LRIG2 — 214 ClinVar variants

All ClinVar germline LRIG2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 140 flagged for review →

6 Pathogenic · 9 Likely pathogenic · 3 Conflicting · 10 Benign · 2 Benign/Likely benign · 27 Likely benign · 157 Uncertain significance

Full LRIG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 140

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 3

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 117

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 20

The independent predictors disagree with each other — read with care.

All LRIG2 variants

Pathogenic 6

c.804-2A>C Single submitter Global developmental delay
p.Leu6fs Single submitter
p.Arg709Ter No assertion criteria urofacial syndrome 2
p.Glu410fs No assertion criteria urofacial syndrome 2
p.Ile662Phefs No assertion criteria urofacial syndrome 2
p.Ser697fs No assertion criteria urofacial syndrome 2

Likely pathogenic 9

c.1799-2_1799-1delAG Single submitter urofacial syndrome 2
c.2530+1G>T Single submitter urofacial syndrome 2
c.306-2A>G Single submitter
p.Gln29Ter Single submitter
p.Glu926fs Single submitter urofacial syndrome 2
p.Ser175fs Single submitter urofacial syndrome 2
p.Thr363_Leu364insTer Single submitter
p.Glu413Ter No assertion criteria
p.Ser523Arg No assertion criteria

Conflicting classifications of pathogenicity 3

p.Arg550Cys Single submitter ⚠
p.Gly1030Arg Single submitter ⚠
p.Gly7Ala Single submitter ⚠

Benign 10

c.2531-22G>A Multiple submitters urofacial syndrome 2
c.2680+10_2680+11del Multiple submitters
p.Asp755Glu Multiple submitters
p.Ser563Thr Multiple submitters
p.Thr708= Multiple submitters urofacial syndrome 2
p.Val469Ile Multiple submitters
c.2680+7A>G Single submitter
p.Pro113= Single submitter
p.Ser163= Single submitter
p.Thr765Ile No assertion criteria LRIG2-related disorder

Benign/Likely benign 2

p.Thr915Ile Multiple submitters
p.Val598Leu Multiple submitters

Likely benign 27

p.Ala2= Multiple submitters
p.Ile155Leu Multiple submitters
p.Pro882Leu Multiple submitters
p.Thr433= Multiple submitters
p.Thr933= Multiple submitters
c.1314-7C>T Single submitter
c.660-18A>C Single submitter
c.-4G>A Single submitter
p.Ala45= Single submitter
p.Ala713= Single submitter
p.Arg166His Single submitter
p.Asn177= Single submitter
p.Glu845= Single submitter
p.Gly39Arg Single submitter
p.Gly990Ser Single submitter
p.Ile299Val Single submitter
p.Ile508Val Single submitter
p.Ile823= Single submitter
p.Pro1009= Single submitter
p.Pro75= Single submitter
p.Ser240= Single submitter
p.Thr181Ile Single submitter
p.Thr771= Single submitter
c.660-7G>A No assertion criteria LRIG2-related disorder
p.Asp760= No assertion criteria LRIG2-related disorder
p.Asp928= No assertion criteria LRIG2-related disorder
p.Phe187= No assertion criteria LRIG2-related disorder

