Sugi Variant

Sugi Variant/F2

F2 — 466 ClinVar variants

All ClinVar germline F2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 118 flagged for review →

20 Pathogenic · 3 Pathogenic/Likely pathogenic · 18 Likely pathogenic · 27 Conflicting · 23 Benign · 8 Benign/Likely benign · 245 Likely benign · 122 Uncertain significance

Full F2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 118

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 2

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

Predictors agree, ClinVar conflicts 6

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

Predictors lean, ClinVar uncertain 67

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

Predictors split 43

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

All F2 variants

Pathogenic 20

  • p.Arg500Gln Multiple submitters congenital prothrombin deficiency ⚠
  • p.Arg596Gln Multiple submitters thrombophilia due to thrombin defect ⚠
  • p.Arg117Ter Single submitter congenital prothrombin deficiency
  • p.Arg314Cys Single submitter thrombophilia due to thrombin defect
  • p.Arg339Ter Single submitter congenital prothrombin deficiency
  • p.Arg560Ter Single submitter congenital prothrombin deficiency
  • p.Arg596Trp Single submitter congenital prothrombin deficiency ⚠
  • p.Arg5Ter Single submitter congenital prothrombin deficiency
  • p.Asp308fs Single submitter congenital prothrombin deficiency
  • p.Glu319Ter Single submitter congenital prothrombin deficiency
  • p.Trp132fs Single submitter congenital prothrombin deficiency
  • p.Val185fs Single submitter congenital prothrombin deficiency
  • p.Arg425His No assertion criteria congenital prothrombin deficiency ⚠
  • p.Arg596Leu No assertion criteria thrombophilia due to thrombin defect ⚠
  • p.Asn155Ter No assertion criteria congenital prothrombin deficiency
  • p.Asp595Glu No assertion criteria congenital prothrombin deficiency ⚠
  • p.Glu343Lys No assertion criteria congenital prothrombin deficiency ⚠
  • p.Glu352Lys No assertion criteria congenital prothrombin deficiency ⚠
  • p.Gly601Val No assertion criteria congenital prothrombin deficiency
  • p.Met380Thr No assertion criteria congenital prothrombin deficiency ⚠

Pathogenic/Likely pathogenic 3

  • p.Arg461Trp Multiple submitters congenital prothrombin deficiency
  • p.Arg581Cys Multiple submitters congenital prothrombin deficiency
  • p.Gln387Ter Multiple submitters congenital prothrombin deficiency

Likely pathogenic 18

  • p.Arg314His Multiple submitters Prolonged prothrombin time ⚠
  • c.1130+1G>A Single submitter congenital prothrombin deficiency
  • c.317-1G>A Single submitter pregnancy loss, recurrent, susceptibility to, 2
  • c.422+1G>A Single submitter congenital prothrombin deficiency
  • p.Arg425Cys Single submitter congenital prothrombin deficiency ⚠
  • p.Arg431His Single submitter F2-related disorder ⚠
  • p.Gln584Ter Single submitter congenital prothrombin deficiency
  • p.Glu357Gly Single submitter congenital prothrombin deficiency ⚠
  • p.Gly332Ala Single submitter congenital prothrombin deficiency ⚠
  • p.Gly499Glu Single submitter congenital prothrombin deficiency
  • p.His406Arg Single submitter congenital prothrombin deficiency
  • p.Leu152fs Single submitter F2-related disorder
  • p.Leu609Pro Single submitter Prolonged prothrombin time
  • p.Lys345del Single submitter Prolonged prothrombin time
  • p.Trp582Ter Single submitter congenital prothrombin deficiency
  • p.Tyr87Cys Single submitter Coagulation factor deficiency syndrome
  • p.Val424Met Single submitter congenital prothrombin deficiency
  • p.Val365Glu No assertion criteria congenital prothrombin deficiency ⚠

