ICOS — 190 ClinVar variants
All ClinVar germline ICOS variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 49 flagged for review →
9 Pathogenic · 3 Likely pathogenic · 9 Conflicting · 27 Benign · 62 Likely benign · 80 Uncertain significance
Full ICOS gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 49
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 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
ICOS p.Val151Leu
Conflicting
Single submitter
immunodeficiency, common variable, 1
Predictors lean, ClinVar uncertain 32
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
ICOS p.Gln134Pro
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ICOS p.Gly24Val
Uncertain significance
Multiple submitters
immunodeficiency, common variable, 1
-
ICOS p.Ile77Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ICOS p.Thr195Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ICOS p.Val151Ile
Uncertain significance
Multiple submitters
immunodeficiency, common variable, 1
-
ICOS p.Ala104Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
ICOS p.Ala26Asp
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Arg14His
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Arg193Lys
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Asn98Asp
Uncertain significance
Single submitter
Inborn genetic diseases
-
ICOS p.Asp175Asn
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Asp175His
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Asp64Asn
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Gln60Lys
Uncertain significance
Single submitter
Inborn genetic diseases
-
ICOS p.Glu29Gly
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Glu29Lys
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Gly126Arg
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Gly58Ala
Uncertain significance
Single submitter
Inborn genetic diseases
-
ICOS p.Gly72Val
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Ile113Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
ICOS p.Ile145Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
ICOS p.Ile15Met
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Ile15Val
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Leu123Val
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Leu156Val
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Leu194Ile
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Leu5Phe
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Leu62Phe
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Lys43Arg
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Lys43Asn
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Phe8Leu
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Ser172Gly
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
Predictors split 16
The independent predictors disagree with each other — read with care.
-
ICOS p.Gly36Arg
Uncertain significance
Multiple submitters
immunodeficiency, common variable, 1
-
ICOS p.Val197Met
Uncertain significance
Multiple submitters
immunodeficiency, common variable, 1
-
ICOS p.Cys136Arg
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Ile159Met
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Leu139Arg
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Lys166Glu
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Lys167Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
ICOS p.Lys168Gln
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Met183Val
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Phe119Ser
Conflicting
Single submitter
Inherited Immunodeficiency Diseases
-
ICOS p.Ser112Pro
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Ser170Leu
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Ser171Tyr
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Ser79Arg
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Ser91Gly
Uncertain significance
Single submitter
immunodeficiency, common variable, 1
-
ICOS p.Val75Met
Likely benign
No assertion criteria
EBV-positive nodal T- and NK-cell lymphoma
All ICOS variants
Pathogenic 9
- p.Glu21Ter Single submitter immunodeficiency, common variable, 1
