INTS2 — 131 ClinVar variants
All ClinVar germline INTS2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 119 flagged for review →
1 Benign · 5 Likely benign · 125 Uncertain significance
Full INTS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 119
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 90
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- INTS2 c.-17A>G Uncertain significance Single submitter
- INTS2 c.-1A>G Uncertain significance Single submitter
- INTS2 c.-3A>G Uncertain significance Single submitter
- INTS2 p.Ala1125Ser Uncertain significance Single submitter
- INTS2 p.Ala57Val Uncertain significance Single submitter
- INTS2 p.Ala599Val Uncertain significance Single submitter
- INTS2 p.Ala662Gly Uncertain significance Single submitter
- INTS2 p.Ala775Thr Uncertain significance Single submitter
- INTS2 p.Ala782Val Uncertain significance Single submitter
- INTS2 p.Arg227Gln Uncertain significance Single submitter
- INTS2 p.Arg237His Uncertain significance Single submitter
- INTS2 p.Arg243His Uncertain significance Single submitter
- INTS2 p.Arg306Trp Uncertain significance Single submitter
- INTS2 p.Arg350Gln Uncertain significance Single submitter
- INTS2 p.Arg410Cys Uncertain significance Single submitter
- INTS2 p.Arg410His Uncertain significance Single submitter
- INTS2 p.Arg634Cys Uncertain significance Single submitter
- INTS2 p.Arg634Gly Uncertain significance Single submitter
- INTS2 p.Arg634His Uncertain significance Single submitter
- INTS2 p.Arg734Gln Uncertain significance Single submitter
- INTS2 p.Asn1074Ser Uncertain significance Single submitter
- INTS2 p.Asn149Lys Uncertain significance Single submitter
- INTS2 p.Asn198Tyr Uncertain significance Single submitter
- INTS2 p.Asn209Asp Uncertain significance Single submitter
- INTS2 p.Asn315Ser Uncertain significance Single submitter
- INTS2 p.Asn539Ser Uncertain significance Single submitter
- INTS2 p.Asn899Ser Uncertain significance Single submitter
- INTS2 p.Asn900Ile Uncertain significance Single submitter
- INTS2 p.Asp1167Asn Uncertain significance Single submitter
- INTS2 p.Cys980Trp Uncertain significance Single submitter
- INTS2 p.Cys990Trp Uncertain significance Single submitter
- INTS2 p.Gln1131Lys Uncertain significance Single submitter
- INTS2 p.Gln252Glu Uncertain significance Single submitter
- INTS2 p.Gln54Arg Uncertain significance Single submitter
- INTS2 p.Gln803Arg Uncertain significance Single submitter
- INTS2 p.Gln893Arg Uncertain significance Single submitter
- INTS2 p.Glu16Gly Uncertain significance Single submitter
- INTS2 p.Glu777Lys Uncertain significance Single submitter
- INTS2 p.Gly903Val Uncertain significance Single submitter
- INTS2 p.His124Tyr Uncertain significance Single submitter
- INTS2 p.His195Arg Uncertain significance Single submitter
- INTS2 p.His581Arg Uncertain significance Single submitter
- INTS2 p.His744Asn Uncertain significance Single submitter
- INTS2 p.His99Arg Uncertain significance Single submitter
- INTS2 p.Ile1047Leu Uncertain significance Single submitter
- INTS2 p.Ile186Met Uncertain significance Single submitter
- INTS2 p.Ile351Met Uncertain significance Single submitter
- INTS2 p.Ile512Val Uncertain significance Single submitter
- INTS2 p.Ile540Val Uncertain significance Single submitter
- INTS2 p.Ile767Thr Uncertain significance Single submitter
- INTS2 p.Ile847Leu Uncertain significance Single submitter
- INTS2 p.Ile902Val Uncertain significance Single submitter
- INTS2 p.Leu1177Val Uncertain significance Single submitter
- INTS2 p.Leu221Pro Uncertain significance Single submitter
- INTS2 p.Leu337Val Uncertain significance Single submitter
- INTS2 p.Leu617Phe Uncertain significance Single submitter
- INTS2 p.Leu703Pro Uncertain significance Single submitter
- INTS2 p.Leu888Met Uncertain significance Single submitter
- INTS2 p.Leu939Val Uncertain significance Single submitter
- INTS2 p.Leu978Trp Uncertain significance Single submitter
- INTS2 p.Lys1148Asn Uncertain significance Single submitter
- INTS2 p.Lys919Arg Uncertain significance Single submitter
- INTS2 p.Met142Leu Uncertain significance Single submitter
- INTS2 p.Met259Val Uncertain significance Single submitter
- INTS2 p.Met340Thr Uncertain significance Single submitter
- INTS2 p.Met444Leu Uncertain significance Single submitter
- INTS2 p.Pro1149Arg Uncertain significance Single submitter
- INTS2 p.Pro32Ser Uncertain significance Single submitter
- INTS2 p.Pro361Arg Uncertain significance Single submitter
- INTS2 p.Pro411His Uncertain significance Single submitter
- INTS2 p.Pro438Leu Uncertain significance Single submitter
- INTS2 p.Pro940Leu Uncertain significance Single submitter
- INTS2 p.Ser105Asn Uncertain significance Single submitter
- INTS2 p.Ser1098Ile Uncertain significance Single submitter
- INTS2 p.Ser232Gly Uncertain significance Single submitter
- INTS2 p.Ser28Cys Uncertain significance Single submitter
- INTS2 p.Ser324Thr Uncertain significance Single submitter
- INTS2 p.Ser348Asn Uncertain significance Single submitter
- INTS2 p.Ser367Leu Uncertain significance Single submitter
- INTS2 p.Ser557Ala Uncertain significance Single submitter
- INTS2 p.Thr1020Met Uncertain significance Single submitter
- INTS2 p.Thr345Pro Uncertain significance Single submitter
- INTS2 p.Thr786Ile Uncertain significance Single submitter
- INTS2 p.Tyr1089His Uncertain significance Single submitter
- INTS2 p.Val1123Ile Uncertain significance Single submitter
- INTS2 p.Val260Ala Uncertain significance Single submitter
- INTS2 p.Val346Ile Uncertain significance Single submitter
- INTS2 p.Val445Met Uncertain significance Single submitter
- INTS2 p.Val590Met Uncertain significance Single submitter
- INTS2 p.Val811Ile Uncertain significance Single submitter
Predictors split 29
The independent predictors disagree with each other — read with care.