Conflicting classifications of pathogenicity 27

  • c.1298+11G>C Single submitter congenital prothrombin deficiency
  • c.1298+19G>A Single submitter thrombophilia due to thrombin defect
  • c.241-26C>G Single submitter
  • c.316+16G>A Single submitter congenital prothrombin deficiency
  • c.317-4G>A Single submitter thrombophilia due to thrombin defect
  • c.874+13G>A Single submitter congenital prothrombin deficiency
  • p.Ala294= Single submitter thrombophilia due to thrombin defect
  • p.Arg363His Single submitter congenital prothrombin deficiency ⚠
  • p.Arg40Trp Single submitter congenital prothrombin deficiency ⚠
  • p.Arg42Trp Single submitter congenital prothrombin deficiency ⚠
  • p.Arg541= Single submitter thrombophilia due to thrombin defect
  • p.Arg541Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg543Leu Single submitter congenital prothrombin deficiency ⚠
  • p.Arg608= Single submitter thrombophilia due to thrombin defect
  • p.Asn514Lys Single submitter ischemic stroke ⚠
  • p.Glu305= Single submitter thrombophilia due to thrombin defect
  • p.His605= Single submitter congenital prothrombin deficiency
  • p.His605fs Single submitter pregnancy loss, recurrent, susceptibility to, 2
  • p.Leu15= Single submitter thrombophilia due to thrombin defect
  • p.Leu210Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro326= Single submitter thrombophilia due to thrombin defect
  • p.Pro534= Single submitter thrombophilia due to thrombin defect
  • p.Ser331Leu Single submitter thrombophilia due to thrombin defect ⚠
  • p.Thr165= Single submitter thrombophilia due to thrombin defect
  • p.Thr488= Single submitter congenital prothrombin deficiency
  • p.Thr78= Single submitter Inborn genetic diseases
  • p.Thr95= Single submitter Inborn genetic diseases

Benign 23

Benign/Likely benign 8

  • c.423-7G>C Multiple submitters thrombophilia due to thrombin defect
  • c.79+7G>A Multiple submitters thrombophilia due to thrombin defect
  • c.875-19G>A Multiple submitters congenital prothrombin deficiency
  • p.Asp266= Multiple submitters congenital prothrombin deficiency
  • p.Gln619= Multiple submitters congenital prothrombin deficiency
  • p.Pro160= Multiple submitters congenital prothrombin deficiency
  • p.Pro411= Multiple submitters congenital prothrombin deficiency
  • p.Thr165Met Multiple submitters thrombophilia due to thrombin defect

