IDH3A — 314 ClinVar variants
All ClinVar germline IDH3A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 103 flagged for review →
12 Pathogenic · 7 Likely pathogenic · 8 Conflicting · 18 Benign · 5 Benign/Likely benign · 142 Likely benign · 122 Uncertain significance
Full IDH3A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 103
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 agree, ClinVar conflicts 5
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
IDH3A p.Ala122Thr
Conflicting
Single submitter
IDH3A-related disorder
- IDH3A p.Arg66Gln Conflicting Single submitter
- IDH3A p.Glu217Asp Conflicting Single submitter
-
IDH3A p.Met313Thr
Conflicting
Single submitter
retinitis pigmentosa 90
-
IDH3A p.Pro304His
Conflicting
Single submitter
IDH3A-related disorder
Predictors lean, ClinVar uncertain 73
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- IDH3A p.Ala197Val Uncertain significance Multiple submitters
- IDH3A p.Ala330Val Uncertain significance Multiple submitters
-
IDH3A p.Ala5Ser
Uncertain significance
Multiple submitters
inherited retinal dystrophy
-
IDH3A p.Arg178Cys
Uncertain significance
Multiple submitters
retinitis pigmentosa 90
- IDH3A p.Gly271Ser Uncertain significance Multiple submitters
- IDH3A p.Gly298Asp Uncertain significance Multiple submitters
- IDH3A p.Ile103Val Uncertain significance Multiple submitters
- IDH3A p.Ile285Val Uncertain significance Multiple submitters
- IDH3A p.Ile71Val Uncertain significance Multiple submitters
- IDH3A p.Lys9Arg Uncertain significance Multiple submitters
- IDH3A p.Met88Thr Uncertain significance Multiple submitters
- IDH3A p.Met93Ile Uncertain significance Multiple submitters
-
IDH3A p.Phe184Leu
Uncertain significance
Multiple submitters
inherited retinal dystrophy
- IDH3A p.Phe321Ser Uncertain significance Multiple submitters
- IDH3A p.Pro4Leu Uncertain significance Multiple submitters
- IDH3A p.Val143Met Uncertain significance Multiple submitters
- IDH3A p.Ala57Pro Uncertain significance Single submitter
- IDH3A p.Arg12Gln Uncertain significance Single submitter
- IDH3A p.Arg12Pro Uncertain significance Single submitter
- IDH3A p.Arg12Trp Uncertain significance Single submitter
- IDH3A p.Arg178His Uncertain significance Single submitter
- IDH3A p.Arg192Gln Uncertain significance Single submitter
- IDH3A p.Arg316His Uncertain significance Single submitter
- IDH3A p.Asn189His Uncertain significance Single submitter
- IDH3A p.Asn190His Uncertain significance Single submitter
- IDH3A p.Asn194Lys Uncertain significance Single submitter
- IDH3A p.Asn238Ser Uncertain significance Single submitter
- IDH3A p.Asn281Lys Uncertain significance Single submitter
- IDH3A p.Asn281Ser Uncertain significance Single submitter
-
IDH3A p.Asn91Lys
Uncertain significance
Single submitter
retinitis pigmentosa 90
- IDH3A p.Asp139Asn Uncertain significance Single submitter
- IDH3A p.Asp139Tyr Uncertain significance Single submitter
- IDH3A p.Asp233His Uncertain significance Single submitter
- IDH3A p.Asp337Val Uncertain significance Single submitter
- IDH3A p.Asp353His Uncertain significance Single submitter
- IDH3A p.Cys127Arg Uncertain significance Single submitter
- IDH3A p.Cys222Ser Uncertain significance Single submitter
- IDH3A p.Cys263Tyr Uncertain significance Single submitter
- IDH3A p.Cys331Tyr Uncertain significance Single submitter
- IDH3A p.Gln166Arg Uncertain significance Single submitter
- IDH3A p.Gln72Glu Uncertain significance Single submitter
- IDH3A p.Glu173Lys Uncertain significance Single submitter
