VAX1 — 82 ClinVar variants
All ClinVar germline VAX1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 46 flagged for review →
1 Pathogenic · 1 Likely pathogenic · 1 Conflicting · 5 Benign · 2 Benign/Likely benign · 17 Likely benign · 55 Uncertain significance
Full VAX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 46
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 36
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
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VAX1 p.Ala227Val
Uncertain significance
Multiple submitters
microphthalmia, syndromic 11
- VAX1 p.Ala232Ser Uncertain significance Multiple submitters
- VAX1 p.Ala239Ser Uncertain significance Multiple submitters
-
VAX1 p.Lys27Thr
Uncertain significance
Multiple submitters
microphthalmia, syndromic 11
-
VAX1 p.Met295Val
Uncertain significance
Multiple submitters
microphthalmia, syndromic 11
-
VAX1 p.Ser213Thr
Uncertain significance
Multiple submitters
microphthalmia, syndromic 11
- VAX1 p.Ala219Val Uncertain significance Single submitter
- VAX1 p.Ala231Thr Uncertain significance Single submitter
- VAX1 p.Ala232Val Uncertain significance Single submitter
- VAX1 p.Ala25Pro Uncertain significance Single submitter
- VAX1 p.Ala263Val Uncertain significance Single submitter
- VAX1 p.Ala265Thr Uncertain significance Single submitter
- VAX1 p.Ala268Val Uncertain significance Single submitter
-
VAX1 p.Ala285Ser
Uncertain significance
Single submitter
microphthalmia, syndromic 11
- VAX1 p.Ala41Gly Uncertain significance Single submitter
- VAX1 p.Ala53Val Uncertain significance Single submitter
- VAX1 p.Ala68Pro Uncertain significance Single submitter
- VAX1 p.Arg180Trp Uncertain significance Single submitter
- VAX1 p.Glu46Gln Uncertain significance Single submitter
- VAX1 p.Gly192Ser Uncertain significance Single submitter
-
VAX1 p.Leu214Phe
Uncertain significance
Single submitter
microphthalmia, syndromic 11
- VAX1 p.Leu261Ser Uncertain significance Single submitter
- VAX1 p.Pro199His Uncertain significance Single submitter
- VAX1 p.Pro199Leu Uncertain significance Single submitter
- VAX1 p.Pro212Ser Uncertain significance Single submitter
- VAX1 p.Pro212Thr Uncertain significance Single submitter
- VAX1 p.Pro215Gln Uncertain significance Single submitter
- VAX1 p.Pro234Leu Uncertain significance Single submitter
- VAX1 p.Pro244Ser Uncertain significance Single submitter
- VAX1 p.Pro40Arg Uncertain significance Single submitter
- VAX1 p.Ser14Trp Uncertain significance Single submitter
- VAX1 p.Ser241Thr Uncertain significance Single submitter
-
VAX1 p.Ser274Ile
Uncertain significance
Single submitter
microphthalmia, syndromic 11
-
VAX1 p.Thr103Met
Uncertain significance
Single submitter
microphthalmia, syndromic 11
- VAX1 p.Thr202Arg Uncertain significance Single submitter
-
VAX1 p.Gly84Arg
Uncertain significance
No assertion criteria
microphthalmia, syndromic 11
Predictors split 10
The independent predictors disagree with each other — read with care.
