OPA3 — 571 ClinVar variants

All ClinVar germline OPA3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 146 flagged for review →

9 Pathogenic · 2 Pathogenic/Likely pathogenic · 22 Likely pathogenic · 58 Conflicting · 34 Benign · 17 Benign/Likely benign · 127 Likely benign · 302 Uncertain significance

Full OPA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 146

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 4

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

Predictors lean, ClinVar uncertain 107

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

Predictors split 33

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

All OPA3 variants

Pathogenic 9

  • c.143-1G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.143-1G>C Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Gln105Glu Multiple submitters OPA3-related disorder ⚠
  • c.143-2_143-1delinsCC Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu35Ter Single submitter 3-methylglutaconic aciduria type 3
  • p.Val19fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Gln108_Glu113del No assertion criteria 3-methylglutaconic aciduria type 3
  • p.Gly93Ser No assertion criteria optic atrophy 3 ⚠
  • p.Leu11Gln No assertion criteria 3-methylglutaconic aciduria type 3

Pathogenic/Likely pathogenic 2

  • p.Gln18Ter Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Gln139Ter No assertion criteria 3-methylglutaconic aciduria type 3

Likely pathogenic 22

  • c.142+1G>A Multiple submitters OPA3-related disorder
  • p.Gly65fs Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Met1Val Multiple submitters optic atrophy 3
  • c.142+2_142+3dup Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala5fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala77fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Arg103fs Single submitter optic atrophy 3
  • p.Arg153fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Arg33Ter Single submitter 3-methylglutaconic aciduria type 3
  • p.Cys96fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Gln107fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Gln137fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Gln47Arg Single submitter 3-methylglutaconic aciduria type 3 ⚠
  • p.Glu158fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu73Ter Single submitter 3-methylglutaconic aciduria type 3
  • p.Gly85fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Ile27_Lys28insTer Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu79Val Single submitter optic atrophy 3 ⚠
  • p.Trp51Ter Single submitter 3-methylglutaconic aciduria type 3
  • p.Lys21Ter No assertion criteria 3-methylglutaconic aciduria type 3
  • p.Ser34fs No assertion criteria 3-methylglutaconic aciduria type 3
  • p.Ter180Trp No assertion criteria 3-methylglutaconic aciduria type 3

Conflicting classifications of pathogenicity 58

  • c.142+5G>C Single submitter 3-methylglutaconic aciduria type 3
  • c.143-13T>G Single submitter optic atrophy 3
  • c.-113T>C Single submitter 3-methylglutaconic aciduria type 3
  • c.*1052C>T Single submitter optic atrophy 3
  • c.*1095C>A Single submitter 3-methylglutaconic aciduria type 3
  • c.*1238G>A Single submitter 3-methylglutaconic aciduria type 3
  • c.*1642A>G Single submitter 3-methylglutaconic aciduria type 3
  • c.*1761A>T Single submitter 3-methylglutaconic aciduria type 3
  • c.*1836C>T Single submitter optic atrophy 3
  • c.*2008C>T Single submitter 3-methylglutaconic aciduria type 3
  • c.*2101A>T Single submitter optic atrophy 3
  • c.*2518A>G Single submitter 3-methylglutaconic aciduria type 3
  • c.*3117C>T Single submitter 3-methylglutaconic aciduria type 3
  • c.*3128C>G Single submitter 3-methylglutaconic aciduria type 3
  • c.*3360G>A Single submitter optic atrophy 3
  • c.*3442A>G Single submitter optic atrophy 3
  • c.*3884G>A Single submitter 3-methylglutaconic aciduria type 3
  • c.*398G>T Single submitter 3-methylglutaconic aciduria type 3
  • c.*422C>T Single submitter 3-methylglutaconic aciduria type 3
  • c.*4439C>T Single submitter optic atrophy 3
  • c.*4949G>A Single submitter optic atrophy 3
  • c.*4954C>T Single submitter optic atrophy 3
  • c.*5277G>A Single submitter optic atrophy 3
  • c.*540G>T Single submitter optic atrophy 3
  • c.*5565C>T Single submitter optic atrophy 3
  • c.*5783G>A Single submitter optic atrophy 3
  • c.*5923G>A Single submitter optic atrophy 3
  • c.*5944G>A Single submitter 3-methylglutaconic aciduria type 3
  • c.*6101A>G Single submitter 3-methylglutaconic aciduria type 3
  • c.*6208C>T Single submitter optic atrophy 3
  • c.*6289A>G Single submitter 3-methylglutaconic aciduria type 3
  • c.*6442A>G Single submitter 3-methylglutaconic aciduria type 3
  • c.*6554G>A Single submitter optic atrophy 3
  • c.*6626G>A Single submitter 3-methylglutaconic aciduria type 3
  • c.*6688G>A Single submitter 3-methylglutaconic aciduria type 3
  • c.*6767G>A Single submitter 3-methylglutaconic aciduria type 3
  • c.*698G>A Single submitter 3-methylglutaconic aciduria type 3
  • c.*7018G>C Single submitter optic atrophy 3
  • c.*7181G>A Single submitter optic atrophy 3
  • c.*80G>T Single submitter optic atrophy 3
  • p.Ala170Thr Single submitter 3-methylglutaconic aciduria type 3 ⚠
  • p.Arg160Cys Single submitter 3-methylglutaconic aciduria type 3 ⚠
  • p.Gln105Ter Single submitter 3-methylglutaconic aciduria type 3
  • p.Gln162Ter Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu73fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu78Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu82Ter Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu86Asp Single submitter Inborn genetic diseases
  • p.Gly147fs Single submitter 3-methylglutaconic aciduria type 3
  • p.Gly62Ser Single submitter optic atrophy 3
  • p.Gly85Asp Single submitter optic atrophy 3 ⚠
  • p.Ile41Met Single submitter OPA3-related disorder ⚠
  • p.Leu11= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu152= Single submitter
  • p.Lys178Glu Single submitter 3-methylglutaconic aciduria type 3 ⚠
  • p.Lys69Thr Single submitter Inborn genetic diseases ⚠
  • p.Ter180Tyr Single submitter 3-methylglutaconic aciduria type 3
  • p.Trp102Arg Single submitter optic atrophy 3