- IDH3A p.Glu287Val Uncertain significance Single submitter
- IDH3A p.Gly268Arg Uncertain significance Single submitter
- IDH3A p.Gly29Arg Uncertain significance Single submitter
- IDH3A p.Gly3Val Uncertain significance Single submitter
- IDH3A p.Ile142Thr Uncertain significance Single submitter
- IDH3A p.Ile168Val Uncertain significance Single submitter
- IDH3A p.Ile296Val Uncertain significance Single submitter
- IDH3A p.Ile335Val Uncertain significance Single submitter
- IDH3A p.Ile46Ser Uncertain significance Single submitter
- IDH3A p.Ile61Leu Uncertain significance Single submitter
- IDH3A p.Ile7Thr Uncertain significance Single submitter
- IDH3A p.Leu210Pro Uncertain significance Single submitter
- IDH3A p.Lys92Gln Uncertain significance Single submitter
- IDH3A p.Met301Ile Uncertain significance Single submitter
- IDH3A p.Met301Val Uncertain significance Single submitter
- IDH3A p.Met314Leu Uncertain significance Single submitter
- IDH3A p.Met318Val Uncertain significance Single submitter
- IDH3A p.Met51Val Uncertain significance Single submitter
- IDH3A p.Pro274Arg Uncertain significance Single submitter
- IDH3A p.Pro274Leu Uncertain significance Single submitter
- IDH3A p.Pro294Leu Uncertain significance Single submitter
- IDH3A p.Pro44Ser Uncertain significance Single submitter
- IDH3A p.Pro4Ser Uncertain significance Single submitter
- IDH3A p.Thr196Ala Uncertain significance Single submitter
- IDH3A p.Thr292Met Uncertain significance Single submitter
- IDH3A p.Thr305Ile Uncertain significance Single submitter
- IDH3A p.Trp78Arg Uncertain significance Single submitter
- IDH3A p.Val165Met Uncertain significance Single submitter
- IDH3A p.Val248Ile Uncertain significance Single submitter
- IDH3A p.Val250Phe Uncertain significance Single submitter
- IDH3A p.Val31Phe Uncertain significance Single submitter
Predictors split 25
The independent predictors disagree with each other — read with care.
- IDH3A p.Ala122Val Uncertain significance Multiple submitters
- IDH3A p.Arg360Cys Likely benign Multiple submitters
- IDH3A p.Arg361Gln Uncertain significance Multiple submitters
- IDH3A p.Gln72Pro Uncertain significance Multiple submitters
- IDH3A p.Gly106Ser Uncertain significance Multiple submitters
- IDH3A p.Lys350Glu Uncertain significance Multiple submitters
- IDH3A p.Lys90Glu Uncertain significance Multiple submitters
- IDH3A p.Met110Thr Uncertain significance Multiple submitters
- IDH3A p.Val195Ile Uncertain significance Multiple submitters
- IDH3A p.Ala104Val Uncertain significance Single submitter
- IDH3A p.Ala302Val Uncertain significance Single submitter
- IDH3A p.Ala48Pro Uncertain significance Single submitter
- IDH3A p.Arg205Gln Uncertain significance Single submitter
- IDH3A p.Arg360His Uncertain significance Single submitter
- IDH3A p.Gln62Leu Uncertain significance Single submitter
- IDH3A p.Glu328Lys Uncertain significance Single submitter
-
IDH3A p.Gly269Ser
Uncertain significance
Single submitter
retinitis pigmentosa 90
- IDH3A p.Ile156Thr Uncertain significance Single submitter
- IDH3A p.Ile267Leu Uncertain significance Single submitter
- IDH3A p.Ile71Phe Uncertain significance Single submitter
- IDH3A p.Leu36Val Uncertain significance Single submitter
- IDH3A p.Lys52Asn Uncertain significance Single submitter
- IDH3A p.Thr149Ala Uncertain significance Single submitter
- IDH3A p.Val68Ile Uncertain significance Single submitter
-
IDH3A p.Gly94Ser
Uncertain significance
No assertion criteria
inherited retinal dystrophy
All IDH3A variants
Pathogenic 12
