submitter Inborn genetic diseases ⚠
  • p.Tyr571Ser Single submitter ⚠
  • p.Val219Phe Single submitter Inborn genetic diseases ⚠
  • p.Val484Glu Single submitter Inborn genetic diseases ⚠
  • c.1856-6T>C No assertion criteria rhizomelic chondrodysplasia punctata type 3
  • c.710-3C>T No assertion criteria rhizomelic chondrodysplasia punctata type 3
  • c.996+9T>C No assertion criteria rhizomelic chondrodysplasia punctata type 3
  • p.Ala318Thr No assertion criteria rhizomelic chondrodysplasia punctata ⚠
  • p.Ala67Val No assertion criteria rhizomelic chondrodysplasia punctata ⚠
  • p.Asp167Asn No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Asp180Gly No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Asp459Gly No assertion criteria rhizomelic chondrodysplasia punctata ⚠
  • p.Gln435Glu No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Gln479Glu No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Gln625Pro No assertion criteria rhizomelic chondrodysplasia punctata ⚠
  • p.Glu141Gly No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.His215= No assertion criteria rhizomelic chondrodysplasia punctata type 3
  • p.His617Pro No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Ile111Thr No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Ile194Met No assertion criteria rhizomelic chondrodysplasia punctata ⚠
  • p.Ile325Met No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Leu305Pro No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Phe103Leu No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Thr213= No assertion criteria rhizomelic chondrodysplasia punctata type 3
  • p.Thr254Pro No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Thr370Ile No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Thr549del No assertion criteria rhizomelic chondrodysplasia punctata type 3
  • p.Val314Ile No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠
  • p.Val567Ala No assertion criteria rhizomelic chondrodysplasia punctata type 3 ⚠