Sugi Variant

Sugi Variant/SLC25A4

SLC25A4 — 301 ClinVar variants

All ClinVar germline SLC25A4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 100 flagged for review →

13 Pathogenic · 2 Pathogenic/Likely pathogenic · 10 Likely pathogenic · 4 Conflicting · 32 Benign · 3 Benign/Likely benign · 77 Likely benign · 160 Uncertain significance

Full SLC25A4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 100

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 1

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

Predictors lean, ClinVar uncertain 84

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 SLC25A4 variants

Pathogenic 13

  • p.Arg80His Multiple submitters Inborn genetic diseases
  • p.Gln175fs Multiple submitters SLC25A4-related disorder
  • p.Gln37fs Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • p.Ala114Pro Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Asn88fs Single submitter
  • p.Gln85Ter Single submitter
  • p.Ser46fs Single submitter
  • c.111+1G>A No assertion criteria mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • p.Arg235Gly No assertion criteria mitochondrial DNA depletion syndrome 12A (cardiomyopathic type), autosomal dominant
  • p.Arg236Pro No assertion criteria mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • p.Gln39fs No assertion criteria mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • p.Leu98Pro No assertion criteria progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Val289Met No assertion criteria progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2

Pathogenic/Likely pathogenic 2

  • p.Ala123Asp Multiple submitters hypertrophic cardiomyopathy
  • p.Phe130fs Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive

Likely pathogenic 10

  • c.599-11_621del Single submitter mitochondrial DNA depletion syndrome 12A (cardiomyopathic type), autosomal dominant
  • p.Ala86fs Single submitter
  • p.Arg235Leu Single submitter SLC25A4-related disorder
  • p.Arg80Gly Single submitter mitochondrial DNA depletion syndrome 12A (cardiomyopathic type), autosomal dominant
  • p.Asp104Gly Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Gly101Arg Single submitter SLC25A4-related disorder
  • p.Gly16fs Single submitter mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • p.Leu141Phe Single submitter mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • p.Lys33Thr Single submitter
  • p.Val278Met Single submitter

Conflicting classifications of pathogenicity 4

  • c.740-3C>T Single submitter
  • p.Arg244= Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Arg80Cys Single submitter mitochondrial DNA depletion syndrome 12A (cardiomyopathic type), autosomal dominant ⚠
  • p.Ile294= Single submitter

Benign 32

  • c.-25G>A Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*1053T>C Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2307T>C Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2943G>A Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3114C>A Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*512A>G Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*873G>A Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Ala189= Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Val227= Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.111+119C>G Single submitter
  • c.111+123CGCC[3] Single submitter
  • c.111+123CGCC[5] Single submitter
  • c.111+330G>A Single submitter
  • c.112-267T>C Single submitter
  • c.112-65dup Single submitter
  • c.112-91dup Single submitter
  • c.740-293A>G Single submitter
  • c.-103C>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*1146T>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*1245T>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*1792C>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*1985T>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2050A>G Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2466C>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2476G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2529C>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*277C>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3070C>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3110G>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*481G>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*497T>G Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*957T>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2

Benign/Likely benign 3

  • p.Ile164Val Multiple submitters
  • p.Thr252= Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Thr84= Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive

