AFP — 97 ClinVar variants
All ClinVar germline AFP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 79 flagged for review →
2 Pathogenic · 1 Likely pathogenic · 6 Benign · 10 Likely benign · 78 Uncertain significance
Full AFP gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 79
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.
-
AFP p.Gly608Arg
Likely pathogenic
Single submitter
primary ovarian failure
Predictors lean, ClinVar uncertain 54
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- AFP p.Ala134Val Uncertain significance Single submitter
- AFP p.Ala471Val Uncertain significance Single submitter
- AFP p.Ala476Thr Uncertain significance Single submitter
- AFP p.Ala605Ser Uncertain significance Single submitter
- AFP p.Ala606Ser Uncertain significance Single submitter
- AFP p.Asp395Tyr Uncertain significance Single submitter
- AFP p.Cys393Tyr Uncertain significance Single submitter
- AFP p.Cys591Trp Uncertain significance Single submitter
- AFP p.Gln140Lys Uncertain significance Single submitter
- AFP p.Gln386Arg Uncertain significance Single submitter
- AFP p.Gln541Lys Uncertain significance Single submitter
- AFP p.Glu321Ala Uncertain significance Single submitter
- AFP p.Glu40Lys Uncertain significance Single submitter
- AFP p.Glu474Lys Uncertain significance Single submitter
- AFP p.Glu489Ala Uncertain significance Single submitter
- AFP p.Glu565Gln Uncertain significance Single submitter
- AFP p.Glu589Asp Uncertain significance Single submitter
- AFP p.Glu96Lys Uncertain significance Single submitter
- AFP p.Gly311Asp Uncertain significance Single submitter
- AFP p.Gly585Asp Uncertain significance Single submitter
-
AFP p.His22Asn
Uncertain significance
Single submitter
Alpha-fetoprotein, hereditary persistence of
- AFP p.Ile136Phe Uncertain significance Single submitter
- AFP p.Ile238Leu Uncertain significance Single submitter
- AFP p.Ile314Thr Uncertain significance Single submitter
- AFP p.Ile315Thr Uncertain significance Single submitter
- AFP p.Ile349Ser Uncertain significance Single submitter
- AFP p.Ile349Val Uncertain significance Single submitter
- AFP p.Ile41Lys Uncertain significance Single submitter
- AFP p.Ile480Thr Uncertain significance Single submitter
- AFP p.Ile49Thr Uncertain significance Single submitter
- AFP p.Ile532Val Uncertain significance Single submitter
-
AFP p.Leu260Val
Uncertain significance
Single submitter
Alpha-fetoprotein, hereditary persistence of
- AFP p.Leu275Val Uncertain significance Single submitter
- AFP p.Leu334Ser Uncertain significance Single submitter
- AFP p.Leu391Val Uncertain significance Single submitter
- AFP p.Leu553Pro Uncertain significance Single submitter
- AFP p.Lys102Glu Uncertain significance Single submitter
- AFP p.Lys211Glu Uncertain significance Single submitter
- AFP p.Lys228Gln Uncertain significance Single submitter
- AFP p.Lys468Asn Uncertain significance Single submitter
- AFP p.Lys558Asn Uncertain significance Single submitter
- AFP p.Phe11Ser Uncertain significance Single submitter
- AFP p.Pro176Thr Uncertain significance Single submitter
- AFP p.Ser117Thr Uncertain significance Single submitter
- AFP p.Ser445Leu Uncertain significance Single submitter
- AFP p.Ser64Asn Uncertain significance Single submitter
- AFP p.Thr132Pro Uncertain significance Single submitter
- AFP p.Thr157Ala Uncertain significance Single submitter
- AFP p.Thr20Lys Uncertain significance Single submitter
- AFP p.Thr232Ile Uncertain significance Single submitter
-
AFP p.Thr253Ser
Uncertain significance
Single submitter
Alpha-fetoprotein, hereditary persistence of
- AFP p.Val145Asp Uncertain significance Single submitter
- AFP p.Val199Ala Uncertain significance Single submitter
- AFP p.Val367Ile Uncertain significance Single submitter
Predictors split 24
The independent predictors disagree with each other — read with care.
