Sugi Variant

Sugi Variant/INTS1

INTS1 — 818 ClinVar variants

All ClinVar germline INTS1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 480 flagged for review →

11 Pathogenic · 17 Likely pathogenic · 14 Conflicting · 46 Benign · 16 Benign/Likely benign · 193 Likely benign · 521 Uncertain significance

Full INTS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 480

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 vs ClinVar 1

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 8

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

Predictors lean, ClinVar uncertain 355

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 355

Predictors split 116

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

All INTS1 variants

Pathogenic 11

  • p.Arg1645fs Single submitter
  • p.Arg1858Ter Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Arg264fs Single submitter Inborn genetic diseases
  • p.Cys643fs Single submitter
  • p.Leu733fs Single submitter Inborn genetic diseases
  • p.Tyr2127Ter Single submitter
  • p.Arg1800fs No assertion criteria neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Gln1961Ter No assertion criteria neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Met549Val No assertion criteria neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies ⚠
  • p.Pro1874Leu No assertion criteria neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Ser1784Ter No assertion criteria neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies

Likely pathogenic 17

  • c.3424_3429+20del Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.3430-2A>C Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Arg101Ter Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Glu182Ter Multiple submitters
  • c.1711+1G>A Single submitter Inborn genetic diseases
  • c.6184+1G>T Single submitter
  • c.-42+1G>C Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Arg801fs Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Gln1717Ter Single submitter
  • p.Gln513Ter Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Glu1926Ter Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Glu619Ter Single submitter
  • p.Leu71fs Single submitter
  • p.Lys803fs Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Met1013fs Single submitter Neurodevelopmental delay
  • p.Trp1028Ter Single submitter
  • p.Val180fs Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies

Conflicting classifications of pathogenicity 14

Benign 46

  • c.1832+18T>C Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.1911-19T>C Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.1911-9A>G Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.2165+15C>T Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.3703+7T>C Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.4074+7T>A Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.546+7G>A Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.950+14T>C Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Ala63= Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Gly1796= Multiple submitters
  • p.Leu649= Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Pro24= Multiple submitters neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • p.Pro378= Multiple submitters
  • c.1137+16G>T Single submitter
  • c.1138-51T>C Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.1602+57A>G Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.1833-64G>T Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.1910+27T>C Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.2319-94G>A Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.2976+80C>T Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.3430-6C>T Single submitter
  • c.3430-70A>G Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.350-47T>C Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.3703+25A>G Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.3950-6C>T Single submitter
  • c.4074+61G>C Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.4489+26C>T Single submitter neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies
  • c.5152-9C>A Single submitter
  • c.6185-15CT[2] Single submitter
  • p.Ala1111= Single submitter
  • p.Ala1181= Single submitter
  • p.Ala2095= Single submitter
  • p.Ala433= Single submitter
  • p.Ala555= Single submitter
  • p.Asp1773Asn Single submitter
  • p.His245= Single submitter
  • p.Ile442= Single submitter
  • p.Leu1978= Single submitter
  • p.Leu2063= Single submitter
  • p.Lys370Arg Single submitter
  • p.Ser1113= Single submitter
  • p.Ser452= Single submitter
  • p.Ser982= Single submitter
  • p.Thr1450= Single submitter
  • p.Tyr2050= Single submitter
  • p.Val1128Met No assertion criteria INTS1-related disorder

Benign/Likely benign 16

Likely benign 193

Uncertain significance 521

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