- p.Ile61fs Single submitter immunodeficiency, common variable, 1
- p.Leu99fs Single submitter immunodeficiency, common variable, 1
- p.Phe119fs Single submitter immunodeficiency, common variable, 1
- p.Ser91fs Single submitter immunodeficiency, common variable, 1
- p.Trp6Ter Single submitter immunodeficiency, common variable, 1
- p.Tyr106Ter Single submitter immunodeficiency, common variable, 1
- p.Tyr97Ter Single submitter immunodeficiency, common variable, 1
- c.59-594_501+93del No assertion criteria immunodeficiency, common variable, 1
Likely pathogenic 3
- c.58+1G>A Multiple submitters Inherited Immunodeficiency Diseases
- c.394+2T>C Single submitter immunodeficiency, common variable, 1
- p.Asp46fs Single submitter immunodeficiency, common variable, 1
Conflicting classifications of pathogenicity 9
- c.58+9T>G Single submitter immunodeficiency, common variable, 1
- p.Arg14= Single submitter immunodeficiency, common variable, 1
- p.Asn35= Single submitter immunodeficiency, common variable, 1
- p.Cys63Ter Single submitter immunodeficiency, common variable, 1
- p.Gly125= Single submitter immunodeficiency, common variable, 1
- p.Phe119Ser Single submitter Inherited Immunodeficiency Diseases ⚠
- p.Ser170= Single submitter immunodeficiency, common variable, 1
- p.Val151Leu Single submitter immunodeficiency, common variable, 1 ⚠
- p.Val197= Single submitter immunodeficiency, common variable, 1
Benign 27
- c.501+6C>T Multiple submitters immunodeficiency, common variable, 1
- c.501+7G>A Multiple submitters immunodeficiency, common variable, 1
- c.502-113C>T Multiple submitters
- c.587-109T>C Multiple submitters
- c.587-26T>G Multiple submitters immunodeficiency, common variable, 1
- c.*1024C>T Multiple submitters immunodeficiency, common variable, 1
- c.*1262A>G Multiple submitters immunodeficiency, common variable, 1
- c.*1407G>A Multiple submitters immunodeficiency, common variable, 1
- c.*1773G>C Multiple submitters immunodeficiency, common variable, 1
- c.*2A>C Multiple submitters immunodeficiency, common variable, 1
- c.*330G>A Multiple submitters immunodeficiency, common variable, 1
- c.*33T>C Multiple submitters immunodeficiency, common variable, 1
- c.*859A>T Multiple submitters immunodeficiency, common variable, 1
- c.*964T>C Multiple submitters immunodeficiency, common variable, 1
- p.Arg14Cys Multiple submitters immunodeficiency, common variable, 1
- p.Gln50= Multiple submitters immunodeficiency, common variable, 1
- c.395-10dup Single submitter immunodeficiency, common variable, 1
- c.395-303G>T Single submitter
- c.501+117C>T Single submitter
- c.501+126C>G Single submitter
- c.502-228C>T Single submitter
- c.502-257A>G Single submitter
- c.58+173T>C Single submitter
- c.59-7dup Single submitter immunodeficiency, common variable, 1
- c.*1095A>G Single submitter immunodeficiency, common variable, 1
- c.*1249G>A Single submitter immunodeficiency, common variable, 1
- c.*855T>C Single submitter immunodeficiency, common variable, 1
Likely benign 62
- c.395-19A>G Multiple submitters immunodeficiency, common variable, 1
- c.394+10T>C Single submitter immunodeficiency, common variable, 1
- c.394+14T>G Single submitter immunodeficiency, common variable, 1
- c.394+17A>G Single submitter immunodeficiency, common variable, 1
- c.394+19C>T Single submitter immunodeficiency, common variable, 1
- c.394+7C>T Single submitter immunodeficiency, common variable, 1
- c.394+9T>C Single submitter immunodeficiency, common variable, 1
- c.395-15T>C Single submitter immunodeficiency, common variable, 1
- c.395-17del Single submitter immunodeficiency, common variable, 1
- c.395-18C>A Single submitter immunodeficiency, common variable, 1
- c.395-4C>A Single submitter immunodeficiency, common variable, 1
- c.501+12C>G Single submitter immunodeficiency, common variable, 1
- c.501+12C>T Single submitter immunodeficiency, common variable, 1
- c.501+16C>G Single submitter immunodeficiency, common variable, 1
- c.501+7G>T Single submitter immunodeficiency, common variable, 1
- c.58+13T>C Single submitter immunodeficiency, common variable, 1
- c.58+17A>C Single submitter immunodeficiency, common variable, 1