- p.Ala16fs Single submitter
- p.Arg316Cys Single submitter retinitis pigmentosa 90
- p.Gly155Ter Single submitter retinitis pigmentosa 90
- p.Lys96fs Single submitter
- p.Thr135fs Single submitter retinitis pigmentosa 90
- p.Thr28fs Single submitter
- p.Trp6Ter Single submitter
- p.Val198fs Single submitter
- p.Ala175Val No assertion criteria retinitis pigmentosa 90
- p.Ala302fs No assertion criteria inherited retinal dystrophy
- p.Met204Ile No assertion criteria retinitis pigmentosa 90
- p.Met239Thr No assertion criteria retinitis pigmentosa 90
Likely pathogenic 7
- c.27+2T>C Single submitter
- c.27+2T>G Single submitter
- c.611+2T>G Single submitter
- c.715-1G>C Single submitter
- c.779+1G>A Single submitter
- c.864+1G>C Single submitter
- c.90+1G>A Single submitter
Conflicting classifications of pathogenicity 8
- c.714+1G>A Single submitter
- p.Ala122Thr Single submitter IDH3A-related disorder ⚠
- p.Arg125Ter Single submitter
- p.Arg66Gln Single submitter ⚠
- p.Glu217Asp Single submitter ⚠
- p.Ile203= Single submitter
- p.Met313Thr Single submitter retinitis pigmentosa 90 ⚠
- p.Pro304His Single submitter IDH3A-related disorder ⚠
Benign 18
- c.1017+153C>T Multiple submitters
- c.175-138C>T Multiple submitters
- c.175-190T>C Multiple submitters
- c.27+114T>G Multiple submitters
- c.289+174T>C Multiple submitters
- c.611+86T>C Multiple submitters
- c.780-92A>G Multiple submitters
- c.864+118G>C Multiple submitters
- c.865-7T>C Multiple submitters
- c.90+173C>G Multiple submitters
- c.91-142G>C Multiple submitters
- c.*110A>G Multiple submitters
- p.Asp337= Multiple submitters
- p.Ser8= Multiple submitters
- c.28-4A>G Single submitter
- c.611+196del Single submitter
- c.864+130dup Single submitter
- p.Asp344= Single submitter
Benign/Likely benign 5
- c.864+8C>T Multiple submitters
- c.865-10C>T Multiple submitters
- p.Ala330= Multiple submitters
- p.Asp139Glu Multiple submitters
- p.Thr342= Multiple submitters
Likely benign 142
- c.175-20C>T Multiple submitters
- c.27+19_27+41dup Multiple submitters
- c.289+19C>T Multiple submitters
- c.477+16A>T Multiple submitters
- c.477+18T>G Multiple submitters
- c.478-10T>C Multiple submitters
- c.611+14G>A Multiple submitters
- c.714+19_714+22del Multiple submitters
- c.715-11A>G Multiple submitters
- c.865-15T>C Multiple submitters
- c.90+11T>C Multiple submitters
- c.90+12_90+14del Multiple submitters
- c.90+14T>C Multiple submitters
- c.91-18A>C Multiple submitters
- c.91-18A>G Multiple submitters
- p.Ala175= Multiple submitters
- p.Ala197= Multiple submitters
- p.Ala302= Multiple submitters
- p.Ala306= Multiple submitters
- p.Ala349= Multiple submitters
- p.Arg360Cys Multiple submitters ⚠
- p.Asn281= Multiple submitters
- p.Asp300= Multiple submitters
- p.Ile267= Multiple submitters
- p.Leu259= Multiple submitters
- p.Pro126= Multiple submitters
- p.Ser129= Multiple submitters
- p.Thr172= Multiple submitters
- p.Thr292= Multiple submitters
- c.1017+6A>G Single submitter
- c.1018-5C>T Single submitter
- c.174+10C>T Single submitter
- c.174+17A>C Single submitter
- c.174+9G>A Single submitter
- c.175-5T>C Single submitter
- c.175-7C>T Single submitter
- c.175-8G>A Single submitter
- c.27+11G>T Single submitter
- c.27+13A>G Single submitter
- c.27+14G>T Single submitter
- c.27+16C>A Single submitter
- c.27+19G>T Single submitter
- c.27+8_27+9delinsGG Single submitter
- c.27+9_27+31dup Single submitter
- c.28-10A>G Single submitter
- c.28-5T>C Single submitter
- c.289+13T>G Single submitter
- c.289+16A>G Single submitter
