OPLAH — 629 ClinVar variants

All ClinVar germline OPLAH variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 302 flagged for review →

20 Pathogenic · 2 Pathogenic/Likely pathogenic · 22 Likely pathogenic · 11 Conflicting · 40 Benign · 14 Benign/Likely benign · 196 Likely benign · 324 Uncertain significance

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

⚑ Evidence disagreements 302

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 agree, ClinVar conflicts 5

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

Predictors lean, ClinVar uncertain 208

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 208

Predictors split 89

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

All OPLAH variants

Pathogenic 20

Pathogenic/Likely pathogenic 2

  • c.587+1G>A Multiple submitters 5-oxoprolinase deficiency
  • p.Gln1006Ter Multiple submitters 5-oxoprolinase deficiency

Likely pathogenic 22

  • p.Tyr248Ter Multiple submitters 5-oxoprolinase deficiency
  • c.1707-2A>G Single submitter 5-oxoprolinase deficiency
  • c.2686+1G>T Single submitter 5-oxoprolinase deficiency
  • c.3018+1G>T Single submitter 5-oxoprolinase deficiency
  • c.3019-2A>G Single submitter 5-oxoprolinase deficiency
  • c.3623-2A>C Single submitter 5-oxoprolinase deficiency
  • p.Arg65fs Single submitter 5-oxoprolinase deficiency
  • p.Arg768His Single submitter 5-oxoprolinase deficiency
  • p.Asp1255fs Single submitter 5-oxoprolinase deficiency
  • p.Gln1285Ter Single submitter 5-oxoprolinase deficiency
  • p.Gln57Ter Single submitter 5-oxoprolinase deficiency
  • p.Gly1132Trp Single submitter 5-oxoprolinase deficiency
  • p.Leu968Ter Single submitter 5-oxoprolinase deficiency
  • p.Ser298Ter Single submitter 5-oxoprolinase deficiency
  • p.Thr1143fs Single submitter 5-oxoprolinase deficiency
  • p.Thr712Ter Single submitter 5-oxoprolinase deficiency
  • p.Val1057fs Single submitter 5-oxoprolinase deficiency
  • p.Val1087fs Single submitter OPLAH-related disorder
  • p.Val332fs Single submitter 5-oxoprolinase deficiency
  • p.Gln950Ter No assertion criteria OPLAH-related disorder
  • p.Gly1015fs No assertion criteria OPLAH-related disorder
  • p.Pro1266fs No assertion criteria OPLAH-related disorder

Conflicting classifications of pathogenicity 11

Benign 40

  • c.2512-7C>A Multiple submitters 5-oxoprolinase deficiency
  • c.3462-9C>T Multiple submitters 5-oxoprolinase deficiency
  • c.3721-11dup Multiple submitters 5-oxoprolinase deficiency
  • c.3721-20del Multiple submitters 5-oxoprolinase deficiency
  • c.3721-20G>C Multiple submitters 5-oxoprolinase deficiency
  • p.Ala1009= Multiple submitters 5-oxoprolinase deficiency
  • p.Ala1055= Multiple submitters 5-oxoprolinase deficiency
  • p.Ala879Val Multiple submitters 5-oxoprolinase deficiency
  • p.Arg269Cys Multiple submitters 5-oxoprolinase deficiency ⚠
  • p.Arg31Gln Multiple submitters 5-oxoprolinase deficiency
  • p.Arg459Cys Multiple submitters 5-oxoprolinase deficiency ⚠
  • p.Arg501Gln Multiple submitters 5-oxoprolinase deficiency
  • p.Arg658Leu Multiple submitters 5-oxoprolinase deficiency
  • p.Asp526= Multiple submitters 5-oxoprolinase deficiency
  • p.Gly148Ala Multiple submitters 5-oxoprolinase deficiency
  • p.Gly584Cys Multiple submitters 5-oxoprolinase deficiency
  • p.Ile717= Multiple submitters 5-oxoprolinase deficiency
  • p.Ile74= Multiple submitters 5-oxoprolinase deficiency
  • p.Phe612= Multiple submitters 5-oxoprolinase deficiency
  • p.Pro4= Multiple submitters 5-oxoprolinase deficiency
  • p.Ser284Arg Multiple submitters 5-oxoprolinase deficiency
  • p.Tyr944= Multiple submitters 5-oxoprolinase deficiency
  • p.Val340Ile Multiple submitters 5-oxoprolinase deficiency
  • p.Val545Met Multiple submitters 5-oxoprolinase deficiency
  • p.Val721= Multiple submitters 5-oxoprolinase deficiency
  • c.1089-5C>T Single submitter 5-oxoprolinase deficiency
  • c.2409+14del Single submitter 5-oxoprolinase deficiency
  • c.3303+9G>T Single submitter 5-oxoprolinase deficiency
  • c.3721-11del Single submitter 5-oxoprolinase deficiency
  • p.Ala237= Single submitter 5-oxoprolinase deficiency
  • p.Ala376= Single submitter 5-oxoprolinase deficiency
  • p.Arg641Cys Single submitter 5-oxoprolinase deficiency
  • p.Asn440= Single submitter 5-oxoprolinase deficiency
  • p.Gly1170Ser Single submitter 5-oxoprolinase deficiency
  • p.Gly683Val Single submitter 5-oxoprolinase deficiency
  • p.His856= Single submitter 5-oxoprolinase deficiency
  • p.Ile245Thr Single submitter 5-oxoprolinase deficiency
  • p.Pro371= Single submitter 5-oxoprolinase deficiency
  • p.Pro841= Single submitter 5-oxoprolinase deficiency
  • p.Pro908Ser Single submitter 5-oxoprolinase deficiency ⚠

