Sugi Variant

Sugi Variant/SERPINC1

SERPINC1 — 439 ClinVar variants

All ClinVar germline SERPINC1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 166 flagged for review →

80 Pathogenic · 5 Pathogenic/Likely pathogenic · 64 Likely pathogenic · 6 Conflicting · 12 Benign · 3 Benign/Likely benign · 109 Likely benign · 160 Uncertain significance

Full SERPINC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 166

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 15

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

Predictors agree, ClinVar conflicts 2

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

Predictors lean, ClinVar uncertain 98

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

Predictors split 51

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

All SERPINC1 variants

Pathogenic 80

  • c.1154-14G>A Expert panel hereditary antithrombin deficiency
  • p.Ala416Pro Expert panel hereditary antithrombin deficiency
  • p.Ala416Ser Expert panel hereditary antithrombin deficiency ⚠
  • p.Arg161Gln Expert panel hereditary antithrombin deficiency ⚠
  • p.Arg161Ter Expert panel hereditary antithrombin deficiency
  • p.Arg164Ter Expert panel hereditary antithrombin deficiency
  • p.Arg391Ter Expert panel hereditary antithrombin deficiency
  • p.Arg425Cys Expert panel hereditary antithrombin deficiency
  • p.Arg425His Expert panel hereditary antithrombin deficiency ⚠
  • p.Arg79Cys Expert panel hereditary antithrombin deficiency ⚠
  • p.Arg79His Expert panel hereditary antithrombin deficiency ⚠
  • p.Asn219Asp Expert panel hereditary antithrombin deficiency
  • p.Asn437Lys Expert panel hereditary antithrombin deficiency
  • p.Gln150fs Expert panel hereditary antithrombin deficiency
  • p.Gln286Pro Expert panel hereditary antithrombin deficiency
  • p.Ile386Thr Expert panel hereditary antithrombin deficiency ⚠
  • p.Leu131Phe Expert panel hereditary antithrombin deficiency ⚠
  • p.Leu256_Trp257insTer Expert panel hereditary antithrombin deficiency
  • p.Lys139_Phe140del Expert panel hereditary antithrombin deficiency
  • p.Lys260Ter Expert panel hereditary antithrombin deficiency
  • p.Phe261fs Expert panel hereditary antithrombin deficiency
  • p.Phe94fs Expert panel hereditary antithrombin deficiency
  • p.Pro318Leu Expert panel hereditary antithrombin deficiency
  • p.Pro439Thr Expert panel hereditary antithrombin deficiency
  • p.Pro73Leu Expert panel hereditary antithrombin deficiency ⚠
  • p.Ser426Leu Expert panel hereditary antithrombin deficiency ⚠
  • p.Trp339Ter Expert panel hereditary antithrombin deficiency
  • p.Val30Glu Expert panel hereditary antithrombin deficiency ⚠
  • c.409-1G>T Multiple submitters coloboma of optic nerve
  • p.Cys53Ter Multiple submitters Deep venous thrombosis
  • p.Gly456Arg Multiple submitters hereditary antithrombin deficiency
  • p.Pro439Ala Multiple submitters hereditary antithrombin deficiency
  • c.409-1G>C Single submitter hereditary antithrombin deficiency
  • c.41+2T>C Single submitter SERPINC1-related disorder
  • c.763-1G>C Single submitter hereditary antithrombin deficiency