- c.289+20G>A Single submitter
- c.289+23_289+24dup Single submitter
- c.290-10T>C Single submitter
- c.290-14C>T Single submitter
- c.477+12C>A Single submitter
- c.478-18G>A Single submitter
- c.478-7C>G Single submitter
- c.611+10T>G Single submitter
- c.611+13C>T Single submitter
- c.611+16G>A Single submitter
- c.611+17G>A Single submitter
- c.611+7T>C Single submitter
- c.612-12G>A Single submitter
- c.612-12G>C Single submitter
- c.612-12G>T Single submitter
- c.612-4A>G Single submitter
- c.714+17A>G Single submitter
- c.714+18C>T Single submitter
- c.715-13G>A Single submitter
- c.715-19A>G Single submitter
- c.715-3T>C Single submitter
- c.715-4G>C Single submitter
- c.715-5T>C Single submitter
- c.779+10G>C Single submitter
- c.779+7C>G Single submitter
- c.780-20A>G Single submitter
- c.780-5G>A Single submitter
- c.780-6C>T Single submitter
- c.864+16C>T Single submitter
- c.864+8C>A Single submitter
- c.864+9C>A Single submitter
- c.865-12C>T Single submitter
- c.865-16T>C Single submitter
- c.865-18A>G Single submitter
- c.865-5T>C Single submitter
- c.865-6G>A Single submitter
- c.865-7_865-6inv Single submitter
- c.865-9G>A Single submitter
- c.90+11T>A Single submitter
- c.91-11C>T Single submitter
- c.91-5T>C Single submitter
- c.91-8A>G Single submitter
- c.-20C>G Single submitter
- c.-2C>T Single submitter
- c.*2A>G Single submitter
- p.Ala105= Single submitter
- p.Ala183= Single submitter
- p.Ala264= Single submitter
- p.Ala311= Single submitter
- p.Ala324= Single submitter
- p.Ala333= Single submitter
- p.Arg146= Single submitter
- p.Arg192= Single submitter
- p.Arg216= Single submitter
- p.Arg360= Single submitter
- p.Asn123= Single submitter
- p.Asn148= Single submitter
- p.Asn194= Single submitter
- p.Asn348= Single submitter
- p.Asn67= Single submitter
- p.Asp40= Single submitter
- p.Asp55= Single submitter
- p.Gln245= Single submitter
- p.Gln62= Single submitter
- p.Glu173= Single submitter
- p.Glu356= Single submitter
- p.Glu65= Single submitter
- p.Gly174Glu Single submitter
- p.Gly209= Single submitter
- p.Gly276= Single submitter
- p.Gly282= Single submitter
- p.His191= Single submitter
- p.Ile130= Single submitter
- p.Ile7= Single submitter
- p.Leu113= Single submitter
- p.Leu262= Single submitter
- p.Leu270= Single submitter
- p.Leu308= Single submitter
- p.Leu315= Single submitter
- p.Lys177Arg Single submitter
- p.Pro108= Single submitter
- p.Pro294= Single submitter
- p.Pro4= Single submitter
- p.Pro74= Single submitter
- p.Pro81= Single submitter
- p.Ser221Asn Single submitter
- p.Thr101= Single submitter
- p.Thr138= Single submitter
- p.Thr196= Single submitter
- p.Tyr121= Single submitter
- p.Tyr186= Single submitter
- p.Val164= Single submitter
- p.Val198= Single submitter
- p.Val68= Single submitter
Uncertain significance 122
- c.289+3A>G Multiple submitters
- p.Ala122Val Multiple submitters ⚠
- p.Ala197Val Multiple submitters ⚠
- p.Ala330Val Multiple submitters ⚠
- p.Ala5Ser Multiple submitters inherited retinal dystrophy ⚠
- p.Arg178Cys Multiple submitters retinitis pigmentosa 90 ⚠
- p.Arg188Trp Multiple submitters
- p.Arg361Gln Multiple submitters ⚠
- p.Arg361Ter Multiple submitters retinitis pigmentosa 90
- p.Gln72Pro Multiple submitters ⚠
- p.Gly106Ser Multiple submitters ⚠
- p.Gly271Ser Multiple submitters ⚠
- p.Gly282Arg Multiple submitters
- p.Gly298Asp Multiple submitters ⚠
- p.Ile103Val Multiple submitters ⚠
- p.Ile285Val Multiple submitters ⚠
- p.Ile71Val Multiple submitters ⚠
- p.Lys350Glu Multiple submitters ⚠
