Sugi Variant

Sugi Variant/TGM1

TGM1 — 1114 ClinVar variants

All ClinVar germline TGM1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 261 flagged for review →

112 Pathogenic · 59 Pathogenic/Likely pathogenic · 114 Likely pathogenic · 63 Conflicting · 23 Benign · 9 Benign/Likely benign · 487 Likely benign · 247 Uncertain significance

Full TGM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 261

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 4

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 35

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

Predictors lean, ClinVar uncertain 168

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 168

Predictors split 54

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

All TGM1 variants

Pathogenic 112

Pathogenic/Likely pathogenic 59

  • c.1160-2_1160-1del Multiple submitters autosomal recessive congenital ichthyosis 1
  • c.1645+1G>T Multiple submitters autosomal recessive congenital ichthyosis 1
  • c.2226-2A>G Multiple submitters autosomal recessive congenital ichthyosis 1
  • c.876+2T>C Multiple submitters autosomal recessive congenital ichthyosis 1
  • c.984+1G>A Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Arg126Cys Multiple submitters TGM1-related disorder
  • p.Arg142Cys Multiple submitters TGM1-related disorder
  • p.Arg142His Multiple submitters TGM1-related disorder
  • p.Arg143His Multiple submitters Ichthyosis and erythrokeratoderma
  • p.Arg264Gln Multiple submitters lamellar ichthyosis ⚠
  • p.Arg264Trp Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Arg286Gln Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Arg286Trp Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Arg307Trp Multiple submitters lamellar ichthyosis ⚠
  • p.Arg315Cys Multiple submitters lamellar ichthyosis
  • p.Arg315Leu Multiple submitters TGM1-related disorder
  • p.Arg323Gln Multiple submitters Ichthyosis and erythrokeratoderma
  • p.Arg323Trp Multiple submitters TGM1-related disorder
  • p.Arg389His Multiple submitters lamellar ichthyosis
  • p.Arg396Cys Multiple submitters lamellar ichthyosis
  • p.Arg396His Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Arg396Leu Multiple submitters TGM1-related disorder
  • p.Arg687His Multiple submitters autosomal recessive congenital ichthyosis 1 ⚠
  • p.Asp333fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Asp408fs Multiple submitters lamellar ichthyosis
  • p.Gln196Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gln221Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gln227Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gln282Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gln582Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gln592Ter Multiple submitters TGM1-related disorder
  • p.Glu133fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gly218Ser Multiple submitters lamellar ichthyosis ⚠
  • p.Gly278Arg Multiple submitters TGM1-related disorder
  • p.Gly291Asp Multiple submitters TGM1-related disorder
  • p.Gly291Ser Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gly473Arg Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gly473Ser Multiple submitters TGM1-related disorder
  • p.Gly626fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gly62Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gly699Ter Multiple submitters TGM1-related disorder
  • p.His148fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ile140Met Multiple submitters TGM1-related disorder
  • p.Ile163fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ile415fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ile469_Cys471delinsMetLeu Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ile480fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ile480Phe Multiple submitters autosomal recessive congenital ichthyosis 1 ⚠
  • p.Pro474Ser Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ser575fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Thr749fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Trp44Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Tyr134Cys Multiple submitters TGM1-related disorder
  • p.Tyr134fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Tyr134His Multiple submitters lamellar ichthyosis
  • p.Tyr544Cys Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Val268fs Multiple submitters lamellar ichthyosis
  • p.Val383Met Multiple submitters lamellar ichthyosis
  • p.Val650fs Multiple submitters TGM1-related disorder