- INTS2 p.Ala400Asp Uncertain significance Single submitter
- INTS2 p.Arg257Gln Uncertain significance Single submitter
- INTS2 p.Arg508Thr Uncertain significance Single submitter
- INTS2 p.Arg799Gly Uncertain significance Single submitter
- INTS2 p.Arg799Trp Uncertain significance Single submitter
- INTS2 p.Asp1000Glu Uncertain significance Single submitter
- INTS2 p.Asp589Ala Uncertain significance Single submitter
- INTS2 p.Cys990Tyr Uncertain significance Single submitter
- INTS2 p.Gln995His Uncertain significance Single submitter
- INTS2 p.Gly316Arg Uncertain significance Single submitter
- INTS2 p.His116Asp Uncertain significance Single submitter
- INTS2 p.Leu1083Ser Uncertain significance Single submitter
- INTS2 p.Leu877His Uncertain significance Single submitter
- INTS2 p.Leu918Ser Uncertain significance Single submitter
- INTS2 p.Lys304Glu Uncertain significance Single submitter
- INTS2 p.Lys320Asn Uncertain significance Single submitter
- INTS2 p.Met248Ile Uncertain significance Single submitter
- INTS2 p.Met444Ile Uncertain significance Single submitter
- INTS2 p.Met509Thr Uncertain significance Single submitter
- INTS2 p.Met996Ile Uncertain significance Single submitter
- INTS2 p.Met996Thr Uncertain significance Single submitter
- INTS2 p.Phe1048Tyr Uncertain significance Single submitter
- INTS2 p.Pro1107Leu Uncertain significance Single submitter
-
INTS2 p.Pro711Leu
Uncertain significance
Single submitter
exstrophy-epispadias complex
- INTS2 p.Pro940Arg Uncertain significance Single submitter
- INTS2 p.Ser1054Cys Uncertain significance Single submitter
- INTS2 p.Thr941Pro Uncertain significance Single submitter
- INTS2 p.Tyr1060Cys Uncertain significance Single submitter
- INTS2 p.Val815Leu Uncertain significance Single submitter
All INTS2 variants
Benign 1
- p.Gln583= No assertion criteria INTS2-related disorder
Likely benign 5
- p.Asn149Ser Single submitter
- p.Cys283Ser Single submitter
- p.Leu62= Single submitter
- c.432+5A>G No assertion criteria INTS2-related disorder
- p.Val352Ala No assertion criteria INTS2-related disorder
Uncertain significance 125
- c.-17A>G Single submitter ⚠
- c.-1A>G Single submitter ⚠
- c.-3A>G Single submitter ⚠
- p.Ala1125Ser Single submitter ⚠
- p.Ala379Val Single submitter
- p.Ala400Asp Single submitter ⚠
- p.Ala57Val Single submitter ⚠
- p.Ala599Val Single submitter ⚠
- p.Ala662Gly Single submitter ⚠
- p.Ala775Thr Single submitter ⚠
- p.Ala782Val Single submitter ⚠
- p.Arg129His Single submitter
- p.Arg227Gln Single submitter ⚠
- p.Arg237His Single submitter ⚠
- p.Arg243His Single submitter ⚠
- p.Arg257Gln Single submitter ⚠
- p.Arg306Trp Single submitter ⚠
- p.Arg350Gln Single submitter ⚠
- p.Arg410Cys Single submitter ⚠
- p.Arg410His Single submitter ⚠
- p.Arg508Thr Single submitter ⚠
- p.Arg634Cys Single submitter ⚠
- p.Arg634Gly Single submitter ⚠
- p.Arg634His Single submitter ⚠
- p.Arg733Trp Single submitter
- p.Arg734Gln Single submitter ⚠
- p.Arg799Gly Single submitter ⚠
- p.Arg799Trp Single submitter ⚠
- p.Asn1074Ser Single submitter ⚠
- p.Asn149Lys Single submitter ⚠
- p.Asn198Tyr Single submitter ⚠
