LIPT2 — 145 ClinVar variants

All ClinVar germline LIPT2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 91 flagged for review →

1 Pathogenic/Likely pathogenic · 1 Likely pathogenic · 4 Conflicting · 10 Benign · 2 Benign/Likely benign · 30 Likely benign · 97 Uncertain significance

Full LIPT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 91

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 4

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

LIPT2 p.Asn231Ser Conflicting Single submitter
LIPT2 p.Gly109Ala Conflicting Single submitter
LIPT2 p.Leu126Arg Conflicting Single submitter
encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities
LIPT2 p.Leu30Pro Conflicting Single submitter
encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities

Predictors lean, ClinVar uncertain 66

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

Predictors split 21

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

All LIPT2 variants

Pathogenic/Likely pathogenic 1

p.Leu105Arg Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities

Likely pathogenic 1

p.Met1Leu Single submitter encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities

Conflicting classifications of pathogenicity 4

p.Asn231Ser Single submitter ⚠
p.Gly109Ala Single submitter ⚠
p.Leu126Arg Single submitter encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities ⚠
p.Leu30Pro Single submitter encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities ⚠

Benign 10

c.466+14A>C Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities
c.466+230T>G Multiple submitters
c.466+85C>T Multiple submitters
c.*176C>T Multiple submitters
p.Ala53Val Multiple submitters
p.Glu207Val Multiple submitters
p.Leu8= Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities
p.Thr190Ser Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities
p.Thr90= Multiple submitters
c.467-186_467-185insT Single submitter

Benign/Likely benign 2

p.Phe91= Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities
p.Pro230= Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities

Likely benign 30

p.Ala5= Multiple submitters
p.Arg107= Multiple submitters
p.Leu20= Multiple submitters
p.Pro139Ser Multiple submitters ⚠
c.466+17A>G Single submitter
c.466+9C>A Single submitter
c.467-16T>C Single submitter
c.467-16T>G Single submitter
c.467-18C>A Single submitter
p.Ala17= Single submitter
p.Ala215= Single submitter
p.Ala71= Single submitter
p.Arg29= Single submitter
p.Asp24= Single submitter
p.Gln3= Single submitter
p.Gly21= Single submitter
p.Leu110= Single submitter
p.Leu187= Single submitter
p.Leu22= Single submitter
p.Leu27= Single submitter
p.Lys197= Single submitter
p.Pro39Ser Single submitter
p.Pro4= Single submitter
p.Pro94= Single submitter
p.Ser118= Single submitter
p.Ser40= Single submitter
p.Thr190= Single submitter
p.Val145= Single submitter
p.Val192= Single submitter
p.Pro139= No assertion criteria LIPT2-related disorder

Uncertain significance 97

c.467del Multiple submitters
p.Ala121Val Multiple submitters ⚠
p.Ala75Thr Multiple submitters ⚠
p.Arg158Cys Multiple submitters ⚠
p.Arg2Gln Multiple submitters ⚠
p.Asp134Ala Multiple submitters ⚠
p.Gln133Glu Multiple submitters ⚠
p.Glu207Lys Multiple submitters ⚠
p.Gly109Asp Multiple submitters early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome ⚠
p.Gly95Asp Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities ⚠
p.Ile36Thr Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities ⚠
p.Leu30Val Multiple submitters ⚠
p.Pro15Leu Multiple submitters ⚠
p.Thr177Met Multiple submitters ⚠
p.Val14Glu Multiple submitters
p.Val56Ala Multiple submitters encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities ⚠
p.6VRL[3] Single submitter
p.Ala135Val Single submitter ⚠
p.Ala32Gly Single submitter ⚠
p.Ala32Thr Single submitter ⚠
p.Ala46Thr Single submitter ⚠
p.Arg10Leu Single submitter ⚠
p.Arg10Pro Single submitter ⚠
p.Arg111Cys Single submitter ⚠
p.Arg125Cys Single submitter ⚠
p.Arg125Leu Single submitter ⚠
p.Arg136Gly Single submitter ⚠
p.Arg158Gly Single submitter ⚠
p.Arg25His Single submitter ⚠
p.Arg25Ser Single submitter ⚠
p.Arg28Gln Single submitter ⚠
p.Arg74Leu Single submitter ⚠
p.Arg81Cys Single submitter ⚠
p.Arg85_Gly87del Single submitter
p.Arg85Cys Single submitter ⚠
p.Asn231Thr Single submitter ⚠
p.Asp104His Single submitter
p.Asp148Glu Single submitter ⚠
p.Asp149Asn Single submitter ⚠
p.Asp149His Single submitter ⚠
p.Asp175Asn Single submitter ⚠
p.Asp24_Gln31del Single submitter
p.Asp24Asn Single submitter ⚠
p.Cys153Gly Single submitter ⚠
p.Cys172Ser Single submitter ⚠
p.Cys50Ser Single submitter ⚠
p.Gln130His Single submitter ⚠
p.Gln31_Ala32insArgLeuGln Single submitter
p.Gln31Arg Single submitter ⚠
p.Gln31His Single submitter ⚠
p.Gln96His Single submitter encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities ⚠
p.Glu18Gln Single submitter ⚠
p.Glu18Lys Single submitter ⚠
p.Glu33Lys Single submitter ⚠
p.Glu68Lys Single submitter ⚠
p.Glu69Ala Single submitter
p.Gly131Asp Single submitter ⚠
p.Gly156Arg Single submitter ⚠
p.Gly35Asp Single submitter ⚠
p.Gly54= Single submitter encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities
p.Gly54Glu Single submitter ⚠
p.Gly84Ala Single submitter ⚠
p.Gly93Ser Single submitter ⚠
p.His166Arg Single submitter ⚠
p.Ile155Val Single submitter ⚠
p.Ile182Met Single submitter ⚠
p.Leu103Arg Single submitter ⚠
p.Leu105Val Single submitter ⚠
p.Leu126fs Single submitter
p.Leu176Phe Single submitter ⚠
p.Leu88Arg Single submitter ⚠
p.Leu88Met Single submitter ⚠
p.Leu8Val Single submitter ⚠
p.Lys197Gln Single submitter ⚠
p.Met1Arg Single submitter
p.Pro101Leu Single submitter ⚠
p.Pro101Ser Single submitter ⚠
p.Pro140Ser Single submitter ⚠
p.Pro15Ser Single submitter ⚠
p.Pro34Thr Single submitter ⚠
p.Pro4Leu Single submitter ⚠
p.Pro67Arg Single submitter ⚠
p.Pro94Leu Single submitter ⚠
p.Pro94Ser Single submitter ⚠
p.Ser196Thr Single submitter ⚠
p.Ser229Asn Single submitter ⚠
p.Thr164Ile Single submitter ⚠
p.Thr223Ile Single submitter ⚠
p.Thr58Ala Single submitter ⚠
p.Val116Ile Single submitter ⚠
p.Val116Leu Single submitter ⚠
p.Val203Ile Single submitter ⚠
p.Val205Met Single submitter ⚠
p.Val56Met Single submitter ⚠
p.Val6Ile Single submitter ⚠
p.Val6Leu Single submitter ⚠
p.Val82Ile Single submitter ⚠