Sugi Variant

Sugi Variant/CUX1

CUX1 — 559 ClinVar variants

All ClinVar germline CUX1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 306 flagged for review →

20 Pathogenic · 6 Pathogenic/Likely pathogenic · 27 Likely pathogenic · 13 Conflicting · 24 Benign · 3 Benign/Likely benign · 115 Likely benign · 351 Uncertain significance

Full CUX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 306

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 5

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

Predicted LoF vs a conflicting call 3

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 193

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 193

Predictors split 105

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

All CUX1 variants

Pathogenic 20

  • p.Pro431fs Multiple submitters global developmental delay with or without impaired intellectual development
  • c.190-2A>G Single submitter global developmental delay with or without impaired intellectual development
  • c.3655+190_*301del Single submitter Inborn genetic diseases
  • p.Arg984Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Gln116Ter Single submitter Inborn genetic diseases
  • p.Gln1186Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Gln1241Ter Single submitter
  • p.Gln156Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Gln180Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Gln433Ter Single submitter Inborn genetic diseases
  • p.Gln520Ter Single submitter Inborn genetic diseases
  • p.Gln563Ter Single submitter neurodevelopmental disorder
  • p.Gln612Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Gln685Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Leu292Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Lys1068fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Met532fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Pro430fs Single submitter Inborn genetic diseases
  • p.Thr619fs Single submitter
  • p.Trp1188Ter Single submitter global developmental delay with or without impaired intellectual development

Pathogenic/Likely pathogenic 6

  • c.1681-1G>A Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Ala1056fs Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Arg661Ter Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Gln862Ter Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Glu866Ter Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Ser526fs Multiple submitters neurodevelopmental disorder

Likely pathogenic 27

  • c.1451-2A>G Multiple submitters global developmental delay with or without impaired intellectual development
  • c.268+1G>A Single submitter Inborn genetic diseases
  • c.2908-1G>T Single submitter CUX1-related disorder
  • c.530+1G>A Single submitter global developmental delay with or without impaired intellectual development
  • c.675-2A>G Single submitter global developmental delay with or without impaired intellectual development
  • p.Ala1415fs Single submitter Inborn genetic diseases
  • p.Ala957fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Arg1167fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Arg254Ser Single submitter global developmental delay with or without impaired intellectual development ⚠
  • p.Arg996Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Gln21Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Gln348Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Gln789fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Glu318Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Glu353fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Gly439fs Single submitter
  • p.Gly6Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Leu1251fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Leu605fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Lys566Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Lys785Ter Single submitter
  • p.Pro1057fs Single submitter
  • p.Trp879Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Tyr1263fs Single submitter global developmental delay with or without impaired intellectual development
  • p.Tyr1295Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Tyr594Ter Single submitter global developmental delay with or without impaired intellectual development
  • p.Tyr938fs Single submitter CUX1-related disorder

Conflicting classifications of pathogenicity 13

  • c.1961-1G>A Single submitter global developmental delay with or without impaired intellectual development ⚠
  • c.63+1G>A Single submitter global developmental delay with or without impaired intellectual development ⚠
  • p.Ala1433Gly Single submitter global developmental delay with or without impaired intellectual development ⚠
  • p.Arg1261Ter Single submitter global developmental delay with or without impaired intellectual development ⚠
  • p.Arg467His Single submitter global developmental delay with or without impaired intellectual development
  • p.Asn701Lys Single submitter global developmental delay with or without impaired intellectual development ⚠
  • p.Asp1385Asn Single submitter global developmental delay with or without impaired intellectual development ⚠
  • p.Gly1394Asp Single submitter Inborn genetic diseases ⚠
  • p.Gly858Arg Single submitter Inborn genetic diseases ⚠
  • p.Met497Thr Single submitter global developmental delay with or without impaired intellectual development ⚠
  • p.Pro1095Leu Single submitter Inborn genetic diseases ⚠
  • p.Thr1344Ile Single submitter global developmental delay with or without impaired intellectual development ⚠
  • p.Val545Ile Single submitter Inborn genetic diseases ⚠

Benign 24

  • c.190-29T>C Multiple submitters global developmental delay with or without impaired intellectual development
  • c.269-34C>A Multiple submitters global developmental delay with or without impaired intellectual development
  • c.269-38T>G Multiple submitters global developmental delay with or without impaired intellectual development
  • c.2907+10C>A Multiple submitters
  • c.607+6A>G Multiple submitters global developmental delay with or without impaired intellectual development
  • c.674+11C>T Multiple submitters global developmental delay with or without impaired intellectual development
  • c.674+31G>A Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Ala464Thr Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Glu1360Lys Multiple submitters ⚠
  • p.Pro1439= Multiple submitters
  • p.Pro368= Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Pro758= Multiple submitters global developmental delay with or without impaired intellectual development
  • p.Ser1066= Multiple submitters
  • p.Thr138= Multiple submitters
  • c.1681-12dup Single submitter global developmental delay with or without impaired intellectual development
  • c.3073+8G>A Single submitter
  • c.3887+4C>T Single submitter
  • p.Glu576Lys Single submitter
  • p.Pro1463= Single submitter
  • p.Pro1475= Single submitter
  • p.Thr1285= Single submitter
  • c.141+8G>A No assertion criteria CUX1-related disorder
  • p.Glu716= No assertion criteria CUX1-related disorder
  • p.Gly859_Gly860insSerGlyGly No assertion criteria CUX1-related disorder

Benign/Likely benign 3

Likely benign 115

Uncertain significance 351

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