Benign 34

  • c.142+69G>C Multiple submitters 3-methylglutaconic aciduria type 3
  • c.143-127C>G Multiple submitters
  • c.-86G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*1387C>T Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*152G>A Multiple submitters optic atrophy 3
  • c.*190A>G Multiple submitters
  • c.*1950G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*2485G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*272G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*3038G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*3212G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*3387G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*3531G>T Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*3722G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*3874G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*3878A>G Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*4318T>C Multiple submitters optic atrophy 3
  • c.*4672G>A Multiple submitters optic atrophy 3
  • c.*4857A>T Multiple submitters optic atrophy 3
  • c.*5523G>A Multiple submitters optic atrophy 3
  • c.*5525C>T Multiple submitters optic atrophy 3
  • c.*577T>C Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*6012A>G Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*638T>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*6790T>C Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Ala77= Multiple submitters optic atrophy 3
  • c.143-16698C>A Single submitter
  • c.143-16757T>C Single submitter
  • c.143-23_143-22del Single submitter
  • c.143-5dup Single submitter 3-methylglutaconic aciduria type 3
  • c.*3111AGC[3] Single submitter
  • c.*3972C>T Single submitter optic atrophy 3
  • c.*4850_*4852del Single submitter
  • c.*5809dup Single submitter

Benign/Likely benign 17

  • c.-38A>G Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*1340C>T Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*1760C>T Multiple submitters optic atrophy 3
  • c.*1855T>C Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*2469G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*2696C>G Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*3222C>T Multiple submitters optic atrophy 3
  • c.*362T>C Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*4794C>T Multiple submitters optic atrophy 3
  • c.*5905G>A Multiple submitters optic atrophy 3
  • c.*6275T>C Multiple submitters optic atrophy 3
  • c.*6294A>C Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*6394G>A Multiple submitters 3-methylglutaconic aciduria type 3
  • c.*7015G>A Multiple submitters optic atrophy 3
  • c.*7085A>G Multiple submitters optic atrophy 3
  • p.Ala138Thr Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Lys179= Multiple submitters 3-methylglutaconic aciduria type 3