Likely benign 245

  • c.1130+16C>T Multiple submitters congenital prothrombin deficiency
  • c.1130+19C>T Multiple submitters congenital prothrombin deficiency
  • c.241-17C>T Multiple submitters congenital prothrombin deficiency
  • c.265+10G>A Multiple submitters congenital prothrombin deficiency
  • c.423-7G>A Multiple submitters congenital prothrombin deficiency
  • p.Ala242= Multiple submitters Inborn genetic diseases
  • p.Ala277= Multiple submitters congenital prothrombin deficiency
  • p.Arg178= Multiple submitters congenital prothrombin deficiency
  • p.Arg58= Multiple submitters congenital prothrombin deficiency
  • p.Asn458= Multiple submitters congenital prothrombin deficiency
  • p.Asn527= Multiple submitters Inborn genetic diseases
  • p.Cys60= Multiple submitters congenital prothrombin deficiency
  • p.Gln494= Multiple submitters Inborn genetic diseases
  • p.Glu293= Multiple submitters congenital prothrombin deficiency
  • p.Glu388= Multiple submitters congenital prothrombin deficiency
  • p.Gly223= Multiple submitters Inborn genetic diseases
  • p.Gly569= Multiple submitters Inborn genetic diseases
  • p.Ile360= Multiple submitters congenital prothrombin deficiency
  • p.Phe572= Multiple submitters Inborn genetic diseases
  • p.Ser239= Multiple submitters Inborn genetic diseases
  • p.Ser331= Multiple submitters Inborn genetic diseases
  • p.Thr403= Multiple submitters Inborn genetic diseases
  • p.Thr418= Multiple submitters congenital prothrombin deficiency
  • p.Thr510= Multiple submitters congenital prothrombin deficiency
  • p.Thr545= Multiple submitters congenital prothrombin deficiency
  • p.Tyr434= Multiple submitters congenital prothrombin deficiency
  • p.Tyr477= Multiple submitters congenital prothrombin deficiency
  • p.Tyr67= Multiple submitters congenital prothrombin deficiency
  • c.1003+15A>G Single submitter congenital prothrombin deficiency
  • c.1003+19G>A Single submitter congenital prothrombin deficiency
  • c.1003+19G>C Single submitter congenital prothrombin deficiency
  • c.1003+19G>T Single submitter congenital prothrombin deficiency
  • c.1003+28C>T Single submitter
  • c.1004-12C>T Single submitter congenital prothrombin deficiency
  • c.1130+10G>C Single submitter congenital prothrombin deficiency
  • c.1130+11G>A Single submitter congenital prothrombin deficiency
  • c.1130+19C>A Single submitter congenital prothrombin deficiency
  • c.1130+20G>A Single submitter congenital prothrombin deficiency
  • c.1130+8C>T Single submitter congenital prothrombin deficiency
  • c.1130+9T>C Single submitter congenital prothrombin deficiency
  • c.1131-13C>T Single submitter congenital prothrombin deficiency
  • c.1131-16C>T Single submitter congenital prothrombin deficiency
  • c.1131-18_1131-15del Single submitter congenital prothrombin deficiency
  • c.1131-9C>T Single submitter congenital prothrombin deficiency
  • c.1298+14G>A Single submitter congenital prothrombin deficiency
  • c.1298+15G>A Single submitter congenital prothrombin deficiency
  • c.1298+18C>T Single submitter congenital prothrombin deficiency
  • c.1298+8A>G Single submitter congenital prothrombin deficiency
  • c.1299-10G>A Single submitter congenital prothrombin deficiency
  • c.1299-15T>C Single submitter congenital prothrombin deficiency
  • c.1299-17_1299-14del Single submitter congenital prothrombin deficiency
  • c.1299-17T>C Single submitter congenital prothrombin deficiency
  • c.1299-17T>G Single submitter congenital prothrombin deficiency
  • c.1299-6C>T Single submitter congenital prothrombin deficiency
  • c.1472+18T>C Single submitter congenital prothrombin deficiency
  • c.1473-20C>T Single submitter congenital prothrombin deficiency
  • c.1473-5C>T Single submitter congenital prothrombin deficiency
  • c.1473-8C>T Single submitter congenital prothrombin deficiency
  • c.1654+16G>A Single submitter congenital prothrombin deficiency
  • c.1654+17C>G Single submitter congenital prothrombin deficiency