Benign/Likely benign 14

  • c.1156+4A>G Multiple submitters 5-oxoprolinase deficiency
  • c.1845-14C>T Multiple submitters 5-oxoprolinase deficiency
  • c.2097-8C>T Multiple submitters 5-oxoprolinase deficiency
  • c.3018+18T>C Multiple submitters 5-oxoprolinase deficiency
  • c.3720+8C>T Multiple submitters 5-oxoprolinase deficiency
  • c.3721-16C>G Multiple submitters 5-oxoprolinase deficiency
  • c.949+12G>A Multiple submitters 5-oxoprolinase deficiency
  • p.Asn350= Multiple submitters 5-oxoprolinase deficiency
  • p.Asp988= Multiple submitters 5-oxoprolinase deficiency
  • p.Glu1274Val Multiple submitters 5-oxoprolinase deficiency
  • p.Leu1191= Multiple submitters 5-oxoprolinase deficiency
  • p.Leu134= Multiple submitters 5-oxoprolinase deficiency
  • p.Leu782= Multiple submitters 5-oxoprolinase deficiency
  • p.Val1089Ile Multiple submitters 5-oxoprolinase deficiency

Likely benign 196

  • c.171+6C>A Multiple submitters 5-oxoprolinase deficiency
  • c.2096+8G>A Multiple submitters 5-oxoprolinase deficiency
  • c.2512-6C>T Multiple submitters 5-oxoprolinase deficiency
  • c.3721-20_3721-18del Multiple submitters 5-oxoprolinase deficiency
  • c.463+15G>A Multiple submitters 5-oxoprolinase deficiency
  • p.Ala960= Multiple submitters 5-oxoprolinase deficiency
  • p.Arg997Cys Multiple submitters 5-oxoprolinase deficiency ⚠
  • p.Asp238= Multiple submitters 5-oxoprolinase deficiency
  • p.Asp479= Multiple submitters 5-oxoprolinase deficiency
  • p.Gly1052= Multiple submitters 5-oxoprolinase deficiency
  • p.Gly272= Multiple submitters 5-oxoprolinase deficiency
  • p.Gly292= Multiple submitters 5-oxoprolinase deficiency
  • p.Gly477= Multiple submitters 5-oxoprolinase deficiency
  • p.Ile499= Multiple submitters 5-oxoprolinase deficiency
  • p.Leu1219= Multiple submitters 5-oxoprolinase deficiency
  • p.Leu191= Multiple submitters 5-oxoprolinase deficiency
  • p.Pro1148= Multiple submitters
  • p.Ser288= Multiple submitters 5-oxoprolinase deficiency
  • p.Ser720= Multiple submitters 5-oxoprolinase deficiency
  • p.Thr320= Multiple submitters 5-oxoprolinase deficiency
  • p.Tyr1281= Multiple submitters 5-oxoprolinase deficiency
  • c.1156+15C>T Single submitter 5-oxoprolinase deficiency
  • c.1422+16C>T Single submitter 5-oxoprolinase deficiency
  • c.1423-5C>T Single submitter 5-oxoprolinase deficiency
  • c.1535+16G>A Single submitter 5-oxoprolinase deficiency
  • c.1536-18T>C Single submitter 5-oxoprolinase deficiency
  • c.1706+8C>T Single submitter 5-oxoprolinase deficiency
  • c.171+12C>T Single submitter 5-oxoprolinase deficiency
  • c.171+13G>A Single submitter 5-oxoprolinase deficiency
  • c.172-13A>G Single submitter 5-oxoprolinase deficiency
  • c.172-5C>T Single submitter 5-oxoprolinase deficiency
  • c.1844+17C>G Single submitter 5-oxoprolinase deficiency
  • c.1844+18T>G Single submitter 5-oxoprolinase deficiency
  • c.1844+20C>T Single submitter 5-oxoprolinase deficiency
  • c.1844+8G>C Single submitter 5-oxoprolinase deficiency
  • c.1845-13G>A Single submitter 5-oxoprolinase deficiency
