OXCT1 — 249 ClinVar variants

All ClinVar germline OXCT1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 77 flagged for review →

9 Pathogenic · 2 Pathogenic/Likely pathogenic · 11 Likely pathogenic · 7 Conflicting · 34 Benign · 9 Benign/Likely benign · 67 Likely benign · 110 Uncertain significance

Full OXCT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 77

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 3

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

Predictors agree, ClinVar conflicts 1

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

Predictors lean, ClinVar uncertain 58

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

Predictors split 15

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

All OXCT1 variants

Pathogenic 9

  • c.1419+1G>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.733-2A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Arg217Ter Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Arg268His Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Gly324Glu Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Cys456Phe No assertion criteria succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly219Glu No assertion criteria succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ser283Ter No assertion criteria succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Thr457Ile No assertion criteria succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠

Pathogenic/Likely pathogenic 2

  • p.Ala292fs Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Arg468Cys Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠

Likely pathogenic 11

  • c.1099+2T>C Multiple submitters OXCT1-related disorder
  • c.278+1G>A Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Arg124Ter Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1248+5G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1339-2A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly151fs Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly65Arg Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Leu429fs Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Leu486fs Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala142Pro No assertion criteria succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Arg355Ter No assertion criteria OXCT1-related disorder

Conflicting classifications of pathogenicity 7

  • c.1339-12T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.565-13C>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.956-15A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Arg217Leu Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Asp360= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Asp497= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Thr159= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency

Benign 34

  • c.1420-33T>C Multiple submitters
  • c.1420-91C>T Multiple submitters
  • c.414+7A>C Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.671+31A>G Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.78+10dup Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.79-11del Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.955+94C>G Multiple submitters
  • c.956-150G>A Multiple submitters
  • c.-192G>A Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.-215A>G Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly160= Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Thr58Met Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • c.1050+212G>C Single submitter
  • c.1099+17C>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1100-18GT[8] Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1100-19del Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1248+273G>A Single submitter
  • c.1338+211A>T Single submitter
  • c.1420-230dup Single submitter
  • c.1521+263G>C Single submitter
  • c.1522-14del Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1522-14dup Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.414+18del Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.414+192A>G Single submitter
  • c.732+135del Single submitter
  • c.733-330A>G Single submitter
  • c.79-22_79-21dup Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.841-278G>T Single submitter
  • c.955+128dup Single submitter
  • c.955+143del Single submitter
  • c.-60C>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1434G>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1444G>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*935A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency

Benign/Likely benign 9

  • c.1173-139G>T Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.279-7C>T Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.733-3T>C Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.79-22dup Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Arg38Cys Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Asn220= Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Asp395Asn Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Leu232= Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Thr502= Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency

Likely benign 67

  • c.564+4A>G Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.564+8A>G Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala2= Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala433= Multiple submitters Inborn genetic diseases
  • p.Leu486= Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Lys79= Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1051-16A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1173-20T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1249-15T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1249-18T>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1521+18C>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1522-20T>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.1522-4C>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.188-14T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.188-14T>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.414+14C>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.415-15G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.564+14T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.564+19C>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.672-7C>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.732+15T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.733-12C>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.733-13del Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.78+12G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.78+17G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.79-11T>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.79-20T>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.841-19A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.841-4A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.955+18G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1345A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*157G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala150= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala215= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala49= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala87= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Asn520= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Asp300= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Cys14= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gln464= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gln499= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Glu239= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Glu291= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly100= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly129= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly148= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly162= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Gly492Asp Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Gly503= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.His450= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ile364= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ile53= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Leu13= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Leu363= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Leu458= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Leu493= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Leu66= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ser170= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ser33= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ser378= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ser382= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ser432= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Tyr275= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Val249= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Val394= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.415-1537del No assertion criteria OXCT1-related disorder
  • c.*1A>G No assertion criteria OXCT1-related disorder

Uncertain significance 110

  • c.671+3A>G Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.-5C>G Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala401Val Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ala519Thr Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Arg110His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg285Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Gly288Ala Multiple submitters Inborn genetic diseases ⚠
  • p.Leu6Phe Multiple submitters Inborn genetic diseases ⚠
  • p.Thr457Arg Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Val245Phe Multiple submitters succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Val394Ile Multiple submitters Inborn genetic diseases ⚠
  • c.564+44C>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.671+6G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.672-3T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.732+6A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.79-12T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.955+4T>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.-103G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.-133G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.-137G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.-305G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.-54G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1011T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1023G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1041G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1072A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1229C>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1266A>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*138C>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1473G>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*1616A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*188A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*191A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*26G>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*362C>A Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*567C>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*583G>T Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*94A>G Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*956T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • c.*965T>C Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ala183Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala215Val Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ala22Ser Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ala319Thr Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ala36Val Single submitter Inborn genetic diseases ⚠
  • p.Ala433Val Single submitter Inborn genetic diseases ⚠
  • p.Ala507Val Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ala87Val Single submitter Inborn genetic diseases ⚠
  • p.Arg104Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg146His Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Arg18Leu Single submitter Inborn genetic diseases ⚠
  • p.Arg281His Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Arg285Trp Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Arg468His Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Arg468Leu Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Asn175Asp Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Asp289His Single submitter Inborn genetic diseases ⚠
  • p.Asp299Gly Single submitter Inborn genetic diseases ⚠
  • p.Asp95His Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Cys14Arg Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Cys30Phe Single submitter Inborn genetic diseases ⚠
  • p.Cys67Arg Single submitter ⚠
  • p.Gln499Glu Single submitter Inborn genetic diseases ⚠
  • p.Gln499His Single submitter Inborn genetic diseases ⚠
  • p.Glu134Asp Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Glu191Gln Single submitter Inborn genetic diseases ⚠
  • p.Glu191Lys Single submitter Inborn genetic diseases ⚠
  • p.Gly139Ser Single submitter ⚠
  • p.Gly19Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly349Cys Single submitter Inborn genetic diseases ⚠
  • p.Gly447Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly81Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly84Glu Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.His357Arg Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ile172Met Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ile270Lys Single submitter ⚠
  • p.Ile325Val Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Ile487fs Single submitter
  • p.Leu311Phe Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Lys109Thr Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Lys173Arg Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Lys225Arg Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Lys271Arg Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Met111Thr Single submitter Inborn genetic diseases ⚠
  • p.Met234Ile Single submitter Inborn genetic diseases ⚠
  • p.Met398Val Single submitter Inborn genetic diseases ⚠
  • p.Met419Ile Single submitter Inborn genetic diseases ⚠
  • p.Met441Val Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Met515Val Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Pro352Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro514Leu Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ser170Pro Single submitter Inborn genetic diseases ⚠
  • p.Ser226Ile Single submitter ⚠
  • p.Ser334Arg Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Ser334Gly Single submitter ⚠
  • p.Thr140Pro Single submitter Inborn genetic diseases ⚠
  • p.Thr23Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr240Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr471= Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Thr485Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr80Pro Single submitter Inborn genetic diseases
  • p.Tyr275Cys Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Val112Phe Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency
  • p.Val221Met Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Val301Ile Single submitter Inborn genetic diseases ⚠
  • p.Val475Ala Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Val498Ile Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Val50Ile Single submitter succinyl-CoA:3-ketoacid CoA transferase deficiency ⚠
  • p.Arg12Gln No assertion criteria ⚠
  • p.Met398Thr No assertion criteria ⚠