Sugi Variant

Sugi Variant/BMP4

BMP4 — 309 ClinVar variants

All ClinVar germline BMP4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 169 flagged for review →

7 Pathogenic · 15 Likely pathogenic · 26 Conflicting · 16 Benign · 9 Benign/Likely benign · 54 Likely benign · 182 Uncertain significance

Full BMP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 169

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 9

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

Predicted LoF vs a conflicting call 3

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 126

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

Predictors split 30

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

All BMP4 variants

Pathogenic 7

Likely pathogenic 15

  • p.Arg223fs Single submitter
  • p.Asn150fs Single submitter Autosomal dominant BMP4-related disorders
  • p.Asp201fs Single submitter microphthalmia with brain and digit anomalies
  • p.Asp85fs Single submitter microphthalmia with brain and digit anomalies
  • p.Cys373Tyr Single submitter Peters anomaly
  • p.Gln63fs Single submitter microphthalmia with brain and digit anomalies
  • p.His41fs Single submitter microphthalmia with brain and digit anomalies
  • p.Ile178Arg Single submitter microphthalmia with brain and digit anomalies
  • p.Leu54fs Single submitter
  • p.Met83fs Single submitter
  • p.Thr116_Val117insTer Single submitter Stickler syndrome
  • p.Trp212Ter Single submitter
  • p.Trp325Ter Single submitter
  • c.371-2A>G No assertion criteria microphthalmia with brain and digit anomalies
  • p.Arg109fs No assertion criteria microphthalmia with brain and digit anomalies

Conflicting classifications of pathogenicity 26

Benign 16

Benign/Likely benign 9

  • c.370+28G>A Multiple submitters microphthalmia with brain and digit anomalies
  • c.*148A>T Multiple submitters orofacial cleft 11
  • c.*88C>T Multiple submitters orofacial cleft 11
  • p.Arg287His Multiple submitters orofacial cleft 11
  • p.Ser76Arg Multiple submitters microphthalmia with brain and digit anomalies
  • p.Val152Ala Multiple submitters orofacial cleft 11
  • c.-155G>A Single submitter microphthalmia with brain and digit anomalies
  • c.*251C>T Single submitter orofacial cleft 11
  • c.*28A>T Single submitter microphthalmia with brain and digit anomalies

Likely benign 54

  • c.371-24C>T Multiple submitters
  • p.Arg84= Multiple submitters microphthalmia with brain and digit anomalies
  • p.Gly31= Multiple submitters microphthalmia with brain and digit anomalies
  • p.Ile254= Multiple submitters microphthalmia with brain and digit anomalies
  • p.Val205= Multiple submitters microphthalmia with brain and digit anomalies
  • c.370+12C>G Single submitter microphthalmia with brain and digit anomalies
  • c.370+19T>C Single submitter orofacial cleft 11
  • c.370+20C>T Single submitter microphthalmia with brain and digit anomalies
  • c.-87C>T Single submitter
  • c.*148del Single submitter
  • c.*4C>G Single submitter microphthalmia with brain and digit anomalies
  • p.Ala111= Single submitter
  • p.Ala21= Single submitter microphthalmia with brain and digit anomalies
  • p.Ala36= Single submitter microphthalmia with brain and digit anomalies
  • p.Ala77= Single submitter microphthalmia with brain and digit anomalies
  • p.Arg173= Single submitter microphthalmia with brain and digit anomalies
  • p.Arg269Gln Single submitter microphthalmia with brain and digit anomalies
  • p.Arg55= Single submitter orofacial cleft 11
  • p.Asn208= Single submitter microphthalmia with brain and digit anomalies
  • p.Asp170= Single submitter orofacial cleft 11
  • p.Asp319= Single submitter microphthalmia with brain and digit anomalies
  • p.Asp56= Single submitter microphthalmia with brain and digit anomalies
  • p.Glu105= Single submitter orofacial cleft 11
  • p.Glu403= Single submitter microphthalmia with brain and digit anomalies
  • p.Glu93Gly Single submitter microphthalmia with brain and digit anomalies
  • p.Gly103= Single submitter microphthalmia with brain and digit anomalies
  • p.Gly40Asp Single submitter Inborn genetic diseases
  • p.His194= Single submitter
  • p.His41= Single submitter orofacial cleft 11
  • p.Leu17= Single submitter
  • p.Leu222= Single submitter microphthalmia with brain and digit anomalies
  • p.Leu271= Single submitter microphthalmia with brain and digit anomalies
  • p.Leu53= Single submitter microphthalmia with brain and digit anomalies
  • p.Leu8= Single submitter orofacial cleft 11
  • p.Phe142= Single submitter
  • p.Phe161= Single submitter orofacial cleft 11
  • p.Pro110= Single submitter
  • p.Pro270= Single submitter microphthalmia with brain and digit anomalies
  • p.Pro344= Single submitter orofacial cleft 11
  • p.Pro80= Single submitter microphthalmia with brain and digit anomalies
  • p.Ser119= Single submitter microphthalmia with brain and digit anomalies
  • p.Ser155= Single submitter orofacial cleft 11
  • p.Ser318= Single submitter microphthalmia with brain and digit anomalies
  • p.Thr116= Single submitter microphthalmia with brain and digit anomalies
  • p.Thr132Ala Single submitter microphthalmia with brain and digit anomalies
  • p.Thr244Ile Single submitter microphthalmia with brain and digit anomalies
  • p.Thr60= Single submitter microphthalmia with brain and digit anomalies
  • p.Val10= Single submitter
  • p.Val191= Single submitter
  • p.Val393= Single submitter microphthalmia with brain and digit anomalies
  • c.-335G>C No assertion criteria BMP4-related disorder
  • p.Pro342= No assertion criteria BMP4-related disorder
  • p.Tyr314= No assertion criteria BMP4-related disorder
  • p.Val392= No assertion criteria BMP4-related disorder

Uncertain significance 182