TSFM — 532 ClinVar variants

All ClinVar germline TSFM variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 151 flagged for review →

21 Pathogenic · 22 Pathogenic/Likely pathogenic · 36 Likely pathogenic · 21 Conflicting · 16 Benign · 6 Benign/Likely benign · 236 Likely benign · 174 Uncertain significance

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

⚑ Evidence disagreements 151

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 3

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

Predictors lean, ClinVar uncertain 121

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

Predictors split 27

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

All TSFM variants

Pathogenic 21

Pathogenic/Likely pathogenic 22

  • c.571+1G>C Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Ala13fs Multiple submitters
  • p.Arg201fs Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Arg201Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Arg312Trp Multiple submitters TSFM-related disorder
  • p.Asp184fs Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gln135Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gln26Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gln286Ter Multiple submitters TSFM-related disorder
  • p.Gln29Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gln303fs Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gln87Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Leu137fs Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Leu186Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Lys133fs Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Lys200Ter Multiple submitters
  • p.Lys84Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Phe10fs Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Ser181Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Ser2Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Ser6Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Tyr216Ter Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3

Likely pathogenic 36

  • c.231+1G>A Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.232-2A>G Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.484-1G>A Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.484-1G>T Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.57+1G>A Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Cys315Tyr Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Leu266fs Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Met1fs Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.231+1G>C Single submitter
  • c.355G>C Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3 ⚠
  • c.360+1G>A Single submitter TSFM-related disorder
  • c.360+1G>C Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.483+1G>A Single submitter
  • c.483+1G>C Single submitter
  • c.484-1003_484-1000dup Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.57+1G>T Single submitter
  • c.57+2T>A Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.58-2A>T Single submitter
  • p.Ala187fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Arg25fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Arg312fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Arg39fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Cys64Ter Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gln139fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gln258His Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gln286Arg Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Glu278fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gly210fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Leu143_Gly144delinsTer Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Leu75fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Lys47Ter Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Met1Arg Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Ser270fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Trp204Ter Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Tyr59_Asn63delinsTer Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Val128fs Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3

Conflicting classifications of pathogenicity 21

  • c.231+1GT[6] Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.361-12T>G Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.361-14A>G Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.484-11C>T Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.58-2A>G Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.*210G>A Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Arg254Cys Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3 ⚠
  • p.Arg8= Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Asp272= Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Cys240Ser Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3 ⚠
  • p.Gly16= Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Gly162Ser Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3 ⚠
  • p.Gly180Ala Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3 ⚠
  • p.Leu266His Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3 ⚠
  • p.Met1Thr Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Met1Val Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Pro156Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser215Phe Single submitter Inborn genetic diseases ⚠
  • p.Ter326= Single submitter
  • p.Val230Leu Single submitter Inborn genetic diseases ⚠
  • c.57+4A>G No assertion criteria fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3

Benign 16

  • c.231+226G>A Multiple submitters
  • c.231+25C>T Multiple submitters
  • c.484-996T>C Multiple submitters
  • c.484-999A>T Multiple submitters
  • c.*114G>A Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.*33G>A Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.*997G>C Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Phe10= Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Ser2Leu Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.484-174A>G Single submitter
  • c.484-175C>T Single submitter
  • c.484-236G>A Single submitter
  • c.484-947A>G Single submitter
  • c.484-963T>C Single submitter
  • c.572-11del Single submitter
  • c.*958C>G Single submitter fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3

Benign/Likely benign 6

  • c.232-19T>G Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • c.484-977A>G Multiple submitters
  • p.Arg39= Multiple submitters
  • p.Leu266Ile Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Trp91Gly Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3
  • p.Val252Ile Multiple submitters fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3

Likely benign 236

Uncertain significance 174