GLI1 — 222 ClinVar variants
All ClinVar germline GLI1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 149 flagged for review →
5 Pathogenic · 9 Likely pathogenic · 3 Conflicting · 9 Benign · 3 Benign/Likely benign · 37 Likely benign · 156 Uncertain significance
Full GLI1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 149
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 2
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
- GLI1 p.Gly600Cys Conflicting Single submitter
-
GLI1 p.Trp272Cys
Conflicting
Single submitter
polydactyly, postaxial, type A8
Predictors lean, ClinVar uncertain 128
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
GLI1 p.Arg293Cys
Uncertain significance
Multiple submitters
polydactyly, postaxial, type A8
- GLI1 p.Arg496Cys Uncertain significance Multiple submitters
- GLI1 p.Gly368Asp Uncertain significance Multiple submitters
- GLI1 p.Pro361Leu Uncertain significance Multiple submitters
- GLI1 p.Pro535Ser Uncertain significance Multiple submitters
- GLI1 p.Pro842Ser Uncertain significance Multiple submitters
- GLI1 p.Ala137Val Uncertain significance Single submitter
- GLI1 p.Ala349Thr Uncertain significance Single submitter
- GLI1 p.Ala391Thr Uncertain significance Single submitter
- GLI1 p.Ala562Thr Uncertain significance Single submitter
- GLI1 p.Ala591Ser Uncertain significance Single submitter
- GLI1 p.Ala645Thr Uncertain significance Single submitter
- GLI1 p.Ala670Ser Uncertain significance Single submitter
- GLI1 p.Ala920Thr Uncertain significance Single submitter
- GLI1 p.Ala978Ser Uncertain significance Single submitter
- GLI1 p.Ala986Thr Uncertain significance Single submitter
- GLI1 p.Arg161Trp Uncertain significance Single submitter
- GLI1 p.Arg191Trp Uncertain significance Single submitter
- GLI1 p.Arg20Trp Uncertain significance Single submitter
- GLI1 p.Arg227His Uncertain significance Single submitter
- GLI1 p.Arg314Cys Uncertain significance Single submitter
- GLI1 p.Arg314His Uncertain significance Single submitter
- GLI1 p.Arg348Gly Uncertain significance Single submitter
- GLI1 p.Arg497His Uncertain significance Single submitter
- GLI1 p.Arg510Pro Uncertain significance Single submitter
- GLI1 p.Arg515Trp Uncertain significance Single submitter
- GLI1 p.Arg532His Uncertain significance Single submitter
- GLI1 p.Arg611Gln Uncertain significance Single submitter
- GLI1 p.Arg623Gln Uncertain significance Single submitter
- GLI1 p.Arg637Gln Uncertain significance Single submitter
- GLI1 p.Arg878Ser Uncertain significance Single submitter
- GLI1 p.Arg940Cys Uncertain significance Single submitter
- GLI1 p.Arg990Gln Uncertain significance Single submitter
- GLI1 p.Asn45Lys Uncertain significance Single submitter
- GLI1 p.Asn460Asp Uncertain significance Single submitter
- GLI1 p.Asn460Ile Uncertain significance Single submitter
- GLI1 p.Asn760Ser Uncertain significance Single submitter
- GLI1 p.Asn834Ser Uncertain significance Single submitter
- GLI1 p.Asp220Gly Uncertain significance Single submitter
- GLI1 p.Asp825Gly Uncertain significance Single submitter
- GLI1 p.Gln352His Uncertain significance Single submitter
- GLI1 p.Gln508His Uncertain significance Single submitter
- GLI1 p.Gln802Arg Uncertain significance Single submitter
- GLI1 p.Gln853Glu Uncertain significance Single submitter
- GLI1 p.Gln896His Uncertain significance Single submitter
- GLI1 p.Glu1030Lys Uncertain significance Single submitter
- GLI1 p.Glu196Asp Uncertain significance Single submitter
- GLI1 p.Glu219Lys Uncertain significance Single submitter
- GLI1 p.Glu225Asp Uncertain significance Single submitter
- GLI1 p.Glu225Lys Uncertain significance Single submitter
- GLI1 p.Glu336Gln Uncertain significance Single submitter
- GLI1 p.Glu483Lys Uncertain significance Single submitter
- GLI1 p.Glu64Lys Uncertain significance Single submitter
- GLI1 p.Gly1021Arg Uncertain significance Single submitter
- GLI1 p.Gly307Glu Uncertain significance Single submitter
- GLI1 p.Gly421Ser Uncertain significance Single submitter
- GLI1 p.Gly49Ser Uncertain significance Single submitter
- GLI1 p.Gly526Ser Uncertain significance Single submitter
- GLI1 p.Gly526Val Uncertain significance Single submitter
