Sugi Variant

Sugi Variant/PTBP1

PTBP1 — 100 ClinVar variants

All ClinVar germline PTBP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 54 flagged for review →

8 Pathogenic · 2 Conflicting · 8 Benign · 2 Benign/Likely benign · 14 Likely benign · 66 Uncertain significance

Full PTBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 54

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 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 40

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

Predictors split 11

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

All PTBP1 variants

Pathogenic 8

  • p.Met1Thr Multiple submitters PTBP1-related neurodevelopmental disorder with skeletal dysplasia
  • p.Arg14Gln Single submitter PTBP1-related neurodevelopmental disorder with skeletal dysplasia ⚠
  • p.Lys46Thr Single submitter PTBP1-related neurodevelopmental disorder with skeletal dysplasia
  • p.Lys48Asn Single submitter PTBP1-related neurodevelopmental disorder with skeletal dysplasia ⚠
  • p.Met1Arg Single submitter PTBP1-related neurodevelopmental disorder with skeletal dysplasia
  • p.Met1Ile Single submitter PTBP1-related neurodevelopmental disorder with skeletal dysplasia
  • p.Met1Leu Single submitter PTBP1-related neurodevelopmental disorder with skeletal dysplasia
  • p.Met1Lys Single submitter PTBP1-related neurodevelopmental disorder with skeletal dysplasia

Conflicting classifications of pathogenicity 2

  • p.Met1Val Single submitter PTBP1-related neurodevelopmental disorder with skeletal dysplasia ⚠
  • p.Val507Ile Single submitter ⚠

Benign 8

Benign/Likely benign 2

Likely benign 14

Uncertain significance 66