LIAS — 437 ClinVar variants

All ClinVar germline LIAS variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 166 flagged for review →

19 Pathogenic · 2 Pathogenic/Likely pathogenic · 11 Likely pathogenic · 13 Conflicting · 39 Benign · 7 Benign/Likely benign · 164 Likely benign · 182 Uncertain significance

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

⚑ Evidence disagreements 166

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 6

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

Predictors lean, ClinVar uncertain 139

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 LIAS variants

Pathogenic 19

  • p.Asn89fs Multiple submitters lipoic acid synthetase deficiency
  • p.Glu37fs Multiple submitters lipoic acid synthetase deficiency
  • p.Lys92_Leu93insTer Multiple submitters lipoic acid synthetase deficiency
  • p.Thr148fs Multiple submitters lipoic acid synthetase deficiency
  • p.Ala222Ter Single submitter lipoic acid synthetase deficiency
  • p.Arg110Ter Single submitter lipoic acid synthetase deficiency
  • p.Arg73fs Single submitter
  • p.Asp44fs Single submitter lipoic acid synthetase deficiency
  • p.Cys22fs Single submitter lipoic acid synthetase deficiency
  • p.Glu122fs Single submitter lipoic acid synthetase deficiency
  • p.Glu37Ter Single submitter lipoic acid synthetase deficiency
  • p.Gly71fs Single submitter lipoic acid synthetase deficiency
  • p.Leu132fs Single submitter lipoic acid synthetase deficiency
  • p.Leu231Ter Single submitter Inborn genetic diseases
  • p.Lys94Ter Single submitter lipoic acid synthetase deficiency
  • p.Tyr161fs Single submitter lipoic acid synthetase deficiency
  • p.Tyr174fs Single submitter lipoic acid synthetase deficiency
  • p.Val334fs Single submitter lipoic acid synthetase deficiency
  • p.Glu159Lys No assertion criteria lipoic acid synthetase deficiency

Pathogenic/Likely pathogenic 2

  • p.Arg217Ter Multiple submitters lipoic acid synthetase deficiency
  • p.Lys34Ter Multiple submitters LIAS-related disorders

Likely pathogenic 11

  • c.218+1G>A Multiple submitters lipoic acid synthetase deficiency
  • c.954+1G>A Multiple submitters lipoic acid synthetase deficiency
  • c.313-38_367del Single submitter lipoic acid synthetase deficiency
  • c.737+1G>A Single submitter lipoic acid synthetase deficiency
  • c.884-1G>A Single submitter lipoic acid synthetase deficiency
  • p.Ala253Pro Single submitter
  • p.Asp215fs Single submitter lipoic acid synthetase deficiency
  • p.Thr196Asn Single submitter lipoic acid synthetase deficiency
  • p.Trp79Ter Single submitter lipoic acid synthetase deficiency
  • p.Ala355Pro No assertion criteria lipoic acid synthetase deficiency
  • p.Glu239fs No assertion criteria

Conflicting classifications of pathogenicity 13

Benign 39

Benign/Likely benign 7

  • c.393+10G>A Multiple submitters lipoic acid synthetase deficiency
  • c.393+8C>A Multiple submitters lipoic acid synthetase deficiency
  • c.*14C>A Multiple submitters
  • p.Arg19Ser Multiple submitters lipoic acid synthetase deficiency
  • p.Asn99= Multiple submitters lipoic acid synthetase deficiency
  • p.Pro242= Multiple submitters lipoic acid synthetase deficiency
  • p.Pro43= Multiple submitters lipoic acid synthetase deficiency

Likely benign 164

  • c.1066+17G>A Multiple submitters lipoic acid synthetase deficiency
  • c.1066+20A>G Multiple submitters lipoic acid synthetase deficiency
  • c.313-152C>A Multiple submitters
  • c.45+161C>T Multiple submitters
  • c.884-18G>A Multiple submitters lipoic acid synthetase deficiency
  • c.954+35_954+37del Multiple submitters
  • p.Gln269= Multiple submitters lipoic acid synthetase deficiency
  • p.Gly6= Multiple submitters lipoic acid synthetase deficiency
  • p.Leu38= Multiple submitters lipoic acid synthetase deficiency
  • p.Thr129= Multiple submitters lipoic acid synthetase deficiency
  • p.Thr343= Multiple submitters lipoic acid synthetase deficiency
  • p.Tyr20= Multiple submitters lipoic acid synthetase deficiency
  • c.1066+12T>C Single submitter lipoic acid synthetase deficiency
  • c.1066+16G>A Single submitter lipoic acid synthetase deficiency
  • c.1066+18G>T Single submitter lipoic acid synthetase deficiency
  • c.1066+19C>T Single submitter lipoic acid synthetase deficiency
  • c.1066+65C>T Single submitter
  • c.1067-11T>C Single submitter lipoic acid synthetase deficiency
  • c.1067-15C>G Single submitter lipoic acid synthetase deficiency
  • c.1067-258T>A Single submitter
  • c.218+14T>A Single submitter lipoic acid synthetase deficiency
  • c.218+15G>A Single submitter lipoic acid synthetase deficiency
  • c.218+19T>C Single submitter lipoic acid synthetase deficiency
  • c.218+29G>A Single submitter
  • c.218+43T>C Single submitter
  • c.218+7_218+13dup Single submitter lipoic acid synthetase deficiency
  • c.219-11G>A Single submitter lipoic acid synthetase deficiency
  • c.219-6C>T Single submitter lipoic acid synthetase deficiency
  • c.312+15T>A Single submitter lipoic acid synthetase deficiency
  • c.312+168A>C Single submitter
  • c.312+17T>G Single submitter lipoic acid synthetase deficiency
  • c.312+8G>T Single submitter lipoic acid synthetase deficiency
  • c.313-12T>G Single submitter lipoic acid synthetase deficiency
  • c.313-14C>T Single submitter lipoic acid synthetase deficiency
  • c.313-19C>T Single submitter lipoic acid synthetase deficiency
  • c.313-6A>G Single submitter lipoic acid synthetase deficiency
  • c.313-7C>T Single submitter lipoic acid synthetase deficiency
  • c.393+147del Single submitter
  • c.393+17C>T Single submitter lipoic acid synthetase deficiency
  • c.393+20C>G Single submitter lipoic acid synthetase deficiency
  • c.393+7C>A Single submitter lipoic acid synthetase deficiency
  • c.393+7C>T Single submitter lipoic acid synthetase deficiency
  • c.45+10G>A Single submitter lipoic acid synthetase deficiency
  • c.45+12G>A Single submitter lipoic acid synthetase deficiency
  • c.45+18C>T Single submitter lipoic acid synthetase deficiency
  • c.45+19G>T Single submitter lipoic acid synthetase deficiency
  • c.45+20G>T Single submitter lipoic acid synthetase deficiency
  • c.45+7G>A Single submitter lipoic acid synthetase deficiency
  • c.46-13A>T Single