Likely benign 77

Uncertain significance 160

  • c.-65C>T Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • c.*1163G>T Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*151T>C Multiple submitters mitochondrial DNA depletion syndrome 12A (cardiomyopathic type), autosomal dominant
  • c.*2475C>T Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • c.*2592C>T Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2616C>T Multiple submitters mitochondrial DNA depletion syndrome 12A (cardiomyopathic type), autosomal dominant
  • c.*2824G>C Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3195T>C Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • c.*3229A>G Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • c.*3276C>T Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3277G>A Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3317G>A Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • c.*824C>T Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*994G>A Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Ala25Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Ala5Gly Multiple submitters ⚠
  • p.Ala76= Multiple submitters
  • p.Arg111Leu Multiple submitters Inborn genetic diseases
  • p.Arg111Ser Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2 ⚠
  • p.Arg244Gln Multiple submitters Family history of sudden cardiac death
  • p.Asp248Asn Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Glu265Lys Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2 ⚠
  • p.Glu48Gln Multiple submitters ⚠
  • p.Gly124Glu Multiple submitters ⚠
  • p.Gly146Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Gly172Val Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive ⚠
  • p.Gly183Asp Multiple submitters Inborn genetic diseases ⚠
  • p.Gly193Arg Multiple submitters ⚠
  • p.Gly243Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Gly284Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Ile161Val Multiple submitters Inborn genetic diseases ⚠
  • p.Ile249Thr Multiple submitters
  • p.Ile261Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Lys107Asn Multiple submitters Inborn genetic diseases ⚠
  • p.Lys263Glu Multiple submitters progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2 ⚠
  • p.Pro205Arg Multiple submitters Inborn genetic diseases
  • p.Thr252Met Multiple submitters mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive ⚠
  • p.Trp6Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Val179Ile Multiple submitters ⚠
  • p.Val17Ile Multiple submitters ⚠
  • c.112-16C>G Single submitter mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive
  • c.739+3A>G Single submitter
  • c.739+5G>C Single submitter
  • c.-15C>A Single submitter
  • c.*1217A>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*1378A>G Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*1546T>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2150G>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2350G>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2363G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2499G>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2510T>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2618C>G Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2697T>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2713G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2720G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2782G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*2802C>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3025G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3264G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3335C>T Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3336G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*3394A>G Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*424A>G Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*448G>A Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*482G>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*571T>G Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*655G>C Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • c.*671A>G Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2
  • p.Ala114Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala125Val Single submitter ⚠
  • p.Ala149Thr Single submitter ⚠
  • p.Ala14Thr Single submitter ⚠
  • p.Ala150Thr Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2 ⚠
  • p.Ala20Thr Single submitter ⚠
  • p.Ala20Val Single submitter ⚠
  • p.Ala224Ser Single submitter
  • p.Ala267Val Single submitter ⚠
  • p.Ala274Gly Single submitter ⚠
  • p.Ala27Val Single submitter familial hypertrophic cardiomyopathy ⚠
  • p.Arg111His Single submitter ⚠
  • p.Arg152Cys Single submitter ⚠
  • p.Arg152Leu Single submitter ⚠
  • p.Arg235Cys Single submitter ⚠
  • p.Arg235His Single submitter ⚠
  • p.Arg236Cys Single submitter mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive ⚠
  • p.Arg236His Single submitter ⚠
  • p.Arg236Leu Single submitter ⚠
  • p.Arg237Gly Single submitter ⚠
  • p.Arg31Gly Single submitter ⚠
  • p.Asn74Lys Single submitter ⚠
  • p.Asp232Val Single submitter mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive ⚠
  • p.Asp256Asn Single submitter Inborn genetic diseases ⚠
  • p.Asp292His Single submitter mitochondrial DNA depletion syndrome 12A (cardiomyopathic type), autosomal dominant ⚠
  • p.Asp3Val Single submitter Inborn genetic diseases ⚠
  • p.Asp93Gly Single submitter ⚠
  • p.Cys160Arg Single submitter Inborn genetic diseases ⚠
  • p.Gln108_Phe109insHisLysGln Single submitter
  • p.Gln108Pro Single submitter ⚠
  • p.Gln175His Single submitter ⚠
  • p.Gln218Pro Single submitter ⚠
  • p.Gln50Lys Single submitter ⚠
  • p.Gln50Pro Single submitter mitochondrial DNA depletion syndrome 12A (cardiomyopathic type), autosomal dominant ⚠
  • p.Glu293Ala Single submitter ⚠
  • p.Glu293Lys Single submitter Inborn genetic diseases ⚠
  • p.Gly101Val Single submitter ⚠
  • p.Gly115Arg Single submitter ⚠
  • p.Gly120Arg Single submitter ⚠
  • p.Gly120Asp Single submitter ⚠
  • p.Gly16Asp Single submitter progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2 ⚠
  • p.Gly183Val Single submitter ⚠
  • p.Gly200Arg Single submitter ⚠
  • p.Gly243Asp Single submitter ⚠
  • p.Gly253Glu Single submitter ⚠
  • p.Gly281Asp Single submitter ⚠
  • p.Gly283Val Single submitter ⚠
  • p.Gly2Asp Single submitter ⚠
  • p.Gly2Ser Single submitter ⚠
  • p.Gly66Asp Single submitter ⚠
  • p.Ile210Val Single submitter ⚠
  • p.Ile294Phe Single submitter ⚠
  • p.Ile55Thr Single submitter ⚠
  • p.Leu117Met Single submitter ⚠
  • p.Leu157Met Single submitter
  • p.Leu290Val Single submitter
  • p.Leu98Val Single submitter Inborn genetic diseases ⚠
  • p.Lys163Gln Single submitter
  • p.Lys199Asn Single submitter mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive ⚠
  • p.Lys206Arg Single submitter Inborn genetic diseases ⚠
  • p.Lys206Glu Single submitter Inborn genetic diseases ⚠
  • p.Lys272Asn Single submitter ⚠
  • p.Lys63Glu Single submitter ⚠
  • p.Lys96_Gln97insTyrLys Single submitter
  • p.Met238Ile Single submitter ⚠
  • p.Met282Thr Single submitter
  • p.Phe109Leu Single submitter ⚠
  • p.Phe130Cys Single submitter ⚠
  • p.Phe165Cys Single submitter
  • p.Phe231fs Single submitter
  • p.Phe271Leu Single submitter ⚠
  • p.Phe89Leu Single submitter mitochondrial DNA depletion syndrome 12B (cardiomyopathic type), autosomal recessive ⚠
  • p.Phe91Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro203Ser Single submitter
  • p.Pro205Ser Single submitter ⚠
  • p.Pro28Ala Single submitter ⚠
  • p.Ser22Tyr Single submitter Inborn genetic diseases ⚠
  • p.Ser69Thr Single submitter ⚠
  • p.Thr197Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr221Arg Single submitter Inborn genetic diseases ⚠
  • p.Trp110Arg Single submitter ⚠
  • p.Trp110Cys Single submitter ⚠
  • p.Trp275Leu Single submitter ⚠
  • p.Tyr191Asp Single submitter ⚠
  • p.Tyr191Cys Single submitter ⚠
  • p.Tyr297fs Single submitter
  • p.Val181Ala Single submitter ⚠
  • p.Val208Met Single submitter
  • p.Val212Met Single submitter ⚠
  • p.Val227Leu Single submitter ⚠
  • p.Val298Ala Single submitter