Likely benign 127

  • c.142+10A>T Multiple submitters 3-methylglutaconic aciduria type 3
  • c.142+16A>G Multiple submitters 3-methylglutaconic aciduria type 3
  • c.142+81T>C Multiple submitters
  • c.143-14C>T Multiple submitters 3-methylglutaconic aciduria type 3
  • c.143-7C>T Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Ala135= Multiple submitters optic atrophy 3
  • p.Ala142= Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Ala143= Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Ala173= Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Ala176= Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Asn72= Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Glu112= Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Gly85= Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Gly94= Multiple submitters optic atrophy 3
  • p.Ile91= Multiple submitters 3-methylglutaconic aciduria type 3
  • p.Leu149= Multiple submitters 3-methylglutaconic aciduria type 3
  • c.142+10A>C Single submitter 3-methylglutaconic aciduria type 3
  • c.142+11C>T Single submitter 3-methylglutaconic aciduria type 3
  • c.142+12C>A Single submitter 3-methylglutaconic aciduria type 3
  • c.142+13C>A Single submitter 3-methylglutaconic aciduria type 3
  • c.142+13C>G Single submitter 3-methylglutaconic aciduria type 3
  • c.142+13C>T Single submitter optic atrophy 3
  • c.142+17T>A Single submitter 3-methylglutaconic aciduria type 3
  • c.142+18T>C Single submitter 3-methylglutaconic aciduria type 3
  • c.142+20C>T Single submitter optic atrophy 3
  • c.142+9G>A Single submitter 3-methylglutaconic aciduria type 3
  • c.142+9G>C Single submitter 3-methylglutaconic aciduria type 3
  • c.143-10T>A Single submitter 3-methylglutaconic aciduria type 3
  • c.143-12C>G Single submitter 3-methylglutaconic aciduria type 3
  • c.143-12C>T Single submitter 3-methylglutaconic aciduria type 3
  • c.143-16C>A Single submitter 3-methylglutaconic aciduria type 3
  • c.143-16C>G Single submitter 3-methylglutaconic aciduria type 3
  • c.143-16CT[2] Single submitter 3-methylglutaconic aciduria type 3
  • c.143-174C>T Single submitter
  • c.143-17C>T Single submitter 3-methylglutaconic aciduria type 3
  • c.143-18C>T Single submitter 3-methylglutaconic aciduria type 3
  • c.143-4G>T Single submitter 3-methylglutaconic aciduria type 3
  • c.143-5C>T Single submitter optic atrophy 3
  • c.143-6C>T Single submitter 3-methylglutaconic aciduria type 3
  • c.143-7C>G Single submitter
  • c.143-8C>T Single submitter optic atrophy 3
  • c.143-9C>A Single submitter 3-methylglutaconic aciduria type 3
  • c.143-9C>G Single submitter 3-methylglutaconic aciduria type 3
  • c.-7C>G Single submitter 3-methylglutaconic aciduria type 3
  • c.*24137T>G Single submitter
  • c.*2A>T Single submitter
  • c.*4696ATAA[8] Single submitter 3-methylglutaconic aciduria type 3
  • c.*4857_*4858insC Single submitter
  • c.*5365C>T Single submitter
  • c.*6104_*6105del Single submitter
  • p.Ala106= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala117= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala118= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala121= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala130= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala138= Single submitter optic atrophy 3
  • p.Ala148= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala161= Single submitter optic atrophy 3
  • p.Ala30= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala5= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ala75= Single submitter optic atrophy 3
  • p.Ala76= Single submitter 3-methylglutaconic aciduria type 3
  • p.Arg103= Single submitter
  • p.Arg109= Single submitter 3-methylglutaconic aciduria type 3
  • p.Arg123= Single submitter optic atrophy 3
  • p.Arg160= Single submitter
  • p.Arg168= Single submitter 3-methylglutaconic aciduria type 3
  • p.Arg33= Single submitter 3-methylglutaconic aciduria type 3
  • p.Arg55= Single submitter 3-methylglutaconic aciduria type 3
  • p.Asn120= Single submitter 3-methylglutaconic aciduria type 3
  • p.Cys42= Single submitter
  • p.Cys96= Single submitter 3-methylglutaconic aciduria type 3
  • p.Gln139= Single submitter 3-methylglutaconic aciduria type 3
  • p.Gln141Arg Single submitter
  • p.Gln157= Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu114= Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu151= Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu158= Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu29= Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu74= Single submitter 3-methylglutaconic aciduria type 3
  • p.Glu82= Single submitter 3-methylglutaconic aciduria type 3
  • p.Gly127= Single submitter 3-methylglutaconic aciduria type 3
  • p.Gly147= Single submitter 3-methylglutaconic aciduria type 3
  • p.Gly167= Single submitter 3-methylglutaconic aciduria type 3
  • p.Gly65= Single submitter optic atrophy 3
  • p.Gly80= Single submitter 3-methylglutaconic aciduria type 3
  • p.Gly93= Single submitter optic atrophy 3
  • p.His172= Single submitter optic atrophy 3
  • p.Ile41= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ile68= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu122= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu131= Single submitter optic atrophy 3
  • p.Leu133= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu156= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu163= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu48= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu71= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu79= Single submitter optic atrophy 3
  • p.Leu83= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu84= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu97= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu99= Single submitter optic atrophy 3
  • p.Lys10= Single submitter optic atrophy 3
  • p.Lys111= Single submitter 3-methylglutaconic aciduria type 3
  • p.Lys28= Single submitter 3-methylglutaconic aciduria type 3
  • p.Phe37= Single submitter 3-methylglutaconic aciduria type 3
  • p.Pro145= Single submitter 3-methylglutaconic aciduria type 3
  • p.Pro173= Single submitter
  • p.Pro44= Single submitter 3-methylglutaconic aciduria type 3
  • p.Pro45= Single submitter 3-methylglutaconic aciduria type 3
  • p.Pro7= Single submitter 3-methylglutaconic aciduria type 3
  • p.Pro70= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ser144= Single submitter
  • p.Ser169= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ser171= Single submitter 3-methylglutaconic aciduria type 3
  • p.Ser177= Single submitter optic atrophy 3
  • p.Ter180= Single submitter 3-methylglutaconic aciduria type 3
  • p.Thr154= Single submitter 3-methylglutaconic aciduria type 3
  • p.Thr39= Single submitter 3-methylglutaconic aciduria type 3
  • p.Thr56= Single submitter 3-methylglutaconic aciduria type 3
  • p.Thr66= Single submitter 3-methylglutaconic aciduria type 3
  • p.Tyr101= Single submitter 3-methylglutaconic aciduria type 3
  • p.Tyr40= Single submitter optic atrophy 3
  • p.Val159= Single submitter 3-methylglutaconic aciduria type 3
  • p.Val174= Single submitter 3-methylglutaconic aciduria type 3
  • p.Val67= Single submitter 3-methylglutaconic aciduria type 3
  • p.Leu129= No assertion criteria OPA3-related disorder

Uncertain significance 302

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