- AFP p.Ala476Val Uncertain significance Single submitter
- AFP p.Arg184Cys Uncertain significance Single submitter
- AFP p.Asp69Val Uncertain significance Single submitter
- AFP p.Gln394Pro Uncertain significance Single submitter
- AFP p.Gln56Arg Uncertain significance Single submitter
- AFP p.Glu119Gln Uncertain significance Single submitter
- AFP p.Glu119Gly Uncertain significance Single submitter
- AFP p.Glu143Ala Uncertain significance Single submitter
- AFP p.Glu267Lys Uncertain significance Single submitter
- AFP p.Glu309Lys Uncertain significance Single submitter
- AFP p.Gly109Arg Benign Single submitter
- AFP p.Gly325Arg Uncertain significance Single submitter
- AFP p.Gly498Val Uncertain significance Single submitter
- AFP p.Leu330Pro Uncertain significance Single submitter
- AFP p.Leu365Phe Uncertain significance Single submitter
- AFP p.Lys535Arg Uncertain significance Single submitter
- AFP p.Phe533Leu Uncertain significance Single submitter
- AFP p.Pro524Leu Uncertain significance Single submitter
- AFP p.Pro77Leu Uncertain significance Single submitter
- AFP p.Ser368Leu Uncertain significance Single submitter
- AFP p.Thr451Asn Uncertain significance Single submitter
- AFP p.Thr48Ala Uncertain significance Single submitter
- AFP p.Val590Phe Uncertain significance Single submitter
- AFP p.Val67Leu Uncertain significance Single submitter
All AFP variants
Pathogenic 2
- p.Leu295fs No assertion criteria Alpha-fetoprotein deficiency
- p.Trp181Ter No assertion criteria Alpha-fetoprotein deficiency
Likely pathogenic 1
- p.Gly608Arg Single submitter primary ovarian failure ⚠
Benign 6
- p.Ser286= Multiple submitters
- p.Ser445= Multiple submitters
- p.Gly109Arg Single submitter ⚠
- p.Thr547= Single submitter Alpha-fetoprotein deficiency
- c.844-10T>C No assertion criteria AFP-related disorder
- p.Thr547Ile No assertion criteria AFP-related disorder
Likely benign 10
- c.714-5C>T Multiple submitters
- c.*10+2T>C Single submitter Alpha-fetoprotein, hereditary persistence of
- p.Gln463= Single submitter
- p.Pro133= Single submitter
- p.Ser368Pro Single submitter
- p.Ser504= Single submitter
- p.Thr294Ile Single submitter
- p.Cys511= No assertion criteria AFP-related disorder
- p.Gly482= No assertion criteria AFP-related disorder
- p.Phe50Tyr No assertion criteria AFP-related disorder
Uncertain significance 78
- p.Ala134Val Single submitter ⚠
- p.Ala471Val Single submitter ⚠
- p.Ala476Thr Single submitter ⚠
- p.Ala476Val Single submitter ⚠
- p.Ala605Ser Single submitter ⚠
- p.Ala606Ser Single submitter ⚠
- p.Arg184Cys Single submitter ⚠
- p.Asp395Tyr Single submitter ⚠
- p.Asp69Val Single submitter ⚠
- p.Cys393Tyr Single submitter ⚠
- p.Cys591Trp Single submitter ⚠
- p.Gln140Lys Single submitter ⚠
- p.Gln386Arg Single submitter ⚠
- p.Gln394Pro Single submitter ⚠
- p.Gln541Lys Single submitter ⚠
- p.Gln56Arg Single submitter ⚠
- p.Glu119Gln Single submitter ⚠
- p.Glu119Gly Single submitter ⚠
- p.Glu143Ala Single submitter ⚠
- p.Glu267Lys Single submitter ⚠
- p.Glu309Lys Single submitter ⚠
- p.Glu321Ala Single submitter ⚠
- p.Glu40Lys Single submitter ⚠
- p.Glu474Lys Single submitter ⚠
- p.Glu489Ala Single submitter ⚠
- p.Glu565Gln Single submitter ⚠
- p.Glu589Asp Single submitter ⚠
- p.Glu96Lys Single submitter ⚠
- p.Gly311Asp Single submitter ⚠
- p.Gly325Arg Single submitter ⚠
- p.Gly498Val Single submitter ⚠
- p.Gly585Asp Single submitter ⚠
- p.His22Asn Single submitter Alpha-fetoprotein, hereditary persistence of ⚠
- p.Ile136Phe Single submitter ⚠
- p.Ile238Leu Single submitter ⚠
- p.Ile314Thr Single submitter ⚠
- p.Ile315Thr Single submitter ⚠
- p.Ile349Ser Single submitter ⚠
- p.Ile349Val Single submitter ⚠
- p.Ile41Lys Single submitter ⚠
- p.Ile480Thr Single submitter ⚠
- p.Ile49Thr Single submitter ⚠
- p.Ile532Val Single submitter ⚠
- p.Leu260Val Single submitter Alpha-fetoprotein, hereditary persistence of ⚠
- p.Leu275Val Single submitter ⚠
- p.Leu330Pro Single submitter ⚠
- p.Leu334Ser Single submitter ⚠
- p.Leu365Phe Single submitter ⚠
- p.Leu391Val Single submitter ⚠
- p.Leu553Pro Single submitter ⚠
- p.Lys102Glu Single submitter ⚠
- p.Lys211Glu Single submitter ⚠
- p.Lys228Gln Single submitter ⚠
- p.Lys322_Pro323delinsAsn Single submitter Alpha-fetoprotein, hereditary persistence of
- p.Lys468Asn Single submitter ⚠
- p.Lys535Arg Single submitter ⚠
- p.Lys558Asn Single submitter ⚠
- p.Phe11Ser Single submitter ⚠
- p.Phe533Leu Single submitter ⚠
- p.Pro176Thr Single submitter ⚠
- p.Pro524Leu Single submitter ⚠
- p.Pro77Leu Single submitter ⚠
- p.Ser117Thr Single submitter ⚠
- p.Ser368Leu Single submitter ⚠
- p.Ser445Leu Single submitter ⚠
- p.Ser64Asn Single submitter ⚠
- p.Thr132Pro Single submitter ⚠
- p.Thr157Ala Single submitter ⚠
- p.Thr20Lys Single submitter ⚠
- p.Thr232Ile Single submitter ⚠
- p.Thr253Ser Single submitter Alpha-fetoprotein, hereditary persistence of ⚠
- p.Thr451Asn Single submitter ⚠
- p.Thr48Ala Single submitter ⚠
- p.Val145Asp Single submitter ⚠
- p.Val199Ala Single submitter ⚠
- p.Val367Ile Single submitter ⚠
- p.Val590Phe Single submitter ⚠
- p.Val67Leu Single submitter ⚠