- GLI1 p.Gly672Ala Uncertain significance Single submitter
- GLI1 p.Gly710Glu Uncertain significance Single submitter
- GLI1 p.Gly823Glu Uncertain significance Single submitter
- GLI1 p.Gly951Ala Uncertain significance Single submitter
- GLI1 p.Gly953Arg Uncertain significance Single submitter
- GLI1 p.His157Arg Uncertain significance Single submitter
- GLI1 p.His664Tyr Uncertain significance Single submitter
- GLI1 p.Ile207Val Uncertain significance Single submitter
- GLI1 p.Ile512Thr Uncertain significance Single submitter
- GLI1 p.Ile512Val Uncertain significance Single submitter
- GLI1 p.Leu403Val Uncertain significance Single submitter
- GLI1 p.Leu753Pro Uncertain significance Single submitter
- GLI1 p.Leu789Met Uncertain significance Single submitter
- GLI1 p.Leu897Val Uncertain significance Single submitter
- GLI1 p.Lys189Thr Uncertain significance Single submitter
- GLI1 p.Lys794Thr Uncertain significance Single submitter
- GLI1 p.Met698Leu Uncertain significance Single submitter
- GLI1 p.Pro1063Leu Uncertain significance Single submitter
- GLI1 p.Pro1076His Uncertain significance Single submitter
- GLI1 p.Pro1077Ser Uncertain significance Single submitter
- GLI1 p.Pro1080Thr Uncertain significance Single submitter
- GLI1 p.Pro145Leu Uncertain significance Single submitter
- GLI1 p.Pro147Ala Uncertain significance Single submitter
- GLI1 p.Pro153Leu Uncertain significance Single submitter
- GLI1 p.Pro166Ser Uncertain significance Single submitter
- GLI1 p.Pro21Thr Uncertain significance Single submitter
- GLI1 p.Pro402Ser Uncertain significance Single submitter
- GLI1 p.Pro404Leu Uncertain significance Single submitter
- GLI1 p.Pro454Leu Uncertain significance Single submitter
- GLI1 p.Pro567Thr Uncertain significance Single submitter
- GLI1 p.Pro571Leu Uncertain significance Single submitter
- GLI1 p.Pro571Ser Uncertain significance Single submitter
- GLI1 p.Pro579Thr Uncertain significance Single submitter
- GLI1 p.Pro618Leu Uncertain significance Single submitter
- GLI1 p.Pro627Ser Uncertain significance Single submitter
- GLI1 p.Pro687Ser Uncertain significance Single submitter
- GLI1 p.Pro755Leu Uncertain significance Single submitter
- GLI1 p.Pro755Ser Uncertain significance Single submitter
- GLI1 p.Pro821Thr Uncertain significance Single submitter
- GLI1 p.Pro842Gln Uncertain significance Single submitter
- GLI1 p.Pro870Ala Uncertain significance Single submitter
- GLI1 p.Pro879Ala Uncertain significance Single submitter
- GLI1 p.Pro967Ser Uncertain significance Single submitter
- GLI1 p.Ser1010Gly Uncertain significance Single submitter
- GLI1 p.Ser104Asn Uncertain significance Single submitter
- GLI1 p.Ser112Trp Uncertain significance Single submitter
- GLI1 p.Ser181Pro Uncertain significance Single submitter
- GLI1 p.Ser311Leu Uncertain significance Single submitter
- GLI1 p.Ser4Leu Uncertain significance Single submitter
- GLI1 p.Ser546Cys Uncertain significance Single submitter
- GLI1 p.Ser716Arg Uncertain significance Single submitter
- GLI1 p.Ser801Asn Uncertain significance Single submitter
- GLI1 p.Ser849Pro Uncertain significance Single submitter
- GLI1 p.Ser982Leu Uncertain significance Single submitter
- GLI1 p.Thr326Met Uncertain significance Single submitter
- GLI1 p.Thr525Pro Uncertain significance Single submitter
- GLI1 p.Thr59Ile Uncertain significance Single submitter
- GLI1 p.Thr997Ser Uncertain significance Single submitter
- GLI1 p.Tyr679Phe Uncertain significance Single submitter
-
GLI1 p.Tyr743His
Uncertain significance
Single submitter
primary ovarian failure
- GLI1 p.Tyr790His Uncertain significance Single submitter
- GLI1 p.Tyr809Phe Uncertain significance Single submitter
- GLI1 p.Tyr948Asp Uncertain significance Single submitter
- GLI1 p.Val431Met Uncertain significance Single submitter
- GLI1 p.Val537Ala Uncertain significance Single submitter
- GLI1 p.Val812Met Uncertain significance Single submitter
- GLI1 p.Val898Leu Uncertain significance Single submitter
-
GLI1 p.Cys177Tyr
Uncertain significance
No assertion criteria
prostate cancer
-
GLI1 p.Gly274Arg
Uncertain significance
No assertion criteria
Bardet-Biedl syndrome
Predictors split 19
The independent predictors disagree with each other — read with care.