- c.58+17A>G Single submitter immunodeficiency, common variable, 1
- c.58+20T>G Single submitter immunodeficiency, common variable, 1
- c.586+11A>G Single submitter immunodeficiency, common variable, 1
- c.586+12T>C Single submitter immunodeficiency, common variable, 1
- c.586+20T>G Single submitter immunodeficiency, common variable, 1
- c.59-10T>C Single submitter immunodeficiency, common variable, 1
- c.59-16C>A Single submitter immunodeficiency, common variable, 1
- c.59-7T>C Single submitter immunodeficiency, common variable, 1
- c.*1025A>G Single submitter immunodeficiency, common variable, 1
- c.*58T>G Single submitter immunodeficiency, common variable, 1
- p.Ala185= Single submitter immunodeficiency, common variable, 1
- p.Ala189= Single submitter immunodeficiency, common variable, 1
- p.Arg184= Single submitter immunodeficiency, common variable, 1
- p.Asn110= Single submitter immunodeficiency, common variable, 1
- p.Asn177= Single submitter immunodeficiency, common variable, 1
- p.Asn98= Single submitter immunodeficiency, common variable, 1
- p.Asp175= Single submitter immunodeficiency, common variable, 1
- p.Cys137= Single submitter immunodeficiency, common variable, 1
- p.Cys63= Single submitter immunodeficiency, common variable, 1
- p.Cys83= Single submitter immunodeficiency, common variable, 1
- p.Gln134= Single submitter immunodeficiency, common variable, 1
- p.Gly146= Single submitter immunodeficiency, common variable, 1
- p.Gly157= Single submitter immunodeficiency, common variable, 1
- p.Gly178Ser Single submitter Inborn genetic diseases
- p.Gly59= Single submitter immunodeficiency, common variable, 1
- p.His129= Single submitter immunodeficiency, common variable, 1
- p.His174= Single submitter immunodeficiency, common variable, 1
- p.His34= Single submitter immunodeficiency, common variable, 1
- p.Ile130= Single submitter immunodeficiency, common variable, 1
- p.Leu143= Single submitter immunodeficiency, common variable, 1
- p.Leu194= Single submitter immunodeficiency, common variable, 1
- p.Leu199= Single submitter immunodeficiency, common variable, 1
- p.Leu55= Single submitter immunodeficiency, common variable, 1
- p.Leu62= Single submitter immunodeficiency, common variable, 1
- p.Leu80= Single submitter immunodeficiency, common variable, 1
- p.Phe31= Single submitter immunodeficiency, common variable, 1
- p.Ser112= Single submitter immunodeficiency, common variable, 1
- p.Ser172= Single submitter immunodeficiency, common variable, 1
- p.Ser192= Single submitter immunodeficiency, common variable, 1
- p.Ser3= Single submitter immunodeficiency, common variable, 1
- p.Ter200= Single submitter immunodeficiency, common variable, 1
- p.Thr165= Single submitter immunodeficiency, common variable, 1
- p.Val152= Single submitter immunodeficiency, common variable, 1
- p.Val38= Single submitter immunodeficiency, common variable, 1
- p.Val75Met No assertion criteria EBV-positive nodal T- and NK-cell lymphoma ⚠
Uncertain significance 80
- c.501+6C>G Multiple submitters immunodeficiency, common variable, 1
- c.59-3C>T Multiple submitters immunodeficiency, common variable, 1
- p.Gln134Pro Multiple submitters Inborn genetic diseases ⚠
- p.Gly24Val Multiple submitters immunodeficiency, common variable, 1 ⚠
- p.Gly36Arg Multiple submitters immunodeficiency, common variable, 1 ⚠
- p.Ile77Val Multiple submitters Inborn genetic diseases ⚠
- p.Thr195Ile Multiple submitters Inborn genetic diseases ⚠
- p.Val151Ile Multiple submitters immunodeficiency, common variable, 1 ⚠
- p.Val197Met Multiple submitters immunodeficiency, common variable, 1 ⚠
- c.502-6_502-5insG Single submitter immunodeficiency, common variable, 1
- c.58+4A>C Single submitter immunodeficiency, common variable, 1
- c.586+2T>A Single submitter immunodeficiency, common variable, 1
- c.586+3A>G Single submitter immunodeficiency, common variable, 1
- c.587-12T>G Single submitter
- c.-24G>T Single submitter immunodeficiency, common variable, 1
- c.*1004C>G Single submitter immunodeficiency, common variable, 1
- c.*1025A>T Single submitter immunodeficiency, common variable, 1
