ALX3 — 95 ClinVar variants
All ClinVar germline ALX3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 62 flagged for review →
9 Pathogenic · 1 Likely pathogenic · 1 Conflicting · 10 Benign · 2 Benign/Likely benign · 10 Likely benign · 62 Uncertain significance
Full ALX3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 62
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 lean, ClinVar uncertain 46
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
ALX3 p.Tyr320Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ALX3 p.Ala34Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Ala65Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Ala7Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Arg154His
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Arg157His
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Arg183Trp
Uncertain significance
Single submitter
frontorhiny
-
ALX3 p.Arg204His
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Arg211Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Arg235His
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Arg329Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Asp116His
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Asp319Gly
Uncertain significance
Single submitter
Inborn genetic diseases
- ALX3 p.Cys54Ser Uncertain significance Single submitter
-
ALX3 p.Glu167Lys
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Glu94Lys
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Gly117Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Gly12Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Gly139Glu
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Gly22Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Gly78Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Gly78Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.His176Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.His278Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.His37Gln
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.His37Tyr
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.His39Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Ile230Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Leu136Val
Uncertain significance
Single submitter
Inborn genetic diseases
- ALX3 p.Leu186Val Uncertain significance Single submitter
-
ALX3 p.Leu260Phe
Uncertain significance
Single submitter
Inborn genetic diseases
- ALX3 p.Leu61Val Uncertain significance Single submitter
-
ALX3 p.Lys170Asn
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Lys331Asn
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Phe172Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro250Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro288Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro40Ala
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro43Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro56Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro64Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro64Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Thr158Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Thr31Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Val232Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Val330Ile
Uncertain significance
Single submitter
Inborn genetic diseases
Predictors split 16
The independent predictors disagree with each other — read with care.
-
ALX3 p.Ser131Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ALX3 p.Arg221Gln
Conflicting
Single submitter
frontorhiny
-
ALX3 p.Arg221Trp
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Asp229His
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Gly296Asp
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.His301Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Leu146Trp
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Leu61His
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Lys333Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro290Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro335Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Pro46Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- ALX3 p.Pro52Leu Likely benign Single submitter
-
ALX3 p.Ser131Asn
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Ser268Phe
Uncertain significance
Single submitter
Inborn genetic diseases
-
ALX3 p.Tyr228Cys
Uncertain significance
Single submitter
Inborn genetic diseases
All ALX3 variants
Pathogenic 9
- p.Gln122Ter Single submitter frontorhiny
- p.Gln185Ter Single submitter frontorhiny
- p.Gln198Ter Single submitter
- c.595-2A>T No assertion criteria frontorhiny