-
GLI1 p.Leu506Gln
Uncertain significance
Multiple submitters
polydactyly of a biphalangeal thumb
- GLI1 p.Ser105Tyr Likely benign Multiple submitters
- GLI1 p.Arg238Cys Uncertain significance Single submitter
- GLI1 p.Arg309Trp Uncertain significance Single submitter
- GLI1 p.Arg405Trp Uncertain significance Single submitter
- GLI1 p.Arg542Cys Uncertain significance Single submitter
- GLI1 p.Arg558Pro Uncertain significance Single submitter
- GLI1 p.Arg81Pro Uncertain significance Single submitter
- GLI1 p.Asp641Tyr Uncertain significance Single submitter
- GLI1 p.Cys662Ser Uncertain significance Single submitter
- GLI1 p.Glu259Gln Uncertain significance Single submitter
- GLI1 p.Gly122Arg Uncertain significance Single submitter
- GLI1 p.Gly273Arg Uncertain significance Single submitter
- GLI1 p.Leu893Pro Uncertain significance Single submitter
- GLI1 p.Met1083Ile Uncertain significance Single submitter
- GLI1 p.Ser84Pro Uncertain significance Single submitter
- GLI1 p.Ser92Asn Uncertain significance Single submitter
- GLI1 p.Thr1099Ile Uncertain significance Single submitter
- GLI1 p.Phe1101Leu Uncertain significance No assertion criteria
All GLI1 variants
Pathogenic 5
- p.Arg113Ter Single submitter polydactyly, postaxial, type A8
- p.Cys338Phe Single submitter polydactyly, postaxial, type A8
- p.Pro454fs Single submitter
- p.Trp780Ter Single submitter polydactyly, postaxial, type A8
- p.Gln644Ter No assertion criteria polydactyly, postaxial, type A8
Likely pathogenic 9
- c.1078-1G>C Single submitter GLI1-related disorder
- c.912+2T>C Single submitter GLI1-related disorders
- p.Cys275fs Single submitter
- p.Gly274fs Single submitter Autosomal recessive GLI1-related disorders
- p.Gly599fs Single submitter
- p.Gly933fs Single submitter polydactyly, postaxial, type A8
- p.Lys329Ter Single submitter polydactyly, postaxial, type A8
- p.Ser474fs Single submitter Autosomal recessive GLI1-related disorders
- p.Arg990Ter No assertion criteria GLI1-related disorder
Conflicting classifications of pathogenicity 3
- p.Gly600Cys Single submitter ⚠
- p.Trp272Cys Single submitter polydactyly, postaxial, type A8 ⚠
- p.Trp620Ter Single submitter
Benign 9
- p.Ala1106= Multiple submitters
- p.Arg405Gln Multiple submitters
- p.Pro168Arg Multiple submitters
- p.Pro520= Multiple submitters
- p.Ser712= Multiple submitters
- p.Gly1012Val Single submitter
- p.Thr97= Single submitter
- p.His262= No assertion criteria GLI1-related disorder
- p.Tyr362= No assertion criteria GLI1-related disorder
Benign/Likely benign 3
- p.Glu1100Gln Multiple submitters polydactyly of a biphalangeal thumb
- p.Glu192= Multiple submitters polydactyly of a biphalangeal thumb
- p.Gly933Asp Multiple submitters polydactyly of a biphalangeal thumb
Likely benign 37
- p.Arg1068Trp Multiple submitters
- p.Arg510= Multiple submitters
- p.Arg510Trp Multiple submitters
- p.Ile99= Multiple submitters
- p.Ser105Tyr Multiple submitters ⚠
- p.Tyr121= Multiple submitters
- c.101-16T>A Single submitter
- c.194-18C>T Single submitter
- c.194-9C>G Single submitter
- p.Ala455= Single submitter
- p.Ala606= Single submitter