Uncertain significance 157

p.Arg86Trp Multiple submitters urofacial syndrome 2 ⚠
p.Glu11Ter Multiple submitters urofacial syndrome 2
p.Lys245Arg Multiple submitters ⚠
c.515+14A>G Single submitter urofacial syndrome 2
p.Ala137Ser Single submitter ⚠
p.Ala28Ser Single submitter ⚠
p.Ala330Asp Single submitter ⚠
p.Ala330Thr Single submitter ⚠
p.Ala374Val Single submitter ⚠
p.Ala383Gly Single submitter ⚠
p.Ala421Thr Single submitter ⚠
p.Ala663Asp Single submitter ⚠
p.Ala964Val Single submitter ⚠
p.Arg1056Gln Single submitter ⚠
p.Arg203Ter Single submitter
p.Arg224fs Single submitter
p.Arg23Gln Single submitter ⚠
p.Arg287Gln Single submitter ⚠
p.Arg325Cys Single submitter
p.Arg339Gly Single submitter ⚠
p.Arg50Gly Single submitter ⚠
p.Arg50Leu Single submitter ⚠
p.Arg534His Single submitter
p.Arg550His Single submitter ⚠
p.Arg650Leu Single submitter ⚠
p.Arg650Ser Single submitter ⚠
p.Arg726His Single submitter ⚠
p.Arg741Gln Single submitter ⚠
p.Arg776Cys Single submitter ⚠
p.Arg832Gly Single submitter ⚠
p.Arg833Lys Single submitter ⚠
p.Arg899Gln Single submitter ⚠
p.Arg916Leu Single submitter ⚠
p.Arg977Ser Single submitter ⚠
p.Arg995Gln Single submitter ⚠
p.Asn274Ser Single submitter ⚠
p.Asn321Lys Single submitter ⚠
p.Asn341His Single submitter ⚠
p.Asn418Ser Single submitter ⚠
p.Asn428Asp Single submitter ⚠
p.Asn461Thr Single submitter ⚠
p.Asn484Ser Single submitter ⚠
p.Asn770Asp Single submitter ⚠
p.Asn788Ser Single submitter ⚠
p.Asp188Asn Single submitter ⚠
p.Asp365His Single submitter ⚠
p.Asp493Gly Single submitter
p.Asp732Gly Single submitter ⚠
p.Asp76Asn Single submitter ⚠
p.Asp893His Single submitter ⚠
p.Asp931Gly Single submitter ⚠
p.Cys49Tyr Single submitter ⚠
p.Gln678Arg Single submitter ⚠
p.Gln940His Single submitter ⚠
p.Gln952Pro Single submitter ⚠
p.Glu158Lys Single submitter ⚠
p.Glu221Asp Single submitter ⚠
p.Glu376Gly Single submitter ⚠
p.Glu560Gly Single submitter ⚠
p.Glu622Lys Single submitter ⚠
p.Glu703Gln Single submitter ⚠
p.Glu958Ala Single submitter ⚠
p.Gly1027Val Single submitter ⚠
p.Gly1064Asp Single submitter ⚠
p.Gly556Arg Single submitter
p.Gly640Ser Single submitter ⚠
p.Gly683Asp Single submitter ⚠
p.Gly819Arg Single submitter ⚠
p.His1008Tyr Single submitter ⚠
p.His1023Pro Single submitter ⚠
p.His1048Arg Single submitter ⚠
p.His129Arg Single submitter
p.His349Tyr Single submitter ⚠
p.His465Asn Single submitter ⚠
p.His566Tyr Single submitter urofacial syndrome 2 ⚠
p.His830Tyr Single submitter ⚠
p.His949Tyr Single submitter ⚠
p.Ile135Val Single submitter ⚠
p.Ile159Asn Single submitter ⚠
p.Ile371Met Single submitter ⚠
p.Ile375Thr Single submitter
p.Ile425Val Single submitter ⚠
p.Ile439Phe Single submitter ⚠
p.Ile482Asn Single submitter ⚠
p.Ile51Val Single submitter ⚠
p.Ile753Thr Single submitter ⚠
p.Ile808Thr Single submitter ⚠
p.Leu169Pro Single submitter ⚠
p.Leu275Arg Single submitter ⚠
p.Leu32Val Single submitter ⚠
p.Leu409Pro Single submitter ⚠
p.Leu458Phe Single submitter ⚠
p.Leu758Ile Single submitter ⚠
p.Leu846Pro Single submitter ⚠
p.Leu848Pro Single submitter urofacial syndrome 2
p.Leu862Pro Single submitter ⚠
p.Lys705Asn Single submitter ⚠
p.Met204Val Single submitter ⚠
p.Met513Thr Single submitter ⚠
p.Met609Val Single submitter ⚠
p.Met881Val Single submitter ⚠
p.Met938Ile Single submitter ⚠
p.Phe331Leu Single submitter ⚠
p.Phe357Tyr Single submitter ⚠
p.Phe586Val Single submitter ⚠
p.Pro209Arg Single submitter ⚠
p.Pro304Ser Single submitter ⚠
p.Pro36Ser Single submitter ⚠
p.Pro44His Single submitter ⚠
p.Pro631Arg Single submitter ⚠
p.Pro655Arg Single submitter ⚠
p.Pro74Thr Single submitter ⚠
p.Pro962Leu Single submitter ⚠
p.Pro996Leu Single submitter ⚠
p.Pro9Thr Single submitter ⚠
p.Ser466Ala Single submitter ⚠
p.Ser48Phe Single submitter ⚠
p.Ser537Thr Single submitter ⚠
p.Ser57Gly Single submitter ⚠
p.Ser795Gly Single submitter ⚠
p.Ser876Asn Single submitter ⚠
p.Ser969Pro Single submitter ⚠
p.Ser985Cys Single submitter ⚠
p.Thr234Ile Single submitter ⚠
p.Thr386Ile Single submitter ⚠
p.Thr531Ser Single submitter ⚠
p.Thr545Ser Single submitter ⚠
p.Thr691Ile Single submitter ⚠
p.Thr695Ile Single submitter ⚠
p.Thr771Ile Single submitter
p.Thr774Lys Single submitter ⚠
p.Thr805Ala Single submitter ⚠
p.Thr861Met Single submitter ⚠
p.Thr955Ala Single submitter ⚠
p.Thr98Ile Single submitter ⚠
p.Thr98Ser Single submitter ⚠
p.Tyr541Cys Single submitter ⚠
p.Tyr590His Single submitter
p.Tyr673Cys Single submitter ⚠
p.Tyr838Cys Single submitter ⚠
p.Tyr855Cys Single submitter
p.Tyr869His Single submitter ⚠
p.Tyr921Ser Single submitter ⚠
p.Val128Ile Single submitter ⚠
p.Val354Ile Single submitter ⚠
p.Val485Met Single submitter ⚠
p.Val570Met Single submitter ⚠
p.Val653Ile Single submitter ⚠
p.Val653Phe Single submitter ⚠
p.Val738Gly Single submitter
p.Val8Gly Single submitter ⚠
p.Arg1044fs No assertion criteria
p.Gln553Ter No assertion criteria
p.Ile826fs No assertion criteria
p.Met1Ile No assertion criteria
p.Phe331fs No assertion criteria
p.Pro696His No assertion criteria ⚠