FGFR2 — 933 ClinVar variants

All ClinVar germline FGFR2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 317 flagged for review →

62 Pathogenic · 25 Pathogenic/Likely pathogenic · 40 Likely pathogenic · 54 Conflicting · 73 Benign · 37 Benign/Likely benign · 254 Likely benign · 388 Uncertain significance

Full FGFR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 317

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 3

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 23

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 212

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 212

Predictors split 78

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

All FGFR2 variants

Pathogenic 62

Pathogenic/Likely pathogenic 25

  • c.940-1G>A Multiple submitters FGFR2-related disorder
  • p.Ala314Ser Multiple submitters Pfeiffer syndrome ⚠
  • p.Ala337Pro Multiple submitters FGFR2-related disorder
  • p.Arg678Gly Multiple submitters FGFR2-related disorder
  • p.Asn549His Multiple submitters FGFR2-related disorder
  • p.Asp336Gly Multiple submitters Crouzon syndrome
  • p.Cys342Tyr Multiple submitters LADD syndrome 1
  • p.Glu565Ala Multiple submitters FGFR2-related disorder
  • p.Glu565Gly Multiple submitters FGFR2-related disorder
  • p.Gly271Val Multiple submitters FGFR2-related craniosynostosis
  • p.Gly338Glu Multiple submitters FGFR2-related craniosynostosis
  • p.Gly338Trp Multiple submitters Common craniosynostosis syndromes
  • p.Gly384Arg Multiple submitters FGFR2-related craniosynostosis
  • p.Ile288Asn Multiple submitters FGFR2-related craniosynostosis
  • p.Leu357Ser Multiple submitters Crouzon syndrome
  • p.Lys526Glu Multiple submitters FGFR2-related craniosynostosis
  • p.Lys641Arg Multiple submitters FGFR2-related disorder
  • p.Pro253Arg Multiple submitters FGFR2-related disorder
  • p.Ser347Cys Multiple submitters FGFR2-related disorder
  • p.Ser354Phe Multiple submitters FGFR2-related craniosynostosis
  • p.Tyr105Cys Multiple submitters FGFR2-related disorder
  • p.Tyr308Cys Multiple submitters Crouzon syndrome
  • p.Tyr328Cys Multiple submitters FGFR2-related disorder ⚠
  • p.Tyr340His Multiple submitters Common craniosynostosis syndromes
  • p.Tyr375Cys Multiple submitters FGFR2-related disorder

Likely pathogenic 40

Conflicting classifications of pathogenicity 54

Benign 73

Benign/Likely benign 37

  • c.1085-13A>T Multiple submitters FGFR2-related craniosynostosis
  • c.109+10T>G Multiple submitters craniosynostosis
  • c.110-54C>T Multiple submitters
  • c.1673-12C>T Multiple submitters FGFR2-related craniosynostosis
  • c.1986+7C>T Multiple submitters FGFR2-related craniosynostosis
  • c.2058-10T>C Multiple submitters FGFR2-related craniosynostosis
  • c.454+14C>T Multiple submitters Isolated Coronal Synostosis
  • c.939+11T>C Multiple submitters FGFR2-related craniosynostosis
  • c.-46G>A Multiple submitters Isolated Coronal Synostosis
  • c.-61G>T Multiple submitters Beare-Stevenson cutis gyrata syndrome
  • c.-74G>A Multiple submitters Beare-Stevenson cutis gyrata syndrome
  • c.*184C>T Multiple submitters craniosynostosis
  • c.*324A>G Multiple submitters Beare-Stevenson cutis gyrata syndrome
  • c.*403A>G Multiple submitters Beare-Stevenson cutis gyrata syndrome
  • p.Ala314= Multiple submitters FGFR2-related craniosynostosis
  • p.Ala53= Multiple submitters FGFR2-related craniosynostosis
  • p.Arg22Trp Multiple submitters Beare-Stevenson cutis gyrata syndrome
  • p.Arg6Pro Multiple submitters Beare-Stevenson cutis gyrata syndrome
  • p.Asp133= Multiple submitters FGFR2-related craniosynostosis
  • p.Glu596= Multiple submitters FGFR2-related craniosynostosis
  • p.His293= Multiple submitters Beare-Stevenson cutis gyrata syndrome
  • p.Leu776= Multiple submitters FGFR2-related craniosynostosis
  • p.Met186Thr Multiple submitters FGFR2-related craniosynostosis
  • p.Pro263= Multiple submitters FGFR2-related craniosynostosis
  • p.Pro744= Multiple submitters Apert syndrome
  • p.Ser57Leu Multiple submitters FGFR2-related craniosynostosis
  • p.Ser587= Multiple submitters Apert syndrome
  • p.Thr188= Multiple submitters FGFR2-related craniosynostosis
  • p.Thr513= Multiple submitters FGFR2-related craniosynostosis
  • p.Thr524= Multiple submitters FGFR2-related craniosynostosis
  • p.Thr98= Multiple submitters FGFR2-related craniosynostosis
  • p.Tyr805= Multiple submitters FGFR2-related craniosynostosis
  • p.Val516= Multiple submitters Beare-Stevenson cutis gyrata syndrome
  • p.Val667= Multiple submitters FGFR2-related craniosynostosis
  • c.-358C>T Single submitter Beare-Stevenson cutis gyrata syndrome
  • c.*1301C>T Single submitter Beare-Stevenson cutis gyrata syndrome
  • c.*1319A>G Single submitter Beare-Stevenson cutis gyrata syndrome

Likely benign 254

Uncertain significance 388

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