  • c.763-33_990del Single submitter hereditary antithrombin deficiency
  • p.Ala403fs Single submitter hereditary antithrombin deficiency
  • p.Arg354fs Single submitter hereditary antithrombin deficiency
  • p.Arg391fs Single submitter hereditary antithrombin deficiency
  • p.Asp106fs Single submitter hereditary antithrombin deficiency
  • p.Cys127Ter Single submitter hereditary antithrombin deficiency
  • p.Gln203Ter Single submitter hereditary antithrombin deficiency
  • p.Gln337Ter Single submitter hereditary antithrombin deficiency
  • p.Glu188Ter Single submitter hereditary antithrombin deficiency
  • p.Glu69Ter Single submitter hereditary antithrombin deficiency
  • p.Gly125Asp Single submitter hereditary antithrombin deficiency
  • p.His33fs Single submitter hereditary antithrombin deficiency
  • p.Ile453Thr Single submitter hereditary antithrombin deficiency
  • p.Leu256fs Single submitter hereditary antithrombin deficiency
  • p.Leu441Pro Single submitter hereditary antithrombin deficiency
  • p.Lys146fs Single submitter hereditary antithrombin deficiency
  • p.Lys146Glu Single submitter hereditary antithrombin deficiency ⚠
  • p.Met1Val Single submitter hereditary antithrombin deficiency
  • p.Met284Thr Single submitter hereditary antithrombin deficiency
  • p.Met370Thr Single submitter
  • p.Ser114Asn Single submitter hereditary antithrombin deficiency ⚠
  • p.Thr10fs Single submitter hereditary antithrombin deficiency
  • p.Thr130Ile Single submitter hereditary antithrombin deficiency
  • p.Trp221Ter Single submitter
  • p.Trp81Ter Single submitter hereditary antithrombin deficiency
  • p.Val244fs Single submitter hereditary antithrombin deficiency
  • c.1154-324_1218+475dup No assertion criteria hereditary antithrombin deficiency
  • c.1154-40_1218+127dup No assertion criteria hereditary antithrombin deficiency
  • c.1154-898_1218+410del No assertion criteria hereditary antithrombin deficiency
  • c.408+948_763-386del No assertion criteria hereditary antithrombin deficiency
  • c.41+297_55del No assertion criteria hereditary antithrombin deficiency
  • c.42-486_1154-846del No assertion criteria hereditary antithrombin deficiency
  • c.763-379_1084del No assertion criteria hereditary antithrombin deficiency
  • c.84_409-536del No assertion criteria hereditary antithrombin deficiency
  • p.Arg425del No assertion criteria hereditary antithrombin deficiency
  • p.Arg89fs No assertion criteria hereditary antithrombin deficiency
  • p.Asn240fs No assertion criteria hereditary antithrombin deficiency
  • p.Asp341fs No assertion criteria hereditary antithrombin deficiency
  • p.Cys127Arg No assertion criteria hereditary antithrombin deficiency ⚠
  • p.Lys402fs No assertion criteria hereditary antithrombin deficiency
  • p.Pro461Leu No assertion criteria hereditary antithrombin deficiency
  • p.Ser223Pro No assertion criteria hereditary antithrombin deficiency
  • p.Ser323fs No assertion criteria hereditary antithrombin deficiency
  • p.Val458_Pro461delinsAla No assertion criteria hereditary antithrombin deficiency
  • p.Val80fs No assertion criteria hereditary antithrombin deficiency