  • c.1654+17C>T Single submitter congenital prothrombin deficiency
  • c.1654+18G>A Single submitter congenital prothrombin deficiency
  • c.1655-13G>A Single submitter congenital prothrombin deficiency
  • c.1655-17G>A Single submitter congenital prothrombin deficiency
  • c.1655-18C>T Single submitter congenital prothrombin deficiency
  • c.1655-4C>T Single submitter congenital prothrombin deficiency
  • c.1725+17C>T Single submitter congenital prothrombin deficiency
  • c.1725+18C>T Single submitter congenital prothrombin deficiency
  • c.1725+19C>T Single submitter congenital prothrombin deficiency
  • c.1725+9C>T Single submitter congenital prothrombin deficiency
  • c.1726-11TTC[2] Single submitter congenital prothrombin deficiency
  • c.1726-20A>C Single submitter congenital prothrombin deficiency
  • c.1726-4T>C Single submitter congenital prothrombin deficiency
  • c.240+17C>T Single submitter congenital prothrombin deficiency
  • c.240+18G>A Single submitter congenital prothrombin deficiency
  • c.240+18G>C Single submitter congenital prothrombin deficiency
  • c.240+7C>T Single submitter congenital prothrombin deficiency
  • c.241-18C>T Single submitter congenital prothrombin deficiency
  • c.241-39G>A Single submitter
  • c.265+6C>T Single submitter
  • c.265+6dup Single submitter congenital prothrombin deficiency
  • c.265+8C>T Single submitter congenital prothrombin deficiency
  • c.265+9C>T Single submitter congenital prothrombin deficiency
  • c.266-19A>G Single submitter congenital prothrombin deficiency
  • c.316+15C>T Single submitter congenital prothrombin deficiency
  • c.316+18G>A Single submitter congenital prothrombin deficiency
  • c.316+8A>C Single submitter congenital prothrombin deficiency
  • c.317-12G>C Single submitter congenital prothrombin deficiency
  • c.317-12G>T Single submitter congenital prothrombin deficiency
  • c.317-14T>C Single submitter congenital prothrombin deficiency
  • c.317-15G>A Single submitter congenital prothrombin deficiency
  • c.317-17G>C Single submitter congenital prothrombin deficiency
  • c.317-18G>A Single submitter congenital prothrombin deficiency
  • c.317-19C>T Single submitter congenital prothrombin deficiency
  • c.317-5C>T Single submitter congenital prothrombin deficiency
  • c.422+14C>T Single submitter congenital prothrombin deficiency
  • c.422+15G>A Single submitter congenital prothrombin deficiency
  • c.423-11T>G Single submitter congenital prothrombin deficiency
  • c.423-13T>A Single submitter congenital prothrombin deficiency
  • c.423-19G>T Single submitter congenital prothrombin deficiency
  • c.423-4C>G Single submitter congenital prothrombin deficiency
  • c.423-7G>T Single submitter congenital prothrombin deficiency
  • c.559+12G>T Single submitter congenital prothrombin deficiency
  • c.559+15G>A Single submitter congenital prothrombin deficiency
  • c.559+19G>A Single submitter congenital prothrombin deficiency
  • c.560-15C>G Single submitter congenital prothrombin deficiency
  • c.560-15C>T Single submitter congenital prothrombin deficiency
  • c.560-19C>G Single submitter congenital prothrombin deficiency
  • c.560-6C>T Single submitter congenital prothrombin deficiency
  • c.560-7C>T Single submitter congenital prothrombin deficiency
  • c.79+10T>C Single submitter congenital prothrombin deficiency
  • c.79+15G>A Single submitter congenital prothrombin deficiency
  • c.79+15G>T Single submitter congenital prothrombin deficiency
  • c.79+17A>G Single submitter congenital prothrombin deficiency
  • c.80-10C>G Single submitter congenital prothrombin deficiency
  • c.80-10C>T Single submitter congenital prothrombin deficiency
  • c.80-12A>C Single submitter congenital prothrombin deficiency
  • c.80-12A>G Single submitter congenital prothrombin deficiency
  • c.80-12dup Single submitter congenital prothrombin deficiency
  • c.80-13C>G Single submitter congenital prothrombin deficiency