- p.Ala624= Single submitter
- p.Arg161Gln Single submitter
- p.Asn632= Single submitter
- p.Gln508= Single submitter
- p.Gly912= Single submitter
- p.His260= Single submitter
- p.His335= Single submitter
- p.Leu495= Single submitter
- p.Leu503= Single submitter
- p.Leu519= Single submitter
- p.Lys226= Single submitter
- p.Phe268= Single submitter
- p.Pro1080= Single submitter
- p.Pro631= Single submitter
- p.Ser378= Single submitter
- p.Ser48= Single submitter
- p.Ser659= Single submitter
- p.Thr326= Single submitter
- p.Thr636= Single submitter
- p.Thr665= Single submitter
- p.Val533Leu Single submitter
- p.Gln1046= No assertion criteria GLI1-related disorder
- p.Leu315= No assertion criteria GLI1-related disorder
- p.Leu379= No assertion criteria GLI1-related disorder
- p.Ser563= No assertion criteria GLI1-related disorder
- p.Ser89= No assertion criteria GLI1-related disorder
Uncertain significance 156
- p.Arg293Cys Multiple submitters polydactyly, postaxial, type A8 ⚠
- p.Arg496Cys Multiple submitters ⚠
- p.Gly368Asp Multiple submitters ⚠
- p.Leu506Gln Multiple submitters polydactyly of a biphalangeal thumb ⚠
- p.Pro361Leu Multiple submitters ⚠
- p.Pro535Ser Multiple submitters ⚠
- p.Pro842Ser Multiple submitters ⚠
- c.1077+20G>A Single submitter
- p.Ala137Val Single submitter ⚠
- p.Ala349Thr Single submitter ⚠
- p.Ala391Thr Single submitter ⚠
- p.Ala562Thr Single submitter ⚠
- p.Ala591Ser Single submitter ⚠
- p.Ala645Thr Single submitter ⚠
- p.Ala670Ser Single submitter ⚠
- p.Ala920Thr Single submitter ⚠
- p.Ala978Ser Single submitter ⚠
- p.Ala986Thr Single submitter ⚠
- p.Arg161Trp Single submitter ⚠
- p.Arg191Trp Single submitter ⚠
- p.Arg20Trp Single submitter ⚠
- p.Arg227His Single submitter ⚠
- p.Arg238Cys Single submitter ⚠
- p.Arg309Trp Single submitter ⚠
- p.Arg314Cys Single submitter ⚠
- p.Arg314His Single submitter ⚠
- p.Arg348Gly Single submitter ⚠
- p.Arg405Trp Single submitter ⚠
- p.Arg497His Single submitter ⚠
- p.Arg510Pro Single submitter ⚠
- p.Arg515Trp Single submitter ⚠
- p.Arg532His Single submitter ⚠
- p.Arg542Cys Single submitter ⚠
- p.Arg558Pro Single submitter ⚠
- p.Arg611Gln Single submitter ⚠
- p.Arg623Gln Single submitter ⚠
- p.Arg623Ter Single submitter
- p.Arg637Gln Single submitter ⚠
- p.Arg81Pro Single submitter ⚠
- p.Arg878Ser Single submitter ⚠
- p.Arg940Cys Single submitter ⚠
- p.Arg990Gln Single submitter ⚠
- p.Asn45Lys Single submitter ⚠
- p.Asn460Asp Single submitter ⚠
- p.Asn460Ile Single submitter ⚠
- p.Asn760Ser Single submitter ⚠
- p.Asn834Ser Single submitter ⚠
- p.Asp220Gly Single submitter ⚠
- p.Asp641Tyr Single submitter ⚠
- p.Asp825Gly Single submitter ⚠
- p.Cys154Arg Single submitter
- p.Cys662Ser Single submitter ⚠
- p.Gln178= Single submitter
- p.Gln352His Single submitter ⚠
- p.Gln508His Single submitter ⚠
- p.Gln802Arg Single submitter ⚠
- p.Gln853Glu Single submitter ⚠
- p.Gln896His Single submitter ⚠
- p.Glu1030Lys Single submitter ⚠
- p.Glu196Asp Single submitter ⚠
- p.Glu219Lys Single submitter ⚠
- p.Glu225Asp Single submitter ⚠
- p.Glu225Lys Single submitter ⚠
- p.Glu259Gln Single submitter ⚠
- p.Glu336Gln Single submitter ⚠
