FGF3 — 168 ClinVar variants
All ClinVar germline FGF3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 75 flagged for review →
10 Pathogenic · 6 Pathogenic/Likely pathogenic · 14 Likely pathogenic · 6 Conflicting · 10 Benign · 6 Benign/Likely benign · 36 Likely benign · 80 Uncertain significance
Full FGF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 75
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.
-
FGF3 p.Arg95Gln
Likely pathogenic
Single submitter
hearing loss disorder
Predictors agree, ClinVar conflicts 5
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
FGF3 p.Gly34Cys
Conflicting
Single submitter
deafness with labyrinthine aplasia, microtia, and microdontia
-
FGF3 p.Leu105His
Conflicting
Single submitter
deafness with labyrinthine aplasia, microtia, and microdontia
-
FGF3 p.Leu56Phe
Conflicting
Single submitter
deafness with labyrinthine aplasia, microtia, and microdontia
-
FGF3 p.Phe178Leu
Conflicting
Single submitter
deafness with labyrinthine aplasia, microtia, and microdontia
-
FGF3 p.Ser108Leu
Conflicting
Single submitter
FGF3-related disorders
Predictors lean, ClinVar uncertain 50
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
FGF3 p.Arg132Trp
Uncertain significance
Multiple submitters
Inborn genetic diseases
- FGF3 p.Arg145Gln Uncertain significance Multiple submitters
- FGF3 p.Arg171His Uncertain significance Multiple submitters
-
FGF3 p.Gln195His
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
FGF3 p.Gly15Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
FGF3 p.Gly90Val
Uncertain significance
Multiple submitters
deafness with labyrinthine aplasia, microtia, and microdontia
-
FGF3 p.Val182Met
Uncertain significance
Multiple submitters
Inborn genetic diseases
- FGF3 p.Val225Ile Uncertain significance Multiple submitters
-
FGF3 p.Val35Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
FGF3 p.Ala113Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Ala18Thr
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Arg104Pro Uncertain significance Single submitter
-
FGF3 p.Arg135Pro
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Arg170His Uncertain significance Single submitter
- FGF3 p.Arg192Gln Uncertain significance Single submitter
-
FGF3 p.Arg211Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Arg212Gln
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Arg212Leu
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Arg32Cys Uncertain significance Single submitter
-
FGF3 p.Arg45Cys
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Arg63His
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Glu116Asp Uncertain significance Single submitter
-
FGF3 p.Glu119Gly
Uncertain significance
Single submitter
deafness with labyrinthine aplasia, microtia, and microdontia
- FGF3 p.Glu150Gln Uncertain significance Single submitter
-
FGF3 p.Glu82Gln
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Gly203Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Gly20Asp Uncertain significance Single submitter
-
FGF3 p.Gly231Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Gly30Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.His122Tyr Uncertain significance Single submitter
- FGF3 p.Leu220Arg Uncertain significance Single submitter
-
FGF3 p.Leu230Val
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Leu234Pro Uncertain significance Single submitter
-
FGF3 p.Leu234Val
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Leu58Pro Uncertain significance Single submitter
-
FGF3 p.Pro147Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Ser228Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Ser237Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Ser67Arg Uncertain significance Single submitter
- FGF3 p.Ser74Asn Uncertain significance Single submitter
- FGF3 p.Thr140Met Uncertain significance Single submitter
-
FGF3 p.Thr169Pro
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Thr52Ala Uncertain significance Single submitter
- FGF3 p.Tyr106Asp Uncertain significance Single submitter
- FGF3 p.Tyr126Ser Uncertain significance Single submitter
- FGF3 p.Tyr129Cys Uncertain significance Single submitter
-
FGF3 p.Tyr36His
Uncertain significance
Single submitter
deafness with labyrinthine aplasia, microtia, and microdontia
-
FGF3 p.Tyr49Cys
Uncertain significance
Single submitter
deafness with labyrinthine aplasia, microtia, and microdontia
- FGF3 p.Val155Met Uncertain significance Single submitter
-
FGF3 p.Arg46Pro
Uncertain significance
No assertion criteria
deafness with labyrinthine aplasia, microtia, and microdontia
Predictors split 19
The independent predictors disagree with each other — read with care.
