Sugi Variant

Sugi Variant/ARFGEF1

ARFGEF1 — 440 ClinVar variants

All ClinVar germline ARFGEF1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 293 flagged for review →

34 Pathogenic · 2 Pathogenic/Likely pathogenic · 30 Likely pathogenic · 2 Conflicting · 11 Benign · 2 Benign/Likely benign · 42 Likely benign · 317 Uncertain significance

Full ARFGEF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 293

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 1

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 207

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 207

Predictors split 84

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

All ARFGEF1 variants

Pathogenic 34

  • p.Arg1272Ter Multiple submitters developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Arg1345Ter Multiple submitters intellectual disability
  • p.Arg1543Ter Multiple submitters Inborn genetic diseases
  • p.Arg1774Ter Multiple submitters developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Arg799Ter Multiple submitters intellectual disability
  • c.1922-2A>G Single submitter
  • c.3289+1G>A Single submitter
  • c.3592-2A>G Single submitter Global developmental delay
  • c.4959+1G>T Single submitter
  • p.Arg1074Ter Single submitter
  • p.Arg1186Ter Single submitter Inborn genetic diseases
  • p.Arg1376fs Single submitter
  • p.Asn474fs Single submitter Inborn genetic diseases
  • p.Cys976fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Gln1233Ter Single submitter intellectual disability
  • p.Gln1267Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Gln1611fs Single submitter
  • p.Gln1722Ter Single submitter Inborn genetic diseases
  • p.Gln212fs Single submitter Inborn genetic diseases
  • p.Gln648Ter Single submitter intellectual disability
  • p.Gln842Ter Single submitter Seizure
  • p.Ile164fs Single submitter
  • p.Leu720fs Single submitter intellectual disability
  • p.Lys414fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Met336fs Single submitter intellectual disability
  • p.Phe818fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Ser773fs Single submitter
  • p.Tyr109Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Tyr1415fs Single submitter
  • p.Tyr1671fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Val333fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Cys1455Ter No assertion criteria DEVELOPMENTAL DELAY, IMPAIRED SPEECH, BEHAVIORAL ABNORMALITIES, AND SEIZURES
  • p.Gln735Ter No assertion criteria
  • p.Ile1180Arg No assertion criteria developmental delay, impaired speech, and behavioral abnormalities, with or without seizures

Pathogenic/Likely pathogenic 2

  • p.Asp798Asn Multiple submitters developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Pro1553fs Multiple submitters developmental delay, impaired speech, and behavioral abnormalities, with or without seizures

Likely pathogenic 30

  • c.1028-2A>T Single submitter intellectual disability
  • c.1203+1G>T Single submitter neurodevelopmental disorder
  • c.1337+1G>C Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • c.2527-1G>A Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • c.2699-1G>T Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • c.2850+1G>A Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • c.2851-1G>T Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • c.3138+1G>A Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • c.4614-2A>G Single submitter Neurodevelopmental delay
  • c.5128+1G>A Single submitter Delayed ability to walk
  • p.Ala1695fs Single submitter Neurodevelopmental delay
  • p.Gln1020Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Gln1233fs Single submitter ARFGEF1-related disorder
  • p.Glu1449Ter Single submitter Neurodevelopmental delay
  • p.Glu802Asp Single submitter Inborn genetic diseases
  • p.Gly1061fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Gly1078Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Gly1178fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.His518Gln Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures ⚠
  • p.Leu1386_Phe1387insTer Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Leu425_Val426insTer Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Leu455fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Ser70Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Thr954fs Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Trp1382Ter Single submitter Neurodevelopmental delay
  • p.Tyr1068Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Tyr1419Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Val25Met Single submitter ⚠
  • p.Leu198Val No assertion criteria developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
  • p.Ser410Ter No assertion criteria ARFGEF1-related disorder

Conflicting classifications of pathogenicity 2

Benign 11

Benign/Likely benign 2

Likely benign 42

Uncertain significance 317

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