- p.Glu483Lys Single submitter ⚠
- p.Glu64Lys Single submitter ⚠
- p.Gly1021Arg Single submitter ⚠
- p.Gly1022fs Single submitter polydactyly, postaxial, type A8
- p.Gly122Arg Single submitter ⚠
- p.Gly273Arg Single submitter ⚠
- p.Gly307Glu Single submitter ⚠
- p.Gly421Ser Single submitter ⚠
- p.Gly49Ser Single submitter ⚠
- p.Gly526Ser Single submitter ⚠
- p.Gly526Val Single submitter ⚠
- p.Gly672Ala Single submitter ⚠
- p.Gly710Glu Single submitter ⚠
- p.Gly823Glu Single submitter ⚠
- p.Gly951Ala Single submitter ⚠
- p.Gly953Arg Single submitter ⚠
- p.His157Arg Single submitter ⚠
- p.His271Arg Single submitter
- p.His664Tyr Single submitter ⚠
- p.Ile207Val Single submitter ⚠
- p.Ile512Thr Single submitter ⚠
- p.Ile512Val Single submitter ⚠
- p.Leu1040fs Single submitter
- p.Leu403Val Single submitter ⚠
- p.Leu753Pro Single submitter ⚠
- p.Leu789Met Single submitter ⚠
- p.Leu893Pro Single submitter ⚠
- p.Leu897Val Single submitter ⚠
- p.Lys189Thr Single submitter ⚠
- p.Lys794Thr Single submitter ⚠
- p.Met1083Ile Single submitter ⚠
- p.Met698Leu Single submitter ⚠
- p.Pro1063Leu Single submitter ⚠
- p.Pro1076His Single submitter ⚠
- p.Pro1077Ser Single submitter ⚠
- p.Pro1080Thr Single submitter ⚠
- p.Pro145Leu Single submitter ⚠
- p.Pro147Ala Single submitter ⚠
- p.Pro153Leu Single submitter ⚠
- p.Pro166Ser Single submitter ⚠
- p.Pro21Thr Single submitter ⚠
- p.Pro402Ser Single submitter ⚠
- p.Pro404Leu Single submitter ⚠
- p.Pro454Leu Single submitter ⚠
- p.Pro567Thr Single submitter ⚠
- p.Pro571Leu Single submitter ⚠
- p.Pro571Ser Single submitter ⚠
- p.Pro579Thr Single submitter ⚠
- p.Pro618Leu Single submitter ⚠
- p.Pro627Ser Single submitter ⚠
- p.Pro687Ser Single submitter ⚠
- p.Pro755Leu Single submitter ⚠
- p.Pro755Ser Single submitter ⚠
- p.Pro821Thr Single submitter ⚠
- p.Pro842Gln Single submitter ⚠
- p.Pro870Ala Single submitter ⚠
- p.Pro879Ala Single submitter ⚠
- p.Pro967Ser Single submitter ⚠
- p.Ser1010Gly Single submitter ⚠
- p.Ser104Asn Single submitter ⚠
- p.Ser112Trp Single submitter ⚠
- p.Ser181Pro Single submitter ⚠
- p.Ser311Leu Single submitter ⚠
- p.Ser4Leu Single submitter ⚠
- p.Ser546Cys Single submitter ⚠
- p.Ser716Arg Single submitter ⚠
- p.Ser801Asn Single submitter ⚠
- p.Ser849Pro Single submitter ⚠
- p.Ser84Pro Single submitter ⚠
- p.Ser92Asn Single submitter ⚠
- p.Ser982Leu Single submitter ⚠
- p.Thr1099Ile Single submitter ⚠
- p.Thr326Met Single submitter ⚠
- p.Thr525= Single submitter
- p.Thr525Pro Single submitter ⚠
- p.Thr59Ile Single submitter ⚠
- p.Thr997Ser Single submitter ⚠
- p.Tyr553Cys Single submitter
- p.Tyr679Phe Single submitter ⚠
- p.Tyr743His Single submitter primary ovarian failure ⚠
- p.Tyr790His Single submitter ⚠
- p.Tyr809Phe Single submitter ⚠
- p.Tyr948Asp Single submitter ⚠
- p.Val431Met Single submitter ⚠
- p.Val537Ala Single submitter ⚠
- p.Val812Met Single submitter ⚠
- p.Val898Leu Single submitter ⚠
- p.Arg238Leu No assertion criteria GLI1-related disorder
- p.Cys177Tyr No assertion criteria prostate cancer ⚠
- p.Gly274Arg No assertion criteria Bardet-Biedl syndrome ⚠
- p.Phe1101Leu No assertion criteria ⚠