TOM1 — 86 ClinVar variants
All ClinVar germline TOM1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 65 flagged for review →
1 Pathogenic · 2 Conflicting · 8 Benign · 9 Likely benign · 66 Uncertain significance
Full TOM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 65
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 vs ClinVar 1
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
-
TOM1 p.Gly307Asp
Pathogenic
No assertion criteria
immunodeficiency 85 and autoimmunity
Predictors agree, ClinVar conflicts 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
Predictors lean, ClinVar uncertain 46
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- TOM1 p.Ala401Pro Uncertain significance Multiple submitters
-
TOM1 p.Asp324Asn
Uncertain significance
Multiple submitters
immunodeficiency 85 and autoimmunity
-
TOM1 p.Ser461Phe
Uncertain significance
Multiple submitters
immunodeficiency 85 and autoimmunity
- TOM1 p.Ala246Ser Uncertain significance Single submitter
- TOM1 p.Ala249Thr Uncertain significance Single submitter
- TOM1 p.Ala276Thr Uncertain significance Single submitter
- TOM1 p.Ala319Ser Uncertain significance Single submitter
- TOM1 p.Ala340Thr Uncertain significance Single submitter
- TOM1 p.Ala408Thr Uncertain significance Single submitter
- TOM1 p.Ala408Val Uncertain significance Single submitter
- TOM1 p.Ala414Pro Uncertain significance Single submitter
- TOM1 p.Ala454Val Uncertain significance Single submitter
- TOM1 p.Ala476Val Uncertain significance Single submitter
- TOM1 p.Arg16His Uncertain significance Single submitter
- TOM1 p.Arg259His Uncertain significance Single submitter
- TOM1 p.Arg297Leu Uncertain significance Single submitter
- TOM1 p.Arg350Thr Uncertain significance Single submitter
- TOM1 p.Arg456Gln Uncertain significance Single submitter
- TOM1 p.Arg478Trp Uncertain significance Single submitter
- TOM1 p.Asp400Glu Uncertain significance Single submitter
- TOM1 p.Cys261Arg Uncertain significance Single submitter
- TOM1 p.Cys415Ser Uncertain significance Single submitter
- TOM1 p.Gln265Pro Uncertain significance Single submitter
-
TOM1 p.Gln422Leu
Uncertain significance
Single submitter
immunodeficiency 85 and autoimmunity
- TOM1 p.Glu28Gln Uncertain significance Single submitter
- TOM1 p.Glu28Lys Uncertain significance Single submitter
- TOM1 p.Gly394Ser Uncertain significance Single submitter
- TOM1 p.Gly437Val Uncertain significance Single submitter
- TOM1 p.Ile17Ser Uncertain significance Single submitter
- TOM1 p.Ile286Val Uncertain significance Single submitter
- TOM1 p.Leu356Pro Uncertain significance Single submitter
- TOM1 p.Leu489Val Uncertain significance Single submitter
- TOM1 p.Lys479Thr Uncertain significance Single submitter
- TOM1 p.Met488Leu Uncertain significance Single submitter
- TOM1 p.Pro318Leu Uncertain significance Single submitter
- TOM1 p.Pro472Arg Uncertain significance Single submitter
- TOM1 p.Pro477Leu Uncertain significance Single submitter
- TOM1 p.Thr239Met Uncertain significance Single submitter
- TOM1 p.Thr244Ile Uncertain significance Single submitter
- TOM1 p.Thr481Ala Uncertain significance Single submitter
- TOM1 p.Val231Met Uncertain significance Single submitter
- TOM1 p.Val268Ile Uncertain significance Single submitter
- TOM1 p.Val287Ile Uncertain significance Single submitter
- TOM1 p.Val411Ala Uncertain significance Single submitter
- TOM1 p.Val59Leu Uncertain significance Single submitter
- TOM1 p.Val59Met Uncertain significance Single submitter
Predictors split 17
The independent predictors disagree with each other — read with care.