  • c.80-13C>T Single submitter congenital prothrombin deficiency
  • c.80-14C>G Single submitter congenital prothrombin deficiency
  • c.80-14C>T Single submitter congenital prothrombin deficiency
  • c.80-17C>G Single submitter congenital prothrombin deficiency
  • c.80-18C>A Single submitter congenital prothrombin deficiency
  • c.80-18C>G Single submitter congenital prothrombin deficiency
  • c.80-18C>T Single submitter congenital prothrombin deficiency
  • c.80-9G>A Single submitter congenital prothrombin deficiency
  • c.874+11dup Single submitter congenital prothrombin deficiency
  • c.874+16A>G Single submitter congenital prothrombin deficiency
  • c.874+20_874+35dup Single submitter congenital prothrombin deficiency
  • c.875-20C>T Single submitter congenital prothrombin deficiency
  • c.875-7C>T Single submitter congenital prothrombin deficiency
  • c.*292G>A Single submitter
  • p.Ala109= Single submitter congenital prothrombin deficiency
  • p.Ala150= Single submitter congenital prothrombin deficiency
  • p.Ala17= Single submitter congenital prothrombin deficiency
  • p.Ala194= Single submitter congenital prothrombin deficiency
  • p.Ala2= Single submitter congenital prothrombin deficiency
  • p.Ala226= Single submitter congenital prothrombin deficiency
  • p.Ala236= Single submitter congenital prothrombin deficiency
  • p.Ala254= Single submitter congenital prothrombin deficiency
  • p.Ala316= Single submitter congenital prothrombin deficiency
  • p.Ala370= Single submitter congenital prothrombin deficiency
  • p.Ala404= Single submitter congenital prothrombin deficiency
  • p.Ala464= Single submitter congenital prothrombin deficiency
  • p.Ala70= Single submitter congenital prothrombin deficiency
  • p.Ala93= Single submitter congenital prothrombin deficiency
  • p.Arg198= Single submitter congenital prothrombin deficiency
  • p.Arg224His Single submitter Inborn genetic diseases
  • p.Arg263= Single submitter congenital prothrombin deficiency
  • p.Arg35= Single submitter congenital prothrombin deficiency
  • p.Arg42= Single submitter congenital prothrombin deficiency
  • p.Arg486= Single submitter congenital prothrombin deficiency
  • p.Arg533= Single submitter congenital prothrombin deficiency
  • p.Arg560= Single submitter congenital prothrombin deficiency
  • p.Asn107= Single submitter congenital prothrombin deficiency
  • p.Asn155= Single submitter congenital prothrombin deficiency
  • p.Asn264= Single submitter congenital prothrombin deficiency
  • p.Asn45= Single submitter congenital prothrombin deficiency
  • p.Asn454= Single submitter congenital prothrombin deficiency
  • p.Asp216= Single submitter congenital prothrombin deficiency
  • p.Asp216Glu Single submitter congenital prothrombin deficiency
  • p.Asp282= Single submitter congenital prothrombin deficiency
  • p.Asp361= Single submitter congenital prothrombin deficiency
  • p.Asp485= Single submitter congenital prothrombin deficiency
  • p.Asp556= Single submitter congenital prothrombin deficiency
  • p.Asp597= Single submitter congenital prothrombin deficiency
  • p.Cys482= Single submitter congenital prothrombin deficiency
  • p.Glu128= Single submitter congenital prothrombin deficiency
  • p.Glu312= Single submitter congenital prothrombin deficiency
  • p.Glu333= Single submitter congenital prothrombin deficiency
  • p.Glu343= Single submitter congenital prothrombin deficiency
  • p.Glu69= Single submitter congenital prothrombin deficiency
  • p.Glu72= Single submitter congenital prothrombin deficiency
  • p.Gly267= Single submitter congenital prothrombin deficiency
  • p.Gly271= Single submitter congenital prothrombin deficiency
  • p.Gly281= Single submitter congenital prothrombin deficiency
  • p.Gly337= Single submitter
  • p.His23= Single submitter congenital prothrombin deficiency
  • p.His429= Single submitter congenital prothrombin deficiency
  • p.His479= Single submitter congenital prothrombin deficiency
