USP19 — 219 ClinVar variants

All ClinVar germline USP19 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 175 flagged for review →

2 Pathogenic · 3 Benign · 18 Likely benign · 196 Uncertain significance

Full USP19 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 175

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.

USP19 p.Glu524Asp Pathogenic No assertion criteria
Epileptic encephalopathy
USP19 p.Val554Leu Pathogenic No assertion criteria
Epileptic encephalopathy

Predictors lean, ClinVar uncertain 149

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

Predictors split 24

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

All USP19 variants

Pathogenic 2

p.Glu524Asp No assertion criteria Epileptic encephalopathy ⚠
p.Val554Leu No assertion criteria Epileptic encephalopathy ⚠

Benign 3

c.2292+7T>C Multiple submitters
p.Pro487= Multiple submitters
c.3698+8G>T Single submitter

Likely benign 18

c.4039-607G>A Single submitter
p.Arg132His Single submitter
p.Arg216Gln Single submitter
p.Arg290Gln Single submitter
p.Arg75Cys Single submitter
p.Arg77His Single submitter
p.Arg840His Single submitter
p.Asp307Glu Single submitter
p.Asp543Glu Single submitter
p.Gly340Arg Single submitter
p.Ile1047Val Single submitter
p.Ile1057Thr Single submitter
p.Met1022Val Single submitter
p.Pro437= Single submitter
p.Ser85Leu Single submitter
p.Thr859Met Single submitter
p.Val889Ile Single submitter
p.Glu378Asp No assertion criteria long QT syndrome