-
FGF3 p.Asp184Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
FGF3 p.Glu150Lys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
FGF3 p.Met190Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
- FGF3 p.Thr136Met Uncertain significance Multiple submitters
-
FGF3 p.Val83Ala
Uncertain significance
Multiple submitters
Inborn genetic diseases
- FGF3 p.Arg120Gln Uncertain significance Single submitter
- FGF3 p.Arg135Gln Uncertain significance Single submitter
-
FGF3 p.Arg144Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Arg24Gln Uncertain significance Single submitter
- FGF3 p.Arg45Ser Uncertain significance Single submitter
- FGF3 p.Glu109Lys Uncertain significance Single submitter
- FGF3 p.Glu116Lys Uncertain significance Single submitter
-
FGF3 p.Gly197Glu
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Gly30Asp
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Leu68Pro
Uncertain significance
Single submitter
deafness with labyrinthine aplasia, microtia, and microdontia
-
FGF3 p.Pro60Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- FGF3 p.Ser175Thr Uncertain significance Single submitter
-
FGF3 p.Ser61Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
FGF3 p.Thr79Lys
Uncertain significance
Single submitter
Inborn genetic diseases
All FGF3 variants
Pathogenic 10
- p.Ala23fs Single submitter deafness with labyrinthine aplasia, microtia, and microdontia
- p.Glu119Ter Single submitter
- p.Met1Arg Single submitter
- p.Ile85fs No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia
- p.Leu6Pro No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia
- p.Leu91fs No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia
- p.Ser156Pro No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia
- p.Trp153fs No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia
- p.Tyr106Cys No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia
- p.Val206fs No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia
Pathogenic/Likely pathogenic 6
- p.Arg104Ter Multiple submitters FGF3-related disorders
- p.Arg209Ter Multiple submitters deafness with labyrinthine aplasia, microtia, and microdontia
- p.Arg95Trp Multiple submitters deafness with labyrinthine aplasia, microtia, and microdontia
- p.Trp16fs Multiple submitters deafness with labyrinthine aplasia, microtia, and microdontia
- p.Tyr106Ter Multiple submitters FGF3-related disorders
- p.Arg104fs No assertion criteria
Likely pathogenic 14
- c.220+1G>A Single submitter deafness with labyrinthine aplasia, microtia, and microdontia
- c.220+2T>C Single submitter FGF3-related disorders
- c.221-1G>C Single submitter
- p.Arg144fs Single submitter deafness with labyrinthine aplasia, microtia, and microdontia
- p.Arg46fs Single submitter FGF3-related disorders
- p.Arg95fs Single submitter FGF3-related disorders
- p.Arg95Gln Single submitter hearing loss disorder ⚠
- p.Gln173Ter Single submitter deafness with labyrinthine aplasia, microtia, and microdontia
- p.Gly66Cys Single submitter deafness with labyrinthine aplasia, microtia, and microdontia
- p.Gly90fs Single submitter deafness with labyrinthine aplasia, microtia, and microdontia
- p.Phe92fs Single submitter FGF3-related disorders
- p.Val157Ala Single submitter deafness with labyrinthine aplasia, microtia, and microdontia
- p.Arg89fs No assertion criteria FGF3-related disorder
- p.Tyr154Ter No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia
Conflicting classifications of pathogenicity 6
- p.Arg162= Single submitter
- p.Gly34Cys Single submitter deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Leu105His Single submitter deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Leu56Phe Single submitter deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Phe178Leu Single submitter deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Ser108Leu Single submitter FGF3-related disorders ⚠
Benign 10
- c.324+110C>T Multiple submitters
- c.324+115C>T Multiple submitters
- c.325-43A>G Multiple submitters
- c.325-5C>T Multiple submitters
- c.-124G>T Multiple submitters
- p.Ala23= Multiple submitters
- p.Thr136= Multiple submitters
- c.220+172G>T Single submitter
- c.325-19T>C Single submitter
- c.325-262C>T Single submitter
Benign/Likely benign 6
- c.324+11G>A Multiple submitters
- c.324+15T>C Multiple submitters
- p.Arg210Gln Multiple submitters
- p.Lys101Asn Multiple submitters
- p.Ser216= Multiple submitters
- p.Ser93= Multiple submitters
Likely benign 36
- c.*260G>A Multiple submitters
- p.Arg26= Multiple submitters
- p.Pro208= Multiple submitters
- p.Thr140= Multiple submitters
- p.Tyr154= Multiple submitters
- p.Val137= Multiple submitters
- c.220+19G>C Single submitter
- c.221-106C>T Single submitter
- c.221-15T>C Single submitter