- c.*1093C>T Single submitter immunodeficiency, common variable, 1
- c.*1094C>T Single submitter immunodeficiency, common variable, 1
- c.*1137C>T Single submitter immunodeficiency, common variable, 1
- c.*1172G>A Single submitter immunodeficiency, common variable, 1
- c.*1269A>C Single submitter immunodeficiency, common variable, 1
- c.*1293T>C Single submitter immunodeficiency, common variable, 1
- c.*1300C>T Single submitter immunodeficiency, common variable, 1
- c.*1416G>T Single submitter immunodeficiency, common variable, 1
- c.*1457A>G Single submitter immunodeficiency, common variable, 1
- c.*1854G>A Single submitter immunodeficiency, common variable, 1
- c.*1869A>C Single submitter immunodeficiency, common variable, 1
- c.*1901A>G Single submitter immunodeficiency, common variable, 1
- c.*1948G>T Single submitter immunodeficiency, common variable, 1
- c.*399G>A Single submitter immunodeficiency, common variable, 1
- c.*474G>T Single submitter immunodeficiency, common variable, 1
- c.*512T>C Single submitter immunodeficiency, common variable, 1
- c.*594C>T Single submitter immunodeficiency, common variable, 1
- c.*73T>C Single submitter immunodeficiency, common variable, 1
- c.*77C>T Single submitter immunodeficiency, common variable, 1
- c.*931A>G Single submitter immunodeficiency, common variable, 1
- c.*939A>G Single submitter immunodeficiency, common variable, 1
- c.*977T>G Single submitter immunodeficiency, common variable, 1
- c.*995C>T Single submitter immunodeficiency, common variable, 1
- p.Ala104Val Single submitter Inborn genetic diseases ⚠
- p.Ala26Asp Single submitter immunodeficiency, common variable, 1 ⚠
- p.Arg14His Single submitter immunodeficiency, common variable, 1 ⚠
- p.Arg193Lys Single submitter immunodeficiency, common variable, 1 ⚠
- p.Asn98Asp Single submitter Inborn genetic diseases ⚠
- p.Asp175Asn Single submitter immunodeficiency, common variable, 1 ⚠
- p.Asp175His Single submitter immunodeficiency, common variable, 1 ⚠
- p.Asp64Asn Single submitter immunodeficiency, common variable, 1 ⚠
- p.Cys136Arg Single submitter immunodeficiency, common variable, 1 ⚠
- p.Gln60Lys Single submitter Inborn genetic diseases ⚠
- p.Glu29Gly Single submitter immunodeficiency, common variable, 1 ⚠
- p.Glu29Lys Single submitter immunodeficiency, common variable, 1 ⚠
- p.Gly126Arg Single submitter immunodeficiency, common variable, 1 ⚠
- p.Gly58Ala Single submitter Inborn genetic diseases ⚠
- p.Gly72Val Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ile113Val Single submitter Inborn genetic diseases ⚠
- p.Ile145Val Single submitter Inborn genetic diseases ⚠
- p.Ile159Met Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ile15Met Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ile15Val Single submitter immunodeficiency, common variable, 1 ⚠
- p.Leu123Val Single submitter immunodeficiency, common variable, 1 ⚠
- p.Leu139Arg Single submitter immunodeficiency, common variable, 1 ⚠
- p.Leu156Val Single submitter immunodeficiency, common variable, 1 ⚠
- p.Leu194Ile Single submitter immunodeficiency, common variable, 1 ⚠
- p.Leu5Phe Single submitter immunodeficiency, common variable, 1 ⚠
- p.Leu62Phe Single submitter immunodeficiency, common variable, 1 ⚠
- p.Lys166Glu Single submitter immunodeficiency, common variable, 1 ⚠
- p.Lys167Met Single submitter Inborn genetic diseases ⚠
- p.Lys168Gln Single submitter immunodeficiency, common variable, 1 ⚠
- p.Lys43Arg Single submitter immunodeficiency, common variable, 1 ⚠
- p.Lys43Asn Single submitter immunodeficiency, common variable, 1 ⚠
- p.Met183Val Single submitter immunodeficiency, common variable, 1 ⚠
- p.Phe8Leu Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ser112Pro Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ser170Leu Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ser171Tyr Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ser172Gly Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ser79Arg Single submitter immunodeficiency, common variable, 1 ⚠
- p.Ser91Gly Single submitter immunodeficiency, common variable, 1 ⚠
- p.Thr188_Lys191del Single submitter immunodeficiency, common variable, 1