Uncertain significance 196

c.4039-440G>A Single submitter ⚠
c.4039-477G>A Single submitter ⚠
c.4039-482C>G Single submitter ⚠
c.4039-518G>A Single submitter ⚠
c.4039-519C>T Single submitter ⚠
c.4039-543A>T Single submitter ⚠
c.4039-548G>C Single submitter ⚠
c.4039-563G>A Single submitter ⚠
c.4039-590G>A Single submitter ⚠
c.4039-591G>A Single submitter ⚠
c.4039-599G>A Single submitter ⚠
c.4039-612C>T Single submitter ⚠
p.Ala1344Thr Single submitter ⚠
p.Ala157Thr Single submitter ⚠
p.Ala268Thr Single submitter
p.Ala301Thr Single submitter
p.Ala30Gly Single submitter ⚠
p.Ala367Val Single submitter ⚠
p.Ala384Val Single submitter ⚠
p.Ala515Thr Single submitter ⚠
p.Ala57Val Single submitter ⚠
p.Ala63Val Single submitter ⚠
p.Ala659Glu Single submitter ⚠
p.Ala659Thr Single submitter ⚠
p.Arg1031Trp Single submitter ⚠
p.Arg1038Gln Single submitter ⚠
p.Arg1038Trp Single submitter ⚠
p.Arg1070Gln Single submitter ⚠
p.Arg1102Gln Single submitter ⚠
p.Arg1127Gln Single submitter ⚠
p.Arg1131His Single submitter ⚠
p.Arg1157Gln Single submitter ⚠
p.Arg121Lys Single submitter ⚠
p.Arg1317Trp Single submitter ⚠
p.Arg132Cys Single submitter ⚠
p.Arg132Leu Single submitter ⚠
p.Arg180Gly Single submitter ⚠
p.Arg180His Single submitter ⚠
p.Arg216Trp Single submitter
p.Arg237Gln Single submitter
p.Arg237Trp Single submitter
p.Arg243Gln Single submitter
p.Arg247Gln Single submitter
p.Arg350Gln Single submitter ⚠
p.Arg46Gln Single submitter ⚠
p.Arg526Trp Single submitter ⚠
p.Arg548Pro Single submitter ⚠
p.Arg631His Single submitter ⚠
p.Arg648His Single submitter
p.Arg658Gln Single submitter ⚠
p.Arg709Cys Single submitter ⚠
p.Arg709Leu Single submitter ⚠
p.Arg724Trp Single submitter ⚠
p.Arg736Gln Single submitter ⚠
p.Arg75His Single submitter ⚠
p.Arg79Trp Single submitter ⚠
p.Arg832His Single submitter ⚠
p.Arg843His Single submitter ⚠
p.Arg874Gln Single submitter ⚠
p.Arg874Trp Single submitter ⚠
p.Arg883His Single submitter ⚠
p.Arg899Gln Single submitter ⚠
p.Arg982Cys Single submitter ⚠
p.Asn1086Asp Single submitter ⚠
p.Asn1277Asp Single submitter ⚠
p.Asn1277Ser Single submitter ⚠
p.Asn220Asp Single submitter
p.Asn640Tyr Single submitter ⚠
p.Asp119Gly Single submitter ⚠
p.Asp357Glu Single submitter ⚠
p.Asp38Gly Single submitter ⚠
p.Asp508Asn Single submitter ⚠
p.Asp539Glu Single submitter ⚠
p.Asp539Gly Single submitter ⚠
p.Asp543Gly Single submitter ⚠
p.Cys1272Trp Single submitter ⚠
p.Cys1272Tyr Single submitter ⚠
p.Cys174Arg Single submitter ⚠
p.Cys359Phe Single submitter ⚠
p.Gln1165Leu Single submitter ⚠
p.Gln1248Lys Single submitter ⚠
p.Glu1066Lys Single submitter ⚠
p.Glu1142Asp Single submitter ⚠
p.Glu1179Asp Single submitter ⚠
p.Glu1301Lys Single submitter ⚠
p.Glu169Ala Single submitter ⚠
p.Glu305Lys Single submitter ⚠
p.Glu392Asp Single submitter ⚠
p.Glu538Ala Single submitter ⚠
p.Glu588Asp Single submitter ⚠
p.Glu591Lys Single submitter ⚠
p.Glu829Lys Single submitter ⚠
p.Glu873Asp Single submitter ⚠
p.Glu95Lys Single submitter ⚠
p.Gly1039Val Single submitter ⚠
p.Gly1117Cys Single submitter ⚠
p.Gly1153Ser Single submitter ⚠
p.Gly159Cys Single submitter ⚠
p.Gly214Val Single submitter
p.Gly252Ser Single submitter
p.Gly255Cys Single submitter
p.Gly282Arg Single submitter
p.Gly483Arg Single submitter ⚠
p.Gly483Ser Single submitter ⚠
p.Gly483Val Single submitter
p.Gly541Ala Single submitter ⚠
p.Gly87Ala Single submitter ⚠
p.His186Tyr Single submitter ⚠
p.His436Tyr Single submitter
p.His442Leu Single submitter ⚠
p.His737Asn Single submitter ⚠
p.Ile800Phe Single submitter ⚠
p.Ile837Thr Single submitter ⚠
p.Ile891Met Single submitter ⚠
p.Ile941Thr Single submitter
p.Leu1116Pro Single submitter ⚠
p.Leu1122Val Single submitter ⚠
p.Leu1163Val Single submitter ⚠
p.Leu1169Phe Single submitter ⚠
p.Leu1210Phe Single submitter ⚠
p.Leu196Val Single submitter ⚠
p.Leu373Met Single submitter ⚠
p.Leu935Phe Single submitter ⚠
p.Leu954Ile Single submitter ⚠
p.Lys1188Arg Single submitter ⚠
p.Lys130Met Single submitter ⚠
p.Lys176Asn Single submitter ⚠
p.Lys181Asn Single submitter ⚠
p.Lys23Asn Single submitter ⚠
p.Lys361Arg Single submitter ⚠
p.Lys532Gln Single submitter ⚠
p.Met1085Leu Single submitter ⚠
p.Met348Val Single submitter ⚠
p.Met611Ile Single submitter ⚠
p.Met739Lys Single submitter ⚠
p.Met983Val Single submitter ⚠
p.Phe744Leu Single submitter ⚠
p.Phe81Leu Single submitter ⚠
p.Pro1010Ser Single submitter ⚠
p.Pro1030His Single submitter ⚠
p.Pro1076Ser Single submitter ⚠
p.Pro1113Ala Single submitter ⚠
p.Pro1334Ser Single submitter ⚠
p.Pro199Leu Single submitter
p.Pro278Leu Single submitter
p.Pro289Ser Single submitter
p.Pro295Leu Single submitter
p.Pro314Leu Single submitter ⚠
p.Pro354Arg Single submitter ⚠
p.Pro395Leu Single submitter ⚠
p.Pro437Leu Single submitter ⚠
p.Pro487Leu Single submitter ⚠
p.Pro512Leu Single submitter ⚠
p.Pro61Ala Single submitter ⚠
p.Pro760Ser Single submitter ⚠
p.Pro780Ser Single submitter ⚠
p.Pro787Ser Single submitter ⚠
p.Pro930Ala Single submitter ⚠
p.Pro938Ala Single submitter ⚠
p.Ser123Arg Single submitter ⚠
p.Ser1284Thr Single submitter ⚠
p.Ser345Phe Single submitter ⚠
p.Ser45fs Single submitter
p.Ser544Asn Single submitter ⚠
p.Ser66Phe Single submitter ⚠
p.Ser6Gly Single submitter ⚠
p.Ser823Arg Single submitter ⚠
p.Ser903Leu Single submitter ⚠
p.Ser903Trp Single submitter
p.Thr1020Ile Single submitter ⚠
p.Thr111Ile Single submitter ⚠
p.Thr1298Met Single submitter ⚠
p.Thr20Ile Single submitter ⚠
p.Thr422Met Single submitter
p.Thr505Ala Single submitter ⚠
p.Thr505Ile Single submitter ⚠
p.Thr555Asn Single submitter ⚠
p.Thr555Ile Single submitter ⚠
p.Thr608Ser Single submitter ⚠
p.Thr91Pro Single submitter ⚠
p.Trp1033Ser Single submitter ⚠
p.Val1068Leu Single submitter ⚠
p.Val402Met Single submitter ⚠
p.Val404Met Single submitter ⚠
p.Val500Met Single submitter ⚠
p.Val584Met Single submitter ⚠
p.Val614Ile Single submitter ⚠
p.Val655Met Single submitter ⚠
p.Val719Met Single submitter ⚠
p.Val729Ala Single submitter ⚠
p.Val785Ile Single submitter ⚠
p.Val804Met Single submitter ⚠
p.Val826Met Single submitter ⚠
p.Val844Met Single submitter ⚠
p.Val875Leu Single submitter ⚠
p.Val947Phe Single submitter ⚠