- c.221-17C>A Single submitter
- c.221-249G>A Single submitter
- c.324+18C>T Single submitter
- c.324+281C>T Single submitter
- c.325-186A>G Single submitter
- c.325-203A>T Single submitter
- c.-32CGC[3] Single submitter
- c.-331G>T Single submitter
- c.-63C>T Single submitter
- p.Ala113= Single submitter
- p.Ala19= Single submitter
- p.Ala238= Single submitter
- p.Arg209= Single submitter
- p.Gln146= Single submitter
- p.Gln215= Single submitter
- p.Glu189= Single submitter
- p.Gly166= Single submitter
- p.Gly34= Single submitter
- p.His224= Single submitter
- p.Ile88= Single submitter
- p.Leu230= Single submitter
- p.Leu25= Single submitter
- p.Lys160= Single submitter
- p.Pro217= Single submitter
- p.Ser228= Single submitter
- p.Thr169= Single submitter
- p.Tyr111= No assertion criteria FGF3-related disorder
Uncertain significance 80
- p.Arg132Trp Multiple submitters Inborn genetic diseases ⚠
- p.Arg145Gln Multiple submitters ⚠
- p.Arg171His Multiple submitters ⚠
- p.Asp184Val Multiple submitters Inborn genetic diseases ⚠
- p.Gln195His Multiple submitters Inborn genetic diseases ⚠
- p.Glu150Lys Multiple submitters Inborn genetic diseases ⚠
- p.Gly15Ser Multiple submitters Inborn genetic diseases ⚠
- p.Gly90Val Multiple submitters deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Gly94Arg Multiple submitters Inborn genetic diseases
- p.Leu8Pro Multiple submitters
- p.Met190Ile Multiple submitters Inborn genetic diseases ⚠
- p.Thr136Met Multiple submitters ⚠
- p.Val182Met Multiple submitters Inborn genetic diseases ⚠
- p.Val225Ile Multiple submitters ⚠
- p.Val35Ile Multiple submitters Inborn genetic diseases ⚠
- p.Val83Ala Multiple submitters Inborn genetic diseases ⚠
- c.325-2A>G Single submitter deafness with labyrinthine aplasia, microtia, and microdontia
- p.Ala113Thr Single submitter Inborn genetic diseases ⚠
- p.Ala18Thr Single submitter Inborn genetic diseases ⚠
- p.Arg102Thr Single submitter
- p.Arg104Pro Single submitter ⚠
- p.Arg120Gln Single submitter ⚠
- p.Arg135Gln Single submitter ⚠
- p.Arg135Pro Single submitter Inborn genetic diseases ⚠
- p.Arg144Cys Single submitter Inborn genetic diseases ⚠
- p.Arg170His Single submitter ⚠
- p.Arg192Gln Single submitter ⚠
- p.Arg211Leu Single submitter Inborn genetic diseases ⚠
- p.Arg212Gln Single submitter Inborn genetic diseases ⚠
- p.Arg212Leu Single submitter Inborn genetic diseases ⚠
- p.Arg24Gln Single submitter ⚠
- p.Arg32Cys Single submitter ⚠
- p.Arg45Cys Single submitter Inborn genetic diseases ⚠
- p.Arg45Ser Single submitter ⚠
- p.Arg63His Single submitter Inborn genetic diseases ⚠
- p.Asn158Ser Single submitter Inborn genetic diseases
- p.Glu109Lys Single submitter ⚠
- p.Glu116Asp Single submitter ⚠
- p.Glu116Gln Single submitter Inborn genetic diseases
- p.Glu116Lys Single submitter ⚠
- p.Glu119Gly Single submitter deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Glu150Gln Single submitter ⚠
- p.Glu82Gln Single submitter Inborn genetic diseases ⚠
- p.Gly159Ser Single submitter
- p.Gly197Glu Single submitter Inborn genetic diseases ⚠
- p.Gly203Ser Single submitter Inborn genetic diseases ⚠
- p.Gly20Asp Single submitter ⚠
- p.Gly231Ser Single submitter Inborn genetic diseases ⚠
- p.Gly30Asp Single submitter Inborn genetic diseases ⚠
- p.Gly30Ser Single submitter Inborn genetic diseases ⚠
- p.His122Tyr Single submitter ⚠
- p.Ile88Val Single submitter
- p.Leu133Pro Single submitter Inborn genetic diseases
- p.Leu220Arg Single submitter ⚠
- p.Leu230Val Single submitter Inborn genetic diseases ⚠
- p.Leu234Pro Single submitter ⚠
- p.Leu234Val Single submitter Inborn genetic diseases ⚠
- p.Leu58Pro Single submitter ⚠
- p.Leu68Pro Single submitter deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Lys174fs Single submitter
- p.Pro147Arg Single submitter Inborn genetic diseases ⚠
- p.Pro60Arg Single submitter Inborn genetic diseases ⚠
- p.Ser108= Single submitter
- p.Ser175Thr Single submitter ⚠
- p.Ser228Leu Single submitter Inborn genetic diseases ⚠
- p.Ser237Cys Single submitter Inborn genetic diseases ⚠
- p.Ser61Arg Single submitter Inborn genetic diseases ⚠
- p.Ser67Arg Single submitter ⚠
- p.Ser74Asn Single submitter ⚠
- p.Thr140Met Single submitter ⚠
- p.Thr169Pro Single submitter Inborn genetic diseases ⚠
- p.Thr52Ala Single submitter ⚠
- p.Thr79Lys Single submitter Inborn genetic diseases ⚠
- p.Tyr106Asp Single submitter ⚠
- p.Tyr126Ser Single submitter ⚠
- p.Tyr129Cys Single submitter ⚠
- p.Tyr36His Single submitter deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Tyr49Cys Single submitter deafness with labyrinthine aplasia, microtia, and microdontia ⚠
- p.Val155Met Single submitter ⚠
- p.Arg46Pro No assertion criteria deafness with labyrinthine aplasia, microtia, and microdontia ⚠