- p.Lys90Glu Multiple submitters ⚠
- p.Lys9Arg Multiple submitters ⚠
- p.Met110Thr Multiple submitters ⚠
- p.Met1Thr Multiple submitters
- p.Met313Leu Multiple submitters retinitis pigmentosa 90
- p.Met88Thr Multiple submitters ⚠
- p.Met93Ile Multiple submitters ⚠
- p.Phe184Leu Multiple submitters inherited retinal dystrophy ⚠
- p.Phe321Ser Multiple submitters ⚠
- p.Pro4Leu Multiple submitters ⚠
- p.Thr196Met Multiple submitters
- p.Val143Met Multiple submitters ⚠
- p.Val195Ile Multiple submitters ⚠
- p.Val312Met Multiple submitters
- c.1017+5C>G Single submitter
- c.27+5G>A Single submitter
- c.27+5G>T Single submitter
- c.290-4A>G Single submitter
- c.478-3C>T Single submitter
- c.612-3C>T Single submitter
- c.612-6A>T Single submitter
- c.715-15A>G Single submitter
- c.864+6G>A Single submitter
- c.91-31A>C Single submitter retinitis pigmentosa 90
- p.Ala104Val Single submitter ⚠
- p.Ala302Val Single submitter ⚠
- p.Ala349Val Single submitter
- p.Ala48Gly Single submitter
- p.Ala48Pro Single submitter ⚠
- p.Ala57Pro Single submitter ⚠
- p.Arg12Gln Single submitter ⚠
- p.Arg12Pro Single submitter ⚠
- p.Arg12Trp Single submitter ⚠
- p.Arg146Ter Single submitter
- p.Arg178His Single submitter ⚠
- p.Arg192Gln Single submitter ⚠
- p.Arg205Gln Single submitter ⚠
- p.Arg316His Single submitter ⚠
- p.Arg360His Single submitter ⚠
- p.Asn189His Single submitter ⚠
- p.Asn190His Single submitter ⚠
- p.Asn194Lys Single submitter ⚠
- p.Asn238Ser Single submitter ⚠
- p.Asn281Lys Single submitter ⚠
- p.Asn281Ser Single submitter ⚠
- p.Asn91= Single submitter
- p.Asn91Lys Single submitter retinitis pigmentosa 90 ⚠
- p.Asp139Asn Single submitter ⚠
- p.Asp139Tyr Single submitter ⚠
- p.Asp224Tyr Single submitter
- p.Asp233His Single submitter ⚠
- p.Asp337Val Single submitter ⚠
- p.Asp353His Single submitter ⚠
- p.Cys127Arg Single submitter ⚠
- p.Cys222Ser Single submitter ⚠
- p.Cys263Tyr Single submitter ⚠
- p.Cys331Tyr Single submitter ⚠
- p.Gln166Arg Single submitter ⚠
- p.Gln62Leu Single submitter ⚠
- p.Gln72Glu Single submitter ⚠
- p.Glu173Lys Single submitter ⚠
- p.Glu287Val Single submitter ⚠
- p.Glu328Lys Single submitter ⚠
- p.Gly268Arg Single submitter ⚠
- p.Gly269Ser Single submitter retinitis pigmentosa 90 ⚠
- p.Gly29Arg Single submitter ⚠
- p.Gly3Val Single submitter ⚠
- p.Ile142Thr Single submitter ⚠
- p.Ile156Thr Single submitter ⚠
- p.Ile168Val Single submitter ⚠
- p.Ile267Leu Single submitter ⚠
- p.Ile296Val Single submitter ⚠
- p.Ile335Val Single submitter ⚠
- p.Ile46Ser Single submitter ⚠
- p.Ile61Leu Single submitter ⚠
- p.Ile71Phe Single submitter ⚠
- p.Ile7Thr Single submitter ⚠
- p.Leu210Pro Single submitter ⚠
- p.Leu36Val Single submitter ⚠
- p.Lys52Asn Single submitter ⚠
- p.Lys92Gln Single submitter ⚠
- p.Met301Ile Single submitter ⚠
- p.Met301Val Single submitter ⚠
- p.Met314Leu Single submitter ⚠
- p.Met318Val Single submitter ⚠
- p.Met51Val Single submitter ⚠
- p.Pro274Arg Single submitter ⚠
- p.Pro274Leu Single submitter ⚠
- p.Pro294Leu Single submitter ⚠
- p.Pro44Ser Single submitter ⚠
- p.Pro4Ser Single submitter ⚠
- p.Ser207= Single submitter
- p.Ser288= Single submitter
- p.Thr149Ala Single submitter ⚠
- p.Thr196Ala Single submitter ⚠
- p.Thr292Met Single submitter ⚠
- p.Thr305Ile Single submitter ⚠
- p.Trp78Arg Single submitter ⚠
- p.Val165Met Single submitter ⚠
- p.Val248Ile Single submitter ⚠
- p.Val250Phe Single submitter ⚠
- p.Val31Phe Single submitter ⚠
- p.Val68Ile Single submitter ⚠
- p.Gly94Ser No assertion criteria inherited retinal dystrophy ⚠