  • p.Ile183= Single submitter congenital prothrombin deficiency
  • p.Ile311= Single submitter congenital prothrombin deficiency
  • p.Ile372= Single submitter congenital prothrombin deficiency
  • p.Ile449= Single submitter congenital prothrombin deficiency
  • p.Ile463= Single submitter congenital prothrombin deficiency
  • p.Ile478= Single submitter congenital prothrombin deficiency
  • p.Ile587= Single submitter congenital prothrombin deficiency
  • p.Ile613= Single submitter congenital prothrombin deficiency
  • p.Leu13= Single submitter congenital prothrombin deficiency
  • p.Leu131= Single submitter congenital prothrombin deficiency
  • p.Leu232= Single submitter congenital prothrombin deficiency
  • p.Leu356= Single submitter Inborn genetic diseases
  • p.Leu389= Single submitter congenital prothrombin deficiency
  • p.Leu408= Single submitter congenital prothrombin deficiency
  • p.Leu409= Single submitter congenital prothrombin deficiency
  • p.Leu422= Single submitter congenital prothrombin deficiency
  • p.Leu465= Single submitter
  • p.Leu483= Single submitter congenital prothrombin deficiency
  • p.Leu492= Single submitter congenital prothrombin deficiency
  • p.Leu493= Single submitter congenital prothrombin deficiency
  • p.Leu56= Single submitter congenital prothrombin deficiency
  • p.Leu7= Single submitter congenital prothrombin deficiency
  • p.Lys428= Single submitter congenital prothrombin deficiency
  • p.Lys554= Single submitter congenital prothrombin deficiency
  • p.Met466Leu Single submitter Inborn genetic diseases
  • p.Phe342= Single submitter congenital prothrombin deficiency
  • p.Phe417= Single submitter congenital prothrombin deficiency
  • p.Phe578Leu Single submitter Inborn genetic diseases
  • p.Phe602= Single submitter congenital prothrombin deficiency
  • p.Phe71= Single submitter congenital prothrombin deficiency
  • p.Pro167= Single submitter congenital prothrombin deficiency
  • p.Pro174= Single submitter congenital prothrombin deficiency
  • p.Pro209= Single submitter congenital prothrombin deficiency
  • p.Pro233= Single submitter Inborn genetic diseases
  • p.Pro386= Single submitter congenital prothrombin deficiency
  • p.Pro471= Single submitter congenital prothrombin deficiency
  • p.Ser144= Single submitter Inborn genetic diseases
  • p.Ser199= Single submitter congenital prothrombin deficiency
  • p.Ser346= Single submitter congenital prothrombin deficiency
  • p.Ser36= Single submitter congenital prothrombin deficiency
  • p.Ser368= Single submitter congenital prothrombin deficiency
  • p.Ser475= Single submitter Inborn genetic diseases
  • p.Ser568= Single submitter congenital prothrombin deficiency
  • p.Ser76= Single submitter congenital prothrombin deficiency
  • p.Ser77= Single submitter congenital prothrombin deficiency
  • p.Thr114= Single submitter congenital prothrombin deficiency
  • p.Thr123= Single submitter congenital prothrombin deficiency
  • p.Thr172= Single submitter congenital prothrombin deficiency
  • p.Thr175= Single submitter congenital prothrombin deficiency
  • p.Thr315= Single submitter congenital prothrombin deficiency
  • p.Thr328= Single submitter congenital prothrombin deficiency
  • p.Thr351= Single submitter congenital prothrombin deficiency
  • p.Thr64= Single submitter congenital prothrombin deficiency
  • p.Tyr116= Single submitter congenital prothrombin deficiency
  • p.Tyr136= Single submitter
  • p.Tyr290= Single submitter congenital prothrombin deficiency
  • p.Tyr87= Single submitter congenital prothrombin deficiency
  • p.Val185= Single submitter congenital prothrombin deficiency
  • p.Val227= Single submitter congenital prothrombin deficiency
  • p.Val379= Single submitter congenital prothrombin deficiency
  • p.Val401= Single submitter congenital prothrombin deficiency
  • p.Val51= Single submitter congenital prothrombin deficiency
  • p.Val573= Single submitter congenital prothrombin deficiency

Uncertain significance 122