- p.Arg196Trp No assertion criteria frontorhiny
- p.Asn203Ser No assertion criteria frontorhiny
- p.Leu168Val No assertion criteria frontorhiny
- p.Thr193fs No assertion criteria frontorhiny
- p.Tyr181Ter No assertion criteria frontorhiny
Likely pathogenic 1
- p.Leu246fs Single submitter frontorhiny
Conflicting classifications of pathogenicity 1
- p.Arg221Gln Single submitter frontorhiny ⚠
Benign 10
- c.277+33C>T Multiple submitters frontorhiny
- p.Pro305= Multiple submitters
- c.277+231A>G Single submitter
- c.277+296T>C Single submitter
- c.278-6T>C Single submitter
- c.594+190T>C Single submitter
- c.594+263G>C Single submitter
- c.*68_*69insCCTGCCTGGACACCACGGAGGAAGCACC Single submitter
- p.Pro138= Single submitter
- p.Pro68= Single submitter
Benign/Likely benign 2
- p.Arg209= Multiple submitters
- p.Pro250Ala Multiple submitters
Likely benign 10
- c.277+18G>A Single submitter
- c.595-5C>A Single submitter
- p.Ala292= Single submitter
- p.Leu146= Single submitter
- p.Phe160= Single submitter
- p.Pro118= Single submitter
- p.Pro28= Single submitter
- p.Pro52Leu Single submitter ⚠
- p.Tyr214= Single submitter
- p.Leu325= No assertion criteria ALX3-related disorder
Uncertain significance 62
- p.Ser131Arg Multiple submitters Inborn genetic diseases ⚠
- p.Tyr320Cys Multiple submitters Inborn genetic diseases ⚠
- p.Ala34Thr Single submitter Inborn genetic diseases ⚠
- p.Ala65Thr Single submitter Inborn genetic diseases ⚠
- p.Ala7Val Single submitter Inborn genetic diseases ⚠
- p.Arg154His Single submitter Inborn genetic diseases ⚠
- p.Arg157His Single submitter Inborn genetic diseases ⚠
- p.Arg183Trp Single submitter frontorhiny ⚠
- p.Arg204His Single submitter Inborn genetic diseases ⚠
- p.Arg211Ser Single submitter Inborn genetic diseases ⚠
- p.Arg221Trp Single submitter Inborn genetic diseases ⚠
- p.Arg235His Single submitter Inborn genetic diseases ⚠
- p.Arg329Ser Single submitter Inborn genetic diseases ⚠
- p.Asp116His Single submitter Inborn genetic diseases ⚠
- p.Asp229His Single submitter Inborn genetic diseases ⚠
- p.Asp319Gly Single submitter Inborn genetic diseases ⚠
- p.Cys54Ser Single submitter ⚠
- p.Glu167Lys Single submitter Inborn genetic diseases ⚠
- p.Glu94Lys Single submitter Inborn genetic diseases ⚠
- p.Glu95del Single submitter
- p.Gly117Arg Single submitter Inborn genetic diseases ⚠
- p.Gly12Arg Single submitter Inborn genetic diseases ⚠
- p.Gly139Glu Single submitter Inborn genetic diseases ⚠
- p.Gly22Arg Single submitter Inborn genetic diseases ⚠
- p.Gly296Asp Single submitter Inborn genetic diseases ⚠
- p.Gly78Arg Single submitter Inborn genetic diseases ⚠
- p.Gly78Ser Single submitter Inborn genetic diseases ⚠
- p.His176Leu Single submitter Inborn genetic diseases ⚠
- p.His278Arg Single submitter Inborn genetic diseases ⚠
- p.His301Arg Single submitter Inborn genetic diseases ⚠
- p.His37Gln Single submitter Inborn genetic diseases ⚠
- p.His37Tyr Single submitter Inborn genetic diseases ⚠
- p.His39Leu Single submitter Inborn genetic diseases ⚠
- p.Ile230Ser Single submitter Inborn genetic diseases ⚠
- p.Leu136Val Single submitter Inborn genetic diseases ⚠
- p.Leu146Trp Single submitter Inborn genetic diseases ⚠
- p.Leu186Val Single submitter ⚠
- p.Leu260Phe Single submitter Inborn genetic diseases ⚠
- p.Leu61His Single submitter Inborn genetic diseases ⚠
- p.Leu61Val Single submitter ⚠
- p.Lys170Asn Single submitter Inborn genetic diseases ⚠
- p.Lys331Asn Single submitter Inborn genetic diseases ⚠
- p.Lys333Thr Single submitter Inborn genetic diseases ⚠
- p.Lys96del Single submitter
- p.Phe172Leu Single submitter Inborn genetic diseases ⚠
- p.Pro250Leu Single submitter Inborn genetic diseases ⚠
- p.Pro288Ser Single submitter Inborn genetic diseases ⚠
- p.Pro290Arg Single submitter Inborn genetic diseases ⚠
- p.Pro335Leu Single submitter Inborn genetic diseases ⚠
- p.Pro40Ala Single submitter Inborn genetic diseases ⚠
- p.Pro43Ser Single submitter Inborn genetic diseases ⚠
- p.Pro46Arg Single submitter Inborn genetic diseases ⚠
- p.Pro56Ser Single submitter Inborn genetic diseases ⚠
- p.Pro64Leu Single submitter Inborn genetic diseases ⚠
- p.Pro64Ser Single submitter Inborn genetic diseases ⚠
- p.Ser131Asn Single submitter Inborn genetic diseases ⚠
- p.Ser268Phe Single submitter Inborn genetic diseases ⚠
- p.Thr158Met Single submitter Inborn genetic diseases ⚠
- p.Thr31Ser Single submitter Inborn genetic diseases ⚠
- p.Tyr228Cys Single submitter Inborn genetic diseases ⚠
- p.Val232Met Single submitter Inborn genetic diseases ⚠
- p.Val330Ile Single submitter Inborn genetic diseases ⚠