- TOM1 p.Arg450Gln Uncertain significance Multiple submitters
-
TOM1 p.Ile40Val
Uncertain significance
Multiple submitters
immunodeficiency 85 and autoimmunity
- TOM1 p.Ala370Val Uncertain significance Single submitter
- TOM1 p.Arg221Cys Uncertain significance Single submitter
- TOM1 p.Arg262Gln Uncertain significance Single submitter
- TOM1 p.Arg303Gln Uncertain significance Single submitter
- TOM1 p.Arg305Gln Uncertain significance Single submitter
- TOM1 p.Arg373Gln Uncertain significance Single submitter
- TOM1 p.Arg373Trp Uncertain significance Single submitter
- TOM1 p.Asn277Ser Conflicting Single submitter
- TOM1 p.Asn7Ser Uncertain significance Single submitter
- TOM1 p.Gln265Arg Uncertain significance Single submitter
- TOM1 p.Glu247Lys Uncertain significance Single submitter
- TOM1 p.Glu441Lys Uncertain significance Single submitter
- TOM1 p.Gly307Cys Uncertain significance Single submitter
- TOM1 p.Gly307Val Uncertain significance Single submitter
- TOM1 p.Pro248Leu Uncertain significance Single submitter
All TOM1 variants
Pathogenic 1
- p.Gly307Asp No assertion criteria immunodeficiency 85 and autoimmunity ⚠
Conflicting classifications of pathogenicity 2
- p.Asn277Ser Single submitter ⚠
- p.Met264Val Single submitter ⚠
Benign 8
- p.Asp38= Multiple submitters
- p.Ser235= Multiple submitters
- c.1284+43G>A Single submitter
- c.1284+86A>G Single submitter
- c.52+104G>C Single submitter
- c.-48+431G>A Single submitter
- p.Gly429= Single submitter
- p.Gly467= Single submitter
Likely benign 9
- c.1324+13G>A Single submitter
- c.1324+13G>C Single submitter
- c.1324+18T>A Single submitter
- c.1324+23G>C Single submitter
- p.Ala378Val Single submitter
- p.Asp393= Single submitter
- p.Asp485= Single submitter
- p.Gly333Ser Single submitter
- p.Tyr386= Single submitter
Uncertain significance 66
- p.Ala401Pro Multiple submitters ⚠
- p.Arg450Gln Multiple submitters ⚠
- p.Asp324Asn Multiple submitters immunodeficiency 85 and autoimmunity ⚠
- p.Ile40Val Multiple submitters immunodeficiency 85 and autoimmunity ⚠
- p.Ser461Phe Multiple submitters immunodeficiency 85 and autoimmunity ⚠
- c.1028-8C>T Single submitter immunodeficiency 85 and autoimmunity
- c.138-6C>T Single submitter
- c.53-8C>A Single submitter
- p.Ala246Ser Single submitter ⚠
- p.Ala249Thr Single submitter ⚠
- p.Ala276Thr Single submitter ⚠
- p.Ala319Ser Single submitter ⚠
- p.Ala340Thr Single submitter ⚠
- p.Ala370Val Single submitter ⚠
- p.Ala408Thr Single submitter ⚠
- p.Ala408Val Single submitter ⚠
- p.Ala414Pro Single submitter ⚠
- p.Ala454Val Single submitter ⚠
- p.Ala476Val Single submitter ⚠
- p.Arg16His Single submitter ⚠
- p.Arg221Cys Single submitter ⚠
- p.Arg259His Single submitter ⚠
- p.Arg262Gln Single submitter ⚠
- p.Arg297Leu Single submitter ⚠
- p.Arg303Gln Single submitter ⚠
- p.Arg305Gln Single submitter ⚠
- p.Arg350Thr Single submitter ⚠
- p.Arg373Gln Single submitter ⚠
- p.Arg373Trp Single submitter ⚠
- p.Arg456Gln Single submitter ⚠
- p.Arg478Trp Single submitter ⚠
- p.Asn7Ser Single submitter ⚠
- p.Asp400Glu Single submitter ⚠
- p.Cys261Arg Single submitter ⚠
- p.Cys415Ser Single submitter ⚠
- p.Gln265Arg Single submitter ⚠
- p.Gln265Pro Single submitter ⚠
- p.Gln422Leu Single submitter immunodeficiency 85 and autoimmunity ⚠
- p.Glu247Lys Single submitter ⚠
- p.Glu28Gln Single submitter ⚠
- p.Glu28Lys Single submitter ⚠
- p.Glu441Lys Single submitter ⚠
- p.Gly307Cys Single submitter ⚠
- p.Gly307Val Single submitter ⚠
- p.Gly394Ser Single submitter ⚠
- p.Gly437Val Single submitter ⚠
- p.Ile17Ser Single submitter ⚠
- p.Ile286Val Single submitter ⚠
- p.Leu356Pro Single submitter ⚠
- p.Leu489Val Single submitter ⚠
- p.Lys479Thr Single submitter ⚠
- p.Met488Leu Single submitter ⚠
- p.Pro248Leu Single submitter ⚠
- p.Pro318Leu Single submitter ⚠
- p.Pro472_Ser473insGlyProPro Single submitter immunodeficiency 85 and autoimmunity
- p.Pro472Arg Single submitter ⚠
- p.Pro477Leu Single submitter ⚠
- p.Thr239Met Single submitter ⚠
- p.Thr244Ile Single submitter ⚠
- p.Thr481Ala Single submitter ⚠
- p.Val231Met Single submitter ⚠
- p.Val268Ile Single submitter ⚠
- p.Val287Ile Single submitter ⚠
- p.Val411Ala Single submitter ⚠
- p.Val59Leu Single submitter ⚠
- p.Val59Met Single submitter ⚠