  • c.1984-10C>T Single submitter 5-oxoprolinase deficiency
  • c.1984-13G>A Single submitter 5-oxoprolinase deficiency
  • c.1984-14C>A Single submitter 5-oxoprolinase deficiency
  • c.2096+15G>A Single submitter 5-oxoprolinase deficiency
  • c.2097-20C>G Single submitter 5-oxoprolinase deficiency
  • c.2248+11G>A Single submitter 5-oxoprolinase deficiency
  • c.2248+19G>T Single submitter 5-oxoprolinase deficiency
  • c.2511+17G>A Single submitter 5-oxoprolinase deficiency
  • c.2512-19G>A Single submitter 5-oxoprolinase deficiency
  • c.2512-5G>A Single submitter 5-oxoprolinase deficiency
  • c.2686+10_2686+15del Single submitter 5-oxoprolinase deficiency
  • c.2871+13A>C Single submitter 5-oxoprolinase deficiency
  • c.2872-4C>T Single submitter 5-oxoprolinase deficiency
  • c.3019-11G>A Single submitter 5-oxoprolinase deficiency
  • c.3019-14C>T Single submitter 5-oxoprolinase deficiency
  • c.3019-5C>T Single submitter 5-oxoprolinase deficiency
  • c.3153+8G>A Single submitter 5-oxoprolinase deficiency
  • c.3154-12C>T Single submitter 5-oxoprolinase deficiency
  • c.3154-20G>T Single submitter 5-oxoprolinase deficiency
  • c.3303+11G>T Single submitter 5-oxoprolinase deficiency
  • c.3304-10C>T Single submitter 5-oxoprolinase deficiency
  • c.3304-11G>A Single submitter 5-oxoprolinase deficiency
  • c.3461+15C>T Single submitter 5-oxoprolinase deficiency
  • c.3461+17G>A Single submitter 5-oxoprolinase deficiency
  • c.3462-4G>A Single submitter 5-oxoprolinase deficiency
  • c.3622+16G>A Single submitter 5-oxoprolinase deficiency
  • c.3622+17C>T Single submitter 5-oxoprolinase deficiency
  • c.3622+7G>C Single submitter 5-oxoprolinase deficiency
  • c.3623-13C>G Single submitter 5-oxoprolinase deficiency
  • c.364-8G>A Single submitter 5-oxoprolinase deficiency
  • c.364-9C>T Single submitter 5-oxoprolinase deficiency
  • c.3721-12_3721-11dup Single submitter
  • c.3721-12_3721-11insCT Single submitter 5-oxoprolinase deficiency
  • c.3721-12C>G Single submitter 5-oxoprolinase deficiency
  • c.3721-13C>T Single submitter 5-oxoprolinase deficiency
  • c.3721-14_3721-13insCA Single submitter 5-oxoprolinase deficiency
  • c.3721-15_3721-6del Single submitter 5-oxoprolinase deficiency
  • c.3721-15C>A Single submitter 5-oxoprolinase deficiency
  • c.3721-15C>T Single submitter 5-oxoprolinase deficiency
  • c.3721-20_3721-17del Single submitter
  • c.3721-20_3721-19del Single submitter 5-oxoprolinase deficiency
  • c.3721-8G>C Single submitter
  • c.463+14C>T Single submitter 5-oxoprolinase deficiency
  • c.587+10G>A Single submitter 5-oxoprolinase deficiency
  • c.587+12G>T Single submitter 5-oxoprolinase deficiency
  • c.783+14G>C Single submitter 5-oxoprolinase deficiency
  • c.784-20C>T Single submitter 5-oxoprolinase deficiency
  • c.784-9C>T Single submitter 5-oxoprolinase deficiency
  • c.949+11C>T Single submitter 5-oxoprolinase deficiency
  • c.950-17C>T Single submitter 5-oxoprolinase deficiency
  • p.Ala1124= Single submitter 5-oxoprolinase deficiency
  • p.Ala1126= Single submitter 5-oxoprolinase deficiency
