Sugi Variant

Sugi Variant/GMPPA

GMPPA — 181 ClinVar variants

All ClinVar germline GMPPA variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 76 flagged for review →

10 Pathogenic · 4 Pathogenic/Likely pathogenic · 3 Likely pathogenic · 4 Conflicting · 12 Benign · 8 Benign/Likely benign · 63 Likely benign · 77 Uncertain significance

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

⚑ Evidence disagreements 76

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 3

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

Predictors lean, ClinVar uncertain 53

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

Predictors split 19

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

All GMPPA variants

Pathogenic 10

  • p.Ala71fs Multiple submitters chromosomal instability with tissue-specific radiosensitivity
  • p.Pro193fs Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • c.243-1G>C Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.853+1G>A Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.His40fs Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.429+1G>A No assertion criteria
  • p.Arg99Ter No assertion criteria alacrima, achalasia, and intellectual disability syndrome
  • p.Ser373Thr No assertion criteria alacrima, achalasia, and intellectual disability syndrome ⚠
  • p.Thr334Pro No assertion criteria alacrima, achalasia, and intellectual disability syndrome
  • p.Trp214Ter No assertion criteria alacrima, achalasia, and intellectual disability syndrome

Pathogenic/Likely pathogenic 4

  • p.Arg264Ter Multiple submitters GMPPA-related disorder
  • p.Arg366Ter Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Gln67Ter Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Trp214fs Multiple submitters alacrima, achalasia, and intellectual disability syndrome

Likely pathogenic 3

  • c.138+1G>T Single submitter
  • p.Gln199Ter Single submitter GMPPA-related disorder
  • p.Glu128Ter Single submitter alacrima, achalasia, and intellectual disability syndrome

Conflicting classifications of pathogenicity 4

  • p.Ala72Thr Single submitter alacrima, achalasia, and intellectual disability syndrome ⚠
  • p.Gly182Asp Single submitter alacrima, achalasia, and intellectual disability syndrome ⚠
  • p.His162Gln Single submitter alacrima, achalasia, and intellectual disability syndrome ⚠
  • p.Phe198Leu Single submitter Inborn genetic diseases ⚠

Benign 12

Benign/Likely benign 8

  • c.40+15G>A Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • c.489+16G>A Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Ala71= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Leu165= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Pro122= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Pro64Ser Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Thr147= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Tyr256= Multiple submitters alacrima, achalasia, and intellectual disability syndrome

Likely benign 63

  • c.40+13G>A Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • c.40+20G>A Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • c.430-36A>G Multiple submitters
  • c.430-78C>T Multiple submitters
  • c.756-10C>T Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • c.854-23C>T Multiple submitters
  • c.994-70A>G Multiple submitters
  • p.Ala115= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Asn286= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Asp100= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Ile307= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Lys379Asn Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Pro291= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Ser250= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • p.Thr292= Multiple submitters alacrima, achalasia, and intellectual disability syndrome
  • c.1162+17G>T Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.138+8C>T Single submitter
  • c.138+9_138+10del Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.242+25G>C Single submitter
  • c.243-13T>A Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.243-17C>T Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.243-4A>G Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.41-16C>T Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.429+114C>T Single submitter
  • c.489+19C>T Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.490-16C>A Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.490-18A>G Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.490-6C>T Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.621-9C>T Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.755+17C>T Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.756-18C>A Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.853+18A>G Single submitter
  • c.854-20G>C Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.900+7A>G Single submitter alacrima, achalasia, and intellectual disability syndrome
  • c.901-10C>T Single submitter
  • c.-21+303T>C Single submitter
  • p.Ala395= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Ala4= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Arg132= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Arg132His Single submitter Inborn genetic diseases
  • p.Arg272= Single submitter
  • p.Arg318= Single submitter
  • p.Arg352= Single submitter
  • p.Asn363= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.His162= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.His276= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.His39= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Ile323= Single submitter
  • p.Leu191= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Phe22= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Ser106Gly Single submitter Inborn genetic diseases
  • p.Ser149= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Ser172= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Ser187= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Ser210= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Ser298= Single submitter
  • p.Ser402= Single submitter
  • p.Tyr261= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Tyr288= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Val112= Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Val156Ile Single submitter alacrima, achalasia, and intellectual disability syndrome
  • p.Val24= Single submitter
  • p.Val391= Single submitter alacrima, achalasia, and intellectual disability syndrome

Uncertain significance 77