Pathogenic/Likely pathogenic 5

  • p.Arg229Ter Multiple submitters hereditary antithrombin deficiency
  • p.Arg45Trp Multiple submitters hereditary antithrombin deficiency ⚠
  • p.Arg56Cys Multiple submitters hereditary antithrombin deficiency ⚠
  • p.Phe155del Multiple submitters hereditary antithrombin deficiency
  • p.Thr93fs Multiple submitters SERPINC1-related disorder

Likely pathogenic 64

  • c.1218+2T>C Expert panel hereditary antithrombin deficiency
  • c.1219-2A>G Expert panel hereditary antithrombin deficiency
  • c.624+1G>A Expert panel hereditary antithrombin deficiency
  • p.Ala414Thr Expert panel hereditary antithrombin deficiency
  • p.Ala436Thr Expert panel hereditary antithrombin deficiency ⚠
  • p.Arg425Pro Expert panel hereditary antithrombin deficiency
  • p.Arg79Ser Expert panel hereditary antithrombin deficiency ⚠
  • p.Gln150Pro Expert panel hereditary antithrombin deficiency ⚠
  • p.Ile39Asn Expert panel hereditary antithrombin deficiency ⚠
  • p.Pro353Leu Expert panel hereditary antithrombin deficiency
  • p.Pro439Leu Expert panel hereditary antithrombin deficiency
  • p.Ser148Pro Expert panel hereditary antithrombin deficiency ⚠
  • p.Ser397Ter Expert panel hereditary antithrombin deficiency
  • p.Thr147Ala Expert panel hereditary antithrombin deficiency ⚠
  • p.Tyr95Cys Expert panel hereditary antithrombin deficiency
  • p.Tyr95His Expert panel hereditary antithrombin deficiency
  • c.1153+5G>T Multiple submitters Thrombophilia with a likely monogenic cause
  • p.Glu227Lys Multiple submitters hereditary antithrombin deficiency ⚠
  • c.1153+1G>A Single submitter hereditary antithrombin deficiency
  • c.1154-50_1218+50del Single submitter hereditary antithrombin deficiency
  • c.1219-1G>A Single submitter hereditary antithrombin deficiency
  • c.41+3A>T Single submitter hereditary antithrombin deficiency
  • c.41+5G>A Single submitter hereditary antithrombin deficiency
  • c.42-1G>C Single submitter
  • c.763-1G>A Single submitter
  • p.Ala42fs Single submitter
  • p.Ala91Val Single submitter hereditary antithrombin deficiency
  • p.Asn107Ter Single submitter hereditary antithrombin deficiency
  • p.Asp374fs Single submitter hereditary antithrombin deficiency
  • p.Cys40Arg Single submitter hereditary antithrombin deficiency
  • p.Cys40Ser Single submitter hereditary antithrombin deficiency
  • p.Gln133_Leu134insTer Single submitter hereditary antithrombin deficiency
  • p.Gln191Arg Single submitter ⚠
  • p.Glu227Ter Single submitter hereditary antithrombin deficiency
  • p.Glu277fs Single submitter hereditary antithrombin deficiency
  • p.Glu59fs Single submitter hereditary antithrombin deficiency
  • p.Glu82Ter Single submitter
  • p.Gly125Cys Single submitter
  • p.Ile108_Phe109del Single submitter hereditary antithrombin deficiency
  • p.Ile151Asn Single submitter hereditary antithrombin deficiency
  • p.Leu205Pro Single submitter hereditary antithrombin deficiency
  • p.Leu23Pro Single submitter hereditary antithrombin deficiency ⚠
  • p.Leu317Val Single submitter ⚠
  • p.Lys220Ter Single submitter
  • p.Lys268fs Single submitter hereditary antithrombin deficiency
  • p.Lys273Asn Single submitter hereditary antithrombin deficiency ⚠
  • p.Met52fs Single submitter hereditary antithrombin deficiency
  • p.Phe179Cys Single submitter hereditary antithrombin deficiency
  • p.Phe434Leu Single submitter hereditary antithrombin deficiency ⚠
  • p.Ser194Arg Single submitter hereditary antithrombin deficiency
  • p.Ser214Tyr Single submitter hereditary antithrombin deficiency
  • p.Ser426Trp Single submitter hereditary antithrombin deficiency
  • p.Thr185fs Single submitter hereditary antithrombin deficiency
  • p.Thr226Ile Single submitter
  • p.Thr299fs Single submitter
  • p.Tyr190Cys Single submitter hereditary antithrombin deficiency
  • p.Val335fs Single submitter hereditary antithrombin deficiency
  • p.Val421fs Single submitter
  • p.Asn128Tyr No assertion criteria hereditary antithrombin deficiency ⚠
  • p.Glu64Ter No assertion criteria SERPINC1-related disorder
  • p.Leu158Pro No assertion criteria hereditary antithrombin deficiency
  • p.Leu317Phe No assertion criteria hereditary antithrombin deficiency
  • p.Met284Arg No assertion criteria hereditary antithrombin deficiency
  • p.Trp257Arg No assertion criteria SERPINC1-related disorder