  • p.Ala1287= Single submitter
  • p.Ala426= Single submitter 5-oxoprolinase deficiency
  • p.Ala564= Single submitter 5-oxoprolinase deficiency
  • p.Arg185= Single submitter 5-oxoprolinase deficiency
  • p.Arg459= Single submitter 5-oxoprolinase deficiency
  • p.Arg501Trp Single submitter 5-oxoprolinase deficiency ⚠
  • p.Arg52Cys Single submitter 5-oxoprolinase deficiency
  • p.Arg615Trp Single submitter 5-oxoprolinase deficiency
  • p.Arg744= Single submitter 5-oxoprolinase deficiency
  • p.Asn462= Single submitter 5-oxoprolinase deficiency
  • p.Asp632= Single submitter 5-oxoprolinase deficiency
  • p.Asp70= Single submitter 5-oxoprolinase deficiency
  • p.Asp947= Single submitter 5-oxoprolinase deficiency
  • p.Gln583Arg Single submitter
  • p.Gln931Arg Single submitter 5-oxoprolinase deficiency
  • p.Glu1152= Single submitter 5-oxoprolinase deficiency
  • p.Glu1274= Single submitter 5-oxoprolinase deficiency
  • p.Glu1274Lys Single submitter 5-oxoprolinase deficiency
  • p.Glu330Lys Single submitter 5-oxoprolinase deficiency
  • p.Glu49= Single submitter 5-oxoprolinase deficiency
  • p.Glu49Lys Single submitter 5-oxoprolinase deficiency
  • p.Glu681= Single submitter 5-oxoprolinase deficiency
  • p.Gly1172= Single submitter 5-oxoprolinase deficiency
  • p.Gly1251= Single submitter 5-oxoprolinase deficiency
  • p.Gly15= Single submitter 5-oxoprolinase deficiency
  • p.Gly379= Single submitter 5-oxoprolinase deficiency
  • p.Gly640Ser Single submitter 5-oxoprolinase deficiency ⚠
  • p.Gly669= Single submitter 5-oxoprolinase deficiency
  • p.Gly730= Single submitter 5-oxoprolinase deficiency
  • p.Gly780= Single submitter 5-oxoprolinase deficiency
  • p.Gly814= Single submitter 5-oxoprolinase deficiency
  • p.Gly889Arg Single submitter 5-oxoprolinase deficiency
  • p.Gly993= Single submitter
  • p.His511= Single submitter 5-oxoprolinase deficiency
  • p.His513= Single submitter 5-oxoprolinase deficiency
  • p.His73Arg Single submitter
  • p.His870Asp Single submitter 5-oxoprolinase deficiency
  • p.Ile12= Single submitter 5-oxoprolinase deficiency
  • p.Ile228= Single submitter 5-oxoprolinase deficiency
  • p.Ile789= Single submitter 5-oxoprolinase deficiency
  • p.Leu1039= Single submitter 5-oxoprolinase deficiency
  • p.Leu1109= Single submitter 5-oxoprolinase deficiency
  • p.Leu1270= Single submitter 5-oxoprolinase deficiency
  • p.Leu180= Single submitter 5-oxoprolinase deficiency
  • p.Leu218= Single submitter 5-oxoprolinase deficiency
  • p.Leu287= Single submitter 5-oxoprolinase deficiency
  • p.Leu485= Single submitter 5-oxoprolinase deficiency
  • p.Leu503= Single submitter 5-oxoprolinase deficiency
  • p.Leu516= Single submitter 5-oxoprolinase deficiency
  • p.Leu63= Single submitter 5-oxoprolinase deficiency
  • p.Leu646= Single submitter
  • p.Leu818= Single submitter 5-oxoprolinase deficiency
  • p.Leu901= Single submitter 5-oxoprolinase deficiency
  • p.Leu98= Single submitter 5-oxoprolinase deficiency
  • p.Phe1186= Single submitter 5-oxoprolinase deficiency
