VDR — 549 ClinVar variants

All ClinVar germline VDR variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 157 flagged for review →

24 Pathogenic · 2 Pathogenic/Likely pathogenic · 13 Likely pathogenic · 31 Conflicting · 35 Benign · 2 Benign/Likely benign · 221 Likely benign · 221 Uncertain significance

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

⚑ Evidence disagreements 157

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 13

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

Predictors lean, ClinVar uncertain 96

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

Predictors split 48

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

All VDR variants

Pathogenic 24

  • p.Arg30Ter Multiple submitters vitamin D-dependent rickets, type 2A
  • p.Arg391His Multiple submitters vitamin D-dependent rickets, type 2A
  • p.Arg50Ter Multiple submitters vitamin D-dependent rickets, type 2A
  • p.Arg73Ter Multiple submitters vitamin D-dependent rickets, type 2A
  • p.Tyr295Ter Multiple submitters vitamin D-dependent rickets, type 2A
  • c.755+1G>C Single submitter
  • p.Arg391Cys Single submitter vitamin D-dependent rickets, type 2A
  • p.Asn394_Ter428delinsXaa Single submitter
  • p.Cys84fs Single submitter
  • p.Gln347Ter Single submitter
  • p.Glu112Ter Single submitter
  • p.Ser187Ter Single submitter
  • p.Ser278fs Single submitter
  • p.Trp286Arg Single submitter vitamin D-dependent rickets, type 2A
  • p.Arg274Leu No assertion criteria vitamin D-dependent rickets, type 2A
  • p.Arg391Ser No assertion criteria vitamin D-dependent rickets, type 2A
  • p.Arg50Gln No assertion criteria vitamin D-dependent rickets, type 2A
  • p.Gln152Ter No assertion criteria vitamin D-dependent rickets, type 2A
  • p.Glu329Lys No assertion criteria vitamin D-dependent rickets, type 2A
  • p.Gly33Asp No assertion criteria vitamin D-dependent rickets, type 2A
  • p.Gly46Asp No assertion criteria vitamin D-dependent rickets, type 2A
  • p.His305Gln No assertion criteria vitamin D-dependent rickets, type 2A
  • p.His397Pro No assertion criteria vitamin D-dependent rickets, type 2A
  • p.Lys123fs No assertion criteria vitamin D-dependent rickets, type 2A

Pathogenic/Likely pathogenic 2

  • p.Arg274His Multiple submitters rickets
  • p.Arg73Gln Multiple submitters vitamin D-dependent rickets, type 2A

Likely pathogenic 13

  • p.Arg343Cys Multiple submitters vitamin D-dependent rickets, type 2A
  • p.Val346Met Multiple submitters vitamin D-dependent rickets, type 2A
  • c.1024+1G>A Single submitter vitamin D-dependent rickets, type 2A
  • c.146+1G>T Single submitter vitamin D-dependent rickets, type 2A
  • c.907+1G>C Single submitter
  • c.-2-1G>A Single submitter vitamin D-dependent rickets, type 2A
  • c.-45A>G Single submitter vitamin D-dependent rickets, type 2A
  • p.Arg80Trp Single submitter
  • p.Gln385Ter Single submitter vitamin D-dependent rickets, type 2A
  • p.Glu127Ter Single submitter vitamin D-dependent rickets, type 2A
  • p.Gly304Arg Single submitter
  • p.Leu313fs Single submitter vitamin D-dependent rickets, type 2A
  • p.Val26Met Single submitter

Conflicting classifications of pathogenicity 31

  • c.1025-49G>T Single submitter vitamin D-dependent rickets, type 2A
  • c.146+9dup Single submitter
  • c.278-5C>T Single submitter vitamin D-dependent rickets, type 2A
  • c.755+13T>C Single submitter vitamin D-dependent rickets, type 2A
  • c.908-14A>G Single submitter vitamin D-dependent rickets, type 2A
  • c.*184T>G Single submitter vitamin D-dependent rickets, type 2A
  • c.*222G>C Single submitter vitamin D-dependent rickets, type 2A
  • p.Ala303= Single submitter vitamin D-dependent rickets, type 2A
  • p.Ala350Thr Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Arg173Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg18Trp Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Arg22Trp Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Arg358His Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Arg80Gln Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Asn290Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn324= Single submitter vitamin D-dependent rickets, type 2A
  • p.Gln259Glu Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Glu311= Single submitter vitamin D-dependent rickets, type 2A
  • p.Glu329Gln Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.His377= Single submitter vitamin D-dependent rickets, type 2A
  • p.Ile268Thr Single submitter familial adenomatous polyposis 2 ⚠
  • p.Ile384= Single submitter vitamin D-dependent rickets, type 2A
  • p.Met52Ile Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Thr192Ser Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Thr362Ile Single submitter vitamin D-dependent rickets, type 2A ⚠
  • p.Thr365= Single submitter vitamin D-dependent rickets, type 2A
  • p.Thr59Ile Single submitter ⚠
  • p.Tyr143= Single submitter vitamin D-dependent rickets, type 2A
  • p.Tyr366= Single submitter vitamin D-dependent rickets, type 2A
  • p.Val297Ile Single submitter Inborn genetic diseases ⚠
  • p.Val339Ala Single submitter vitamin D-dependent rickets, type 2A ⚠

Benign 35

Benign/Likely benign 2

  • p.Arg402= Multiple submitters vitamin D-dependent rickets, type 2A
  • p.Ser148= Multiple submitters vitamin D-dependent rickets, type 2A

Likely benign 221

Uncertain significance 221