- p.Asn209Asp Single submitter ⚠
- p.Asn315Ser Single submitter ⚠
- p.Asn539Ser Single submitter ⚠
- p.Asn899Ser Single submitter ⚠
- p.Asn900Ile Single submitter ⚠
- p.Asp1000Glu Single submitter ⚠
- p.Asp1167Asn Single submitter ⚠
- p.Asp589Ala Single submitter ⚠
- p.Cys980Trp Single submitter ⚠
- p.Cys990Trp Single submitter ⚠
- p.Cys990Tyr Single submitter ⚠
- p.Gln1119Arg Single submitter
- p.Gln1131Lys Single submitter ⚠
- p.Gln252Glu Single submitter ⚠
- p.Gln54Arg Single submitter ⚠
- p.Gln803Arg Single submitter ⚠
- p.Gln893Arg Single submitter ⚠
- p.Gln995His Single submitter ⚠
- p.Glu16Gly Single submitter ⚠
- p.Glu777Lys Single submitter ⚠
- p.Gly316Arg Single submitter ⚠
- p.Gly903Val Single submitter ⚠
- p.His116Asp Single submitter ⚠
- p.His124Tyr Single submitter ⚠
- p.His195Arg Single submitter ⚠
- p.His581Arg Single submitter ⚠
- p.His744Asn Single submitter ⚠
- p.His99Arg Single submitter ⚠
- p.Ile1047Leu Single submitter ⚠
- p.Ile186Met Single submitter ⚠
- p.Ile351Met Single submitter ⚠
- p.Ile512Val Single submitter ⚠
- p.Ile540Val Single submitter ⚠
- p.Ile767Thr Single submitter ⚠
- p.Ile847Leu Single submitter ⚠
- p.Ile902Val Single submitter ⚠
- p.Leu1083Ser Single submitter ⚠
- p.Leu1177Val Single submitter ⚠
- p.Leu221Pro Single submitter ⚠
- p.Leu337Val Single submitter ⚠
- p.Leu617Phe Single submitter ⚠
- p.Leu703Pro Single submitter ⚠
- p.Leu877His Single submitter ⚠
- p.Leu888Met Single submitter ⚠
- p.Leu918Ser Single submitter ⚠
- p.Leu939Val Single submitter ⚠
- p.Leu978Trp Single submitter ⚠
- p.Lys1148Asn Single submitter ⚠
- p.Lys304Glu Single submitter ⚠
- p.Lys320Asn Single submitter ⚠
- p.Lys919Arg Single submitter ⚠
- p.Met142Leu Single submitter ⚠
- p.Met248Ile Single submitter ⚠
- p.Met259Val Single submitter ⚠
- p.Met340Thr Single submitter ⚠
- p.Met444Ile Single submitter ⚠
- p.Met444Leu Single submitter ⚠
- p.Met509Thr Single submitter ⚠
- p.Met664Arg Single submitter
- p.Met996Ile Single submitter ⚠
- p.Met996Thr Single submitter ⚠
- p.Phe1048Tyr Single submitter ⚠
- p.Pro1107Leu Single submitter ⚠
- p.Pro1149Arg Single submitter ⚠
- p.Pro32Ser Single submitter ⚠
- p.Pro361Arg Single submitter ⚠
- p.Pro411His Single submitter ⚠
- p.Pro438Leu Single submitter ⚠
- p.Pro711Leu Single submitter exstrophy-epispadias complex ⚠
- p.Pro940Arg Single submitter ⚠
- p.Pro940Leu Single submitter ⚠
- p.Ser1054Cys Single submitter ⚠
- p.Ser105Asn Single submitter ⚠
- p.Ser1098Ile Single submitter ⚠
- p.Ser232Gly Single submitter ⚠
- p.Ser28Cys Single submitter ⚠
- p.Ser324Thr Single submitter ⚠
- p.Ser348Asn Single submitter ⚠
- p.Ser367Leu Single submitter ⚠
- p.Ser557Ala Single submitter ⚠
- p.Thr1020Met Single submitter ⚠
- p.Thr345Pro Single submitter ⚠
- p.Thr408Met Single submitter
- p.Thr786Ile Single submitter ⚠
- p.Thr941Pro Single submitter ⚠
- p.Tyr1060Cys Single submitter ⚠
- p.Tyr1089His Single submitter ⚠
- p.Val1123Ile Single submitter ⚠
- p.Val260Ala Single submitter ⚠
- p.Val346Ile Single submitter ⚠
- p.Val445Met Single submitter ⚠
- p.Val590Met Single submitter ⚠
- p.Val811Ile Single submitter ⚠
- p.Val815Leu Single submitter ⚠