VPS33B — 590 ClinVar variants

All ClinVar germline VPS33B variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 194 flagged for review →

28 Pathogenic · 7 Pathogenic/Likely pathogenic · 26 Likely pathogenic · 24 Conflicting · 61 Benign · 19 Benign/Likely benign · 170 Likely benign · 255 Uncertain significance

Full VPS33B gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 194

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 4

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

Predictors lean, ClinVar uncertain 139

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

Predictors split 51

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

All VPS33B variants

Pathogenic 28

  • c.403+2T>A Multiple submitters cholestasis, progressive familial intrahepatic, 12
  • p.Arg416Ter Multiple submitters keratoderma-ichthyosis-deafness syndrome, autosomal recessive
  • p.Arg438Ter Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Arg507Ter Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Arg51Ter Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Arg523Ter Multiple submitters cholestasis, progressive familial intrahepatic, 12
  • p.Leu81fs Multiple submitters cholestasis, progressive familial intrahepatic, 12
  • p.Lys504fs Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Pro117fs Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Pro412fs Multiple submitters cholestasis, progressive familial intrahepatic, 12
  • p.Tyr28Ter Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • c.1106-35_1106-7delinsGGT Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.1479+1G>A Single submitter
  • c.290-2_291del Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.778+2T>G Single submitter
  • c.940-2A>G Single submitter
  • p.Arg23Ter Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Arg532Ter Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Asp450fs Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Glu539fs Single submitter
  • p.Leu278fs Single submitter Inborn genetic diseases
  • p.Leu584Pro Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Trp172Ter Single submitter
  • c.240-577_290-156del No assertion criteria arthrogryposis, renal dysfunction, and cholestasis 1
  • c.700+1G>A No assertion criteria arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Cys576Arg No assertion criteria cholestasis, progressive familial intrahepatic, 12
  • p.Gln421fs No assertion criteria arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Leu30Pro No assertion criteria arthrogryposis, renal dysfunction, and cholestasis 1

Pathogenic/Likely pathogenic 7

  • c.1225+5G>C Multiple submitters Inborn genetic diseases
  • c.239+5G>A Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • c.240-1G>C Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Arg107Ter Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Arg542fs Multiple submitters keratoderma-ichthyosis-deafness syndrome, autosomal recessive
  • p.Arg93Ter Multiple submitters Autosomal recessive VPS33B-related disorders
  • p.Glu500Ter Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1

Likely pathogenic 26

  • c.1030+1G>A Multiple submitters cholestasis, progressive familial intrahepatic, 12
  • c.1106-2A>C Single submitter Inborn genetic diseases
  • c.1480-1G>T Single submitter cholestasis, progressive familial intrahepatic, 12
  • c.1609_1657+9del Single submitter
  • c.177+1G>A Single submitter cholestasis, progressive familial intrahepatic, 12
  • c.290-1G>A Single submitter cholestasis, progressive familial intrahepatic, 12
  • c.290-1G>C Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.357+1G>A Single submitter VPS33B-related disorder
  • c.701-1G>A Single submitter
  • c.778+1G>T Single submitter cholestasis, progressive familial intrahepatic, 12
  • c.853-1G>C Single submitter cholestasis, progressive familial intrahepatic, 12
  • c.96+1G>T Single submitter
  • p.Arg585fs Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Glu224fs Single submitter cholestasis, progressive familial intrahepatic, 12
  • p.Gly131Glu Single submitter keratoderma-ichthyosis-deafness syndrome, autosomal recessive
  • p.Leu153del Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Lys201fs Single submitter cholestasis, progressive familial intrahepatic, 12
  • p.Lys413fs Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Pro428fs Single submitter cholestasis, progressive familial intrahepatic, 12
  • p.Trp534Ter Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Tyr187fs Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.1480-1G>A No assertion criteria VPS33B-related disorder
  • p.Leu166= No assertion criteria arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Phe298fs No assertion criteria VPS33B-related disorder
  • p.Ser488fs No assertion criteria VPS33B-related disorder
  • p.Trp207Ter No assertion criteria arthrogryposis, renal dysfunction, and cholestasis 1

Conflicting classifications of pathogenicity 24

  • c.1105+10G>A Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.1170+5G>A Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.1171-6A>G Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.1658-7C>T Single submitter
  • c.1775-14A>G Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.240-9C>T Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • c.498+4A>G Single submitter keratoderma-ichthyosis-deafness syndrome, autosomal recessive
  • p.Ala454= Single submitter
  • p.Ala583= Single submitter
  • p.Ala617= Single submitter
  • p.Arg315Gln Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Arg594Gly Single submitter arthrogryposis, renal dysfunction, and cholestasis 1 ⚠
  • p.Asn296= Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Asp135Asn Single submitter keratoderma-ichthyosis-deafness syndrome, autosomal recessive
  • p.Gln25= Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.His227Arg Single submitter arthrogryposis, renal dysfunction, and cholestasis 1 ⚠
  • p.Ile383Thr Single submitter arthrogryposis, renal dysfunction, and cholestasis 1 ⚠
  • p.Leu152= Single submitter
  • p.Leu403= Single submitter
  • p.Leu462= Single submitter arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Leu66= Single submitter
  • p.Phe572Val Single submitter ⚠
  • p.Ser425Asn Single submitter cholestasis, progressive familial intrahepatic, 12 ⚠
  • p.Ser97Asn Single submitter Inborn genetic diseases ⚠

Benign 61

Benign/Likely benign 19

  • c.1405+36G>A Multiple submitters
  • c.1406-20G>C Multiple submitters
  • c.1480-20G>A Multiple submitters
  • c.240-13_240-12del Multiple submitters
  • c.289+18C>G Multiple submitters
  • c.604-14T>C Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • c.779-17T>A Multiple submitters
  • c.852+13G>A Multiple submitters
  • c.-7C>G Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • c.-8C>T Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • c.*16G>C Multiple submitters
  • p.Ala281Gly Multiple submitters
  • p.Arg389Gln Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Arg51= Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Leu567= Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Lys119= Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Thr444= Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1
  • p.Thr464= Multiple submitters
  • p.Tyr121= Multiple submitters arthrogryposis, renal dysfunction, and cholestasis 1

Likely benign 170

Uncertain significance 255