-
VAX1 p.Ala230Thr
Likely benign
Multiple submitters
microphthalmia, syndromic 11
- VAX1 p.Ala109Thr Uncertain significance Single submitter
- VAX1 p.Cys12Arg Uncertain significance Single submitter
-
VAX1 p.Glu183Ala
Uncertain significance
Single submitter
microphthalmia, syndromic 11
- VAX1 p.Gly206Val Uncertain significance Single submitter
-
VAX1 p.Leu181Met
Uncertain significance
Single submitter
microphthalmia, syndromic 11
-
VAX1 p.Lys157Arg
Uncertain significance
Single submitter
microphthalmia, syndromic 11
- VAX1 p.Met295Ile Uncertain significance Single submitter
- VAX1 p.Pro278His Uncertain significance Single submitter
- VAX1 p.Thr103Lys Uncertain significance Single submitter
All VAX1 variants
Pathogenic 1
- p.Arg152Ser No assertion criteria microphthalmia, syndromic 11
Likely pathogenic 1
- p.Pro71fs Single submitter microphthalmia
Conflicting classifications of pathogenicity 1
- p.Leu214= Single submitter microphthalmia, syndromic 11
Benign 5
- c.*288T>C Multiple submitters
- c.-65del Single submitter
- p.Ala231_Ala233dup Single submitter microphthalmia, syndromic 11
- p.Ala315= Single submitter microphthalmia, syndromic 11
- p.Leu193= Single submitter
Benign/Likely benign 2
Likely benign 17
- p.Ala230Thr Multiple submitters microphthalmia, syndromic 11 ⚠
- p.Pro236= Multiple submitters microphthalmia, syndromic 11
- c.241+19G>T Single submitter microphthalmia, syndromic 11
- c.242-5C>T Single submitter microphthalmia, syndromic 11
- c.430-18C>G Single submitter microphthalmia, syndromic 11
- p.Ala208= Single submitter microphthalmia, syndromic 11
- p.Ala222= Single submitter
- p.Ala226= Single submitter microphthalmia, syndromic 11
- p.Gly238= Single submitter microphthalmia, syndromic 11
- p.Gly94= Single submitter
- p.Leu187= Single submitter microphthalmia, syndromic 11
- p.Phe51= Single submitter microphthalmia, syndromic 11
- p.Ser170= Single submitter microphthalmia, syndromic 11
- p.Ser207= Single submitter microphthalmia, syndromic 11
- p.Ser225= Single submitter microphthalmia, syndromic 11
- p.Ser313= Single submitter
- p.Val125= Single submitter microphthalmia, syndromic 11
Uncertain significance 55
- p.Ala227Val Multiple submitters microphthalmia, syndromic 11 ⚠
- p.Ala232Ser Multiple submitters ⚠
- p.Ala239Ser Multiple submitters ⚠
- p.Lys27Thr Multiple submitters microphthalmia, syndromic 11 ⚠
- p.Met295Val Multiple submitters microphthalmia, syndromic 11 ⚠
- p.Ser213Thr Multiple submitters microphthalmia, syndromic 11 ⚠
- p.Ala109Thr Single submitter ⚠
- p.Ala219Val Single submitter ⚠
- p.Ala231Thr Single submitter ⚠
- p.Ala232Val Single submitter ⚠
- p.Ala25Pro Single submitter ⚠
- p.Ala263Val Single submitter ⚠
- p.Ala265Thr Single submitter ⚠
- p.Ala268= Single submitter
- p.Ala268Val Single submitter ⚠
- p.Ala285Ser Single submitter microphthalmia, syndromic 11 ⚠
- p.Ala332fs Single submitter microphthalmia, syndromic 11
- p.Ala41Gly Single submitter ⚠
- p.Ala53Val Single submitter ⚠
- p.Ala68Pro Single submitter ⚠
- p.Arg180Trp Single submitter ⚠
- p.Arg186fs Single submitter microphthalmia, syndromic 11
- p.Asp70Glu Single submitter microphthalmia, syndromic 11
- p.Cys12Arg Single submitter ⚠
- p.Glu17Ter Single submitter microphthalmia, syndromic 11
- p.Glu183Ala Single submitter microphthalmia, syndromic 11 ⚠
- p.Glu46Gln Single submitter ⚠
- p.Gly160Ser Single submitter
- p.Gly192Ser Single submitter ⚠
- p.Gly206Val Single submitter ⚠
- p.Gly224_Ala228dup Single submitter microphthalmia, syndromic 11
- p.Leu181Met Single submitter microphthalmia, syndromic 11 ⚠
- p.Leu214Phe Single submitter microphthalmia, syndromic 11 ⚠
- p.Leu261Ser Single submitter ⚠
- p.Lys157Arg Single submitter microphthalmia, syndromic 11 ⚠
- p.Lys7Asn Single submitter
- p.Met295Ile Single submitter ⚠
- p.Pro199His Single submitter ⚠
- p.Pro199Leu Single submitter ⚠
- p.Pro212Ser Single submitter ⚠
- p.Pro212Thr Single submitter ⚠
- p.Pro215Gln Single submitter ⚠
- p.Pro234Leu Single submitter ⚠
- p.Pro244Ser Single submitter ⚠
- p.Pro278His Single submitter ⚠
- p.Pro40Arg Single submitter ⚠
- p.Ser14Trp Single submitter ⚠
- p.Ser241Thr Single submitter ⚠
- p.Ser274Ile Single submitter microphthalmia, syndromic 11 ⚠
- p.Ser307Ala Single submitter
- p.Thr103Lys Single submitter ⚠
- p.Thr103Met Single submitter microphthalmia, syndromic 11 ⚠
- p.Thr105fs Single submitter microphthalmia, syndromic 11
- p.Thr202Arg Single submitter ⚠
- p.Gly84Arg No assertion criteria microphthalmia, syndromic 11 ⚠