Likely pathogenic 114

  • c.319+2T>C Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ala571fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ala588fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ala664fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Arg315Pro Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Arg389Cys Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gln292Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gln662fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gly144Glu Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Gly273Arg Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ile304Phe Multiple submitters autosomal recessive congenital ichthyosis 1 ⚠
  • p.Leu153del Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Pro318fs Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Pro352Leu Multiple submitters
  • p.Ser272Pro Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ser772Arg Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Thr491Met Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Thr529Ile Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Trp455Arg Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Trp505Ter Multiple submitters autosomal recessive congenital ichthyosis 1
  • c.1159+1G>A Single submitter autosomal recessive congenital ichthyosis 1
  • c.1491+1G>C Single submitter
  • c.1491+1G>T Single submitter lamellar ichthyosis
  • c.1645+2T>C Single submitter
  • c.1928-1G>C Single submitter autosomal recessive congenital ichthyosis 1
  • c.1928-2A>C Single submitter autosomal recessive congenital ichthyosis 1
  • c.2089-1G>C Single submitter
  • c.319+2T>G Single submitter
  • c.320-10_320-9delinsAGAGCATGCTACAG Single submitter autosomal recessive congenital ichthyosis 1
  • c.320-2A>C Single submitter autosomal recessive congenital ichthyosis 1
  • c.757+1G>C Single submitter autosomal recessive congenital ichthyosis 1
  • c.758-1G>A Single submitter
  • c.758-2A>G Single submitter
  • c.877-2_892dup Single submitter autosomal recessive congenital ichthyosis 1
  • c.984+2T>G Single submitter
  • p.Ala200fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ala404fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ala522fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Arg142Gln Single submitter autosomal recessive congenital ichthyosis 1
  • p.Arg142Pro Single submitter autosomal recessive congenital ichthyosis 1
  • p.Arg155fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Arg286Leu Single submitter
  • p.Arg315_Asp317del Single submitter Ichthyosis and erythrokeratoderma
  • p.Arg396Pro Single submitter
  • p.Arg687Cys Single submitter autosomal recessive congenital ichthyosis 1
  • p.Asn428fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Asn535fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Asn572fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Cys377fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Cys472Arg Single submitter
  • p.Cys472Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Cys53Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gln145fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gln586fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gln683Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gln754fs Single submitter
  • p.Glu166Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Glu497fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Glu548Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gly176fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gly278Ala Single submitter
  • p.Gly309fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gly344Ala Single submitter
  • p.Gly357Asp Single submitter lamellar ichthyosis ⚠
  • p.Gly375Asp Single submitter lamellar ichthyosis
  • p.Gly392fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gly392Val Single submitter
  • p.Gly468fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gly524Asp Single submitter autosomal recessive congenital ichthyosis 1
  • p.His436Pro Single submitter
  • p.His658fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ile216fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Leu139fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Leu167fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Leu207Pro Single submitter autosomal recessive congenital ichthyosis 1
  • p.Leu298Arg Single submitter
  • p.Leu298Pro Single submitter
  • p.Leu388Pro Single submitter autosomal recessive congenital ichthyosis 1
  • p.Leu526fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Leu543fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Lys634fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Met443fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Phe435Leu Single submitter autosomal recessive congenital ichthyosis 1
  • p.Phe435Val Single submitter
  • p.Pro318Arg Single submitter Congenital ichthyosiform erythroderma
  • p.Pro474Ala Single submitter TGM1-related disorder
  • p.Ser122Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ser326fs Single submitter
  • p.Ser358Asn Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ser364fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ser643Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ser85Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Thr22fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Thr622fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Trp288Arg Single submitter autosomal recessive congenital ichthyosis 1
  • p.Trp378Cys Single submitter
  • p.Trp438Cys Single submitter
  • p.Tyr257Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Tyr346Ter Single submitter autosomal recessive congenital ichthyosis 1
  • p.Val112fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Val224_Thr226del Single submitter Ichthyosis and erythrokeratoderma
  • p.Val268Phe Single submitter
  • p.Val321Phe Single submitter
  • p.Val437Gly Single submitter
  • p.Val477fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Val528fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Val557fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Val679fs Single submitter autosomal recessive congenital ichthyosis 1
  • p.Val750fs Single submitter autosomal recessive congenital ichthyosis 1
  • c.1298+2T>C No assertion criteria autosomal recessive congenital ichthyosis 1
  • c.320-1G>T No assertion criteria autosomal recessive congenital ichthyosis 1
  • p.Arg348fs No assertion criteria autosomal recessive congenital ichthyosis 1
  • p.Ser550Ter No assertion criteria autosomal recessive congenital ichthyosis 1
  • p.Val618fs No assertion criteria autosomal recessive congenital ichthyosis 1

Conflicting classifications of pathogenicity 63

  • c.1298+9G>A Single submitter autosomal recessive congenital ichthyosis 1
  • c.1403-15C>T Single submitter autosomal recessive congenital ichthyosis 1
  • c.2088+14G>T Single submitter autosomal recessive congenital ichthyosis 1
  • c.319+15T>C Single submitter autosomal recessive congenital ichthyosis 1
  • c.319+9G>A Single submitter autosomal recessive congenital ichthyosis 1
  • c.876+10G>A Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ala381= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ala56Val Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Ala588Thr Single submitter Inborn genetic diseases ⚠
  • p.Arg11= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Arg155Trp Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Arg240His Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Arg307Gln Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Arg308Gln Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Arg34Cys Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Arg36His Single submitter Inborn genetic diseases ⚠
  • p.Arg36Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg507Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg607His Single submitter Inborn genetic diseases ⚠
  • p.Arg656Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg753His Single submitter Inborn genetic diseases ⚠
  • p.Arg764Cys Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Arg83Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg83Trp Single submitter Inborn genetic diseases ⚠
  • p.Asn439= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Asp137Asn Single submitter Inborn genetic diseases ⚠
  • p.Asp490Gly Single submitter lamellar ichthyosis ⚠
  • p.Asp587= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Asp59= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Cys707= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Glu280Lys Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Glu497= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Glu520Gly Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Glu635Asp Single submitter Inborn genetic diseases ⚠
  • p.Gly192Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly33Arg Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Gly524Val Single submitter ⚠
  • p.Gly677Arg Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Gly70Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly84= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Gly94Asp Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.His295= Single submitter autosomal recessive congenital ichthyosis 1
  • p.His779= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ile361Thr Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Phe435= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Phe495Leu Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Pro173= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Pro184Ser Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Pro446= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Ser212Phe Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Ser42Tyr Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Thr211Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr21Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr22Met Single submitter Inborn genetic diseases ⚠
  • p.Thr368= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Trp342Leu Single submitter ⚠
  • p.Tyr374Cys Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Tyr489= Single submitter autosomal recessive congenital ichthyosis 1
  • p.Tyr621Cys Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Val359Met Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Val518Met Single submitter autosomal recessive congenital ichthyosis 1 ⚠
  • p.Val725Ile Single submitter Inborn genetic diseases ⚠
  • p.Val741Ala Single submitter Inborn genetic diseases ⚠

Benign 23

Benign/Likely benign 9

  • c.1492-12dup Multiple submitters
  • c.1645+5C>A Multiple submitters autosomal recessive congenital ichthyosis 1
  • c.1927+20C>T Multiple submitters
  • c.2225+19C>T Multiple submitters
  • p.Ala99= Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Arg121Cys Multiple submitters autosomal recessive congenital ichthyosis 1 ⚠
  • p.Asp802Val Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ser122Leu Multiple submitters autosomal recessive congenital ichthyosis 1
  • p.Ser95= Multiple submitters autosomal recessive congenital ichthyosis 1

Likely benign 487

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 247