Conflicting classifications of pathogenicity 6

Benign 12

Benign/Likely benign 3

  • c.409-12dup Multiple submitters hereditary antithrombin deficiency
  • p.Arg291= Multiple submitters hereditary antithrombin deficiency
  • p.Val335= Multiple submitters hereditary antithrombin deficiency

Likely benign 109

  • c.1154-5T>C Expert panel hereditary antithrombin deficiency
  • c.1218+7A>G Expert panel hereditary antithrombin deficiency
  • c.408+4C>T Expert panel hereditary antithrombin deficiency
  • c.-57G>A Expert panel hereditary antithrombin deficiency
  • p.Arg294His Expert panel hereditary antithrombin deficiency
  • p.Asn240Ser Expert panel hereditary antithrombin deficiency ⚠
  • p.Asn450= Expert panel hereditary antithrombin deficiency
  • p.Asp100Gly Expert panel hereditary antithrombin deficiency
  • p.Gly7= Expert panel hereditary antithrombin deficiency
  • p.Leu304= Expert panel hereditary antithrombin deficiency
  • p.Phe290= Expert panel hereditary antithrombin deficiency
  • p.Thr10Asn Expert panel hereditary antithrombin deficiency
  • p.Thr185Ala Expert panel hereditary antithrombin deficiency
  • p.Thr418= Expert panel hereditary antithrombin deficiency
  • p.Tyr17= Expert panel hereditary antithrombin deficiency
  • p.Tyr198= Expert panel hereditary antithrombin deficiency
  • p.Val16Ala Expert panel hereditary antithrombin deficiency
  • c.1154-15C>T Multiple submitters hereditary antithrombin deficiency
  • c.409-20T>C Multiple submitters hereditary antithrombin deficiency
  • c.624+18C>T Multiple submitters hereditary antithrombin deficiency
  • c.624+9C>T Multiple submitters hereditary antithrombin deficiency
  • p.Ala414= Multiple submitters hereditary antithrombin deficiency
  • p.Leu124= Multiple submitters hereditary antithrombin deficiency
  • c.1153+7C>T Single submitter hereditary antithrombin deficiency
  • c.1154-14G>C Single submitter hereditary antithrombin deficiency
  • c.1218+11C>T Single submitter hereditary antithrombin deficiency
  • c.1218+8C>T Single submitter hereditary antithrombin deficiency
  • c.1219-16C>T Single submitter hereditary antithrombin deficiency
  • c.1219-25_1219-21del Single submitter
  • c.409-11G>T Single submitter hereditary antithrombin deficiency
  • c.409-8T>C Single submitter hereditary antithrombin deficiency
  • c.41+10G>A Single submitter hereditary antithrombin deficiency
  • c.41+12G>A Single submitter hereditary antithrombin deficiency
  • c.41+14G>C Single submitter hereditary antithrombin deficiency
  • c.41+8G>A Single submitter hereditary antithrombin deficiency
  • c.42-10C>A Single submitter hereditary antithrombin deficiency
  • c.42-15T>C Single submitter hereditary antithrombin deficiency
  • c.624+10A>G Single submitter hereditary antithrombin deficiency
  • c.624+14G>C Single submitter hereditary antithrombin deficiency
  • c.625-10T>C Single submitter hereditary antithrombin deficiency
  • c.625-5C>G Single submitter hereditary antithrombin deficiency
  • c.625-9T>C Single submitter hereditary antithrombin deficiency
  • c.762+19G>C Single submitter hereditary antithrombin deficiency
  • c.762+7A>G Single submitter hereditary antithrombin deficiency
  • p.Ala156= Single submitter hereditary antithrombin deficiency
  • p.Ala175= Single submitter hereditary antithrombin deficiency
  • p.Ala211= Single submitter hereditary antithrombin deficiency
  • p.Ala216= Single submitter hereditary antithrombin deficiency
  • p.Arg215= Single submitter hereditary antithrombin deficiency
  • p.Arg293= Single submitter hereditary antithrombin deficiency
  • p.Arg293Gln Single submitter hereditary antithrombin deficiency
  • p.Arg294= Single submitter hereditary antithrombin deficiency
