Sugi Variant

Sugi Variant/BMP2

BMP2 — 253 ClinVar variants

All ClinVar germline BMP2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 141 flagged for review →

15 Pathogenic · 6 Pathogenic/Likely pathogenic · 18 Likely pathogenic · 6 Conflicting · 8 Benign · 1 Benign/Likely benign · 48 Likely benign · 151 Uncertain significance

Full BMP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 141

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 113

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

Predictors split 24

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

All BMP2 variants

Pathogenic 15

  • p.Tyr78fs Multiple submitters short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • c.346+2T>C Single submitter
  • p.Arg298Ter Single submitter
  • p.Arg66fs Single submitter
  • p.Gln15Ter Single submitter
  • p.Gln252Ter Single submitter
  • p.Glu205Ter Single submitter brachydactyly type A2
  • p.Glu280fs Single submitter
  • p.Glu48Ter Single submitter
  • p.Val74fs Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies
  • c.-7-2_-7-1delinsCC No assertion criteria short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Glu328Lys No assertion criteria ventricular septal defect 1 ⚠
  • p.His321Leu No assertion criteria dextro-looped transposition of the great arteries ⚠
  • p.Ser351Cys No assertion criteria atrial septal defect 1
  • p.Tyr320fs No assertion criteria short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1

Pathogenic/Likely pathogenic 6

  • p.Arg154Ter Multiple submitters BMP2-related disorder
  • p.Arg170Ter Multiple submitters short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Asn135fs Multiple submitters short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Gln89Ter Multiple submitters BMP2-related disorder
  • p.Glu229Ter Multiple submitters
  • p.Ser92Ter Multiple submitters short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1

Likely pathogenic 18

  • p.Cys329Ter Multiple submitters short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies
  • c.346+1G>C Single submitter BMP2-related disorder
  • p.Ala212fs Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Ala343fs Single submitter BMP2-related disorder
  • p.Glu205fs Single submitter
  • p.Glu27Ter Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies
  • p.His274fs Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Pro363Leu Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Ser42Ter Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Ter397Ser Single submitter Inborn genetic diseases
  • p.Ter397Tyr Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Thr141fs Single submitter BMP2-related disorder
  • p.Trp204Ter Single submitter BMP2-related disorder
  • p.Trp216Ter Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Trp313Ter Single submitter short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies
  • p.Tyr320Ter Single submitter Inborn genetic diseases
  • p.Arg282fs No assertion criteria short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
  • p.Val109fs No assertion criteria BMP2-related disorder

Conflicting classifications of pathogenicity 6

Benign 8

  • c.*244A>C Multiple submitters
  • c.*465T>C Multiple submitters
  • p.Arg190Ser Multiple submitters short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies
  • p.Asp387= Multiple submitters
  • p.Ser37Ala Multiple submitters ventricular septal defect 1
  • p.Ser87= Multiple submitters short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies
  • c.346+197A>G Single submitter
  • c.*23AT[9] Single submitter

Benign/Likely benign 1

Likely benign 48

Uncertain significance 151