  • p.Phe457= Single submitter 5-oxoprolinase deficiency
  • p.Phe544= Single submitter 5-oxoprolinase deficiency
  • p.Phe608= Single submitter 5-oxoprolinase deficiency
  • p.Pro1062= Single submitter 5-oxoprolinase deficiency
  • p.Pro1203= Single submitter 5-oxoprolinase deficiency
  • p.Pro1239= Single submitter 5-oxoprolinase deficiency
  • p.Pro126= Single submitter 5-oxoprolinase deficiency
  • p.Pro224= Single submitter 5-oxoprolinase deficiency
  • p.Pro243= Single submitter 5-oxoprolinase deficiency
  • p.Pro290= Single submitter 5-oxoprolinase deficiency
  • p.Pro345= Single submitter 5-oxoprolinase deficiency
  • p.Pro380= Single submitter 5-oxoprolinase deficiency
  • p.Pro628= Single submitter 5-oxoprolinase deficiency
  • p.Pro64= Single submitter 5-oxoprolinase deficiency
  • p.Pro68= Single submitter 5-oxoprolinase deficiency
  • p.Pro778= Single submitter 5-oxoprolinase deficiency
  • p.Ser1083= Single submitter 5-oxoprolinase deficiency
  • p.Ser1129= Single submitter 5-oxoprolinase deficiency
  • p.Ser1193= Single submitter
  • p.Ser1277= Single submitter 5-oxoprolinase deficiency
  • p.Ser270= Single submitter 5-oxoprolinase deficiency
  • p.Ser281= Single submitter 5-oxoprolinase deficiency
  • p.Ser336= Single submitter 5-oxoprolinase deficiency
  • p.Ser642Cys Single submitter 5-oxoprolinase deficiency
  • p.Ser911= Single submitter 5-oxoprolinase deficiency
  • p.Thr1108= Single submitter 5-oxoprolinase deficiency
  • p.Thr1146= Single submitter 5-oxoprolinase deficiency
  • p.Thr1181Ile Single submitter
  • p.Thr149= Single submitter 5-oxoprolinase deficiency
  • p.Thr151= Single submitter 5-oxoprolinase deficiency
  • p.Thr157= Single submitter 5-oxoprolinase deficiency
  • p.Thr234= Single submitter 5-oxoprolinase deficiency
  • p.Thr279Ala Single submitter
  • p.Thr301Ser Single submitter 5-oxoprolinase deficiency
  • p.Thr507= Single submitter 5-oxoprolinase deficiency
  • p.Thr654= Single submitter 5-oxoprolinase deficiency
  • p.Thr844= Single submitter 5-oxoprolinase deficiency
  • p.Tyr248= Single submitter 5-oxoprolinase deficiency
  • p.Tyr383= Single submitter 5-oxoprolinase deficiency
  • p.Val1059= Single submitter 5-oxoprolinase deficiency
  • p.Val1087= Single submitter 5-oxoprolinase deficiency
  • p.Val140= Single submitter 5-oxoprolinase deficiency
  • p.Val167= Single submitter 5-oxoprolinase deficiency
  • p.Val189= Single submitter 5-oxoprolinase deficiency
  • p.Val21= Single submitter
  • p.Val434Ile Single submitter 5-oxoprolinase deficiency
  • p.Val528= Single submitter 5-oxoprolinase deficiency
  • p.Val630= Single submitter 5-oxoprolinase deficiency
  • p.Val838= Single submitter 5-oxoprolinase deficiency
  • p.Val984= Single submitter 5-oxoprolinase deficiency
  • c.1535+10G>A No assertion criteria OPLAH-related disorder
  • p.Ala1073Val No assertion criteria EBV-positive nodal T- and NK-cell lymphoma ⚠
  • p.Pro1069= No assertion criteria OPLAH-related disorder

Uncertain significance 324

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