  • p.Arg79= Single submitter hereditary antithrombin deficiency
  • p.Asn167= Single submitter hereditary antithrombin deficiency
  • p.Asn240Asp Single submitter Inborn genetic diseases
  • p.Asn428= Single submitter hereditary antithrombin deficiency
  • p.Asn87= Single submitter
  • p.Asp141= Single submitter hereditary antithrombin deficiency
  • p.Asp359= Single submitter hereditary antithrombin deficiency
  • p.Asp369= Single submitter hereditary antithrombin deficiency
  • p.Asp46= Single submitter hereditary antithrombin deficiency
  • p.Cys462= Single submitter hereditary antithrombin deficiency
  • p.Glu241= Single submitter hereditary antithrombin deficiency
  • p.Glu338= Single submitter
  • p.Glu358= Single submitter hereditary antithrombin deficiency
  • p.Glu446= Single submitter hereditary antithrombin deficiency
  • p.Glu64= Single submitter hereditary antithrombin deficiency
  • p.Gly199= Single submitter hereditary antithrombin deficiency
  • p.Gly298= Single submitter hereditary antithrombin deficiency
  • p.Gly67= Single submitter hereditary antithrombin deficiency
  • p.His33= Single submitter hereditary antithrombin deficiency
  • p.Ile115= Single submitter hereditary antithrombin deficiency
  • p.Ile452= Single submitter hereditary antithrombin deficiency
  • p.Leu113= Single submitter hereditary antithrombin deficiency
  • p.Leu196= Single submitter hereditary antithrombin deficiency
  • p.Leu270= Single submitter hereditary antithrombin deficiency
  • p.Leu336= Single submitter hereditary antithrombin deficiency
  • p.Leu340= Single submitter hereditary antithrombin deficiency
  • p.Lys139= Single submitter hereditary antithrombin deficiency
  • p.Lys165= Single submitter hereditary antithrombin deficiency
  • p.Met49Val Single submitter Inborn genetic diseases
  • p.Phe271= Single submitter hereditary antithrombin deficiency
  • p.Phe361= Single submitter hereditary antithrombin deficiency
  • p.Pro235= Single submitter hereditary antithrombin deficiency
  • p.Pro44= Single submitter hereditary antithrombin deficiency
  • p.Pro58= Single submitter hereditary antithrombin deficiency
  • p.Pro73= Single submitter hereditary antithrombin deficiency
  • p.Ser111= Single submitter hereditary antithrombin deficiency
  • p.Ser114= Single submitter hereditary antithrombin deficiency
  • p.Ser223= Single submitter hereditary antithrombin deficiency
  • p.Ser236= Single submitter hereditary antithrombin deficiency
  • p.Ser259= Single submitter hereditary antithrombin deficiency
  • p.Ser278= Single submitter hereditary antithrombin deficiency
  • p.Ser35= Single submitter hereditary antithrombin deficiency
  • p.Ser57= Single submitter hereditary antithrombin deficiency
  • p.Thr10= Single submitter hereditary antithrombin deficiency
  • p.Thr117= Single submitter hereditary antithrombin deficiency
  • p.Thr122= Single submitter hereditary antithrombin deficiency
  • p.Thr226= Single submitter hereditary antithrombin deficiency
  • p.Thr250= Single submitter hereditary antithrombin deficiency
  • p.Tyr252= Single submitter hereditary antithrombin deficiency
  • p.Tyr292= Single submitter hereditary antithrombin deficiency
  • p.Val197= Single submitter hereditary antithrombin deficiency
  • p.Val295= Single submitter hereditary antithrombin deficiency
  • p.Val314= Single submitter hereditary antithrombin deficiency
  • p.Val349= Single submitter hereditary antithrombin deficiency
  • p.Val373= Single submitter hereditary antithrombin deficiency
  • p.Val5= Single submitter hereditary antithrombin deficiency
  • p.Val80= Single submitter hereditary antithrombin deficiency

Uncertain significance 160