Sugi Variant

Sugi Variant/UPF3B

UPF3B — 353 ClinVar variants

All ClinVar germline UPF3B variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 126 flagged for review →

22 Pathogenic · 15 Likely pathogenic · 18 Conflicting · 43 Benign · 15 Benign/Likely benign · 104 Likely benign · 136 Uncertain significance

Full UPF3B gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 126

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 10

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

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 81

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

Predictors split 34

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

All UPF3B variants

Pathogenic 22

  • p.Arg225fs Multiple submitters UPF3B-related disorder
  • p.Arg233fs Multiple submitters syndromic X-linked intellectual disability 14
  • p.Glu230fs Multiple submitters Inborn genetic diseases
  • p.Arg229fs Single submitter
  • p.Arg242Ter Single submitter
  • p.Arg430Ter Single submitter syndromic X-linked intellectual disability 14
  • p.Arg451fs Single submitter syndromic X-linked intellectual disability 14
  • p.Asn206fs Single submitter UPF3B-related neurodevelopmental disorder
  • p.Asp148fs Single submitter syndromic X-linked intellectual disability 14
  • p.Glu191_Leu192insTer Single submitter syndromic X-linked intellectual disability 14
  • p.Glu216fs Single submitter syndromic X-linked intellectual disability 14
  • p.Glu224Ter Single submitter syndromic X-linked intellectual disability 14
  • p.Glu364fs Single submitter
  • p.Glu6Ter Single submitter Inborn genetic diseases
  • p.Lys384fs Single submitter
  • p.Lys389fs Single submitter syndromic X-linked intellectual disability 14
  • p.Met1fs Single submitter
  • p.Thr385_Phe386insTer Single submitter
  • p.Tyr94fs Single submitter syndromic X-linked intellectual disability 14
  • p.Val54fs Single submitter syndromic X-linked intellectual disability 14
  • p.Gly290fs No assertion criteria syndromic X-linked intellectual disability 14
  • p.Tyr160Asp No assertion criteria syndromic X-linked intellectual disability 14

Likely pathogenic 15

  • p.Arg13Ter Multiple submitters syndromic X-linked intellectual disability 14
  • p.Arg354Ter Multiple submitters intellectual disability
  • c.263+2_263+3insTAAAAAAAA Single submitter syndromic X-linked intellectual disability 14
  • c.624+2T>G Single submitter syndromic X-linked intellectual disability 14
  • p.Glu328Ter Single submitter syndromic X-linked intellectual disability 14
  • p.Glu347fs Single submitter UPF3B-related disorder
  • p.Glu383Ter Single submitter syndromic X-linked intellectual disability 14
  • p.Glu392Ter Single submitter
  • p.Glu423fs Single submitter
  • p.Glu424fs Single submitter
  • p.Lys306Ter Single submitter UPF3B-related disorder
  • p.Lys421fs Single submitter UPF3B-related disorder
  • p.Lys422fs Single submitter syndromic X-linked intellectual disability 14
  • p.Phe80fs Single submitter syndromic X-linked intellectual disability 14
  • p.Tyr90Ter Single submitter syndromic X-linked intellectual disability 14

Conflicting classifications of pathogenicity 18

Benign 43

Benign/Likely benign 15

  • c.1302+8T>C Multiple submitters syndromic X-linked intellectual disability 14
  • c.263+18del Multiple submitters syndromic X-linked intellectual disability 14
  • c.263+18dup Multiple submitters syndromic X-linked intellectual disability 14
  • c.263+7_263+18dup Multiple submitters syndromic X-linked intellectual disability 14
  • p.Arg358Cys Multiple submitters syndromic X-linked intellectual disability 14 ⚠
  • p.Arg358His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg373Cys Multiple submitters Inborn genetic diseases
  • p.Arg374Cys Multiple submitters Inborn genetic diseases
  • p.Arg401Trp Multiple submitters Inborn genetic diseases
  • p.Glu420= Multiple submitters Inborn genetic diseases
  • p.Gly31= Multiple submitters Inborn genetic diseases
  • p.Leu295= Multiple submitters Inborn genetic diseases
  • p.Lys35= Multiple submitters syndromic X-linked intellectual disability 14
  • p.Lys367Asn Multiple submitters syndromic X-linked intellectual disability 14 ⚠
  • p.Thr18Ile Multiple submitters syndromic X-linked intellectual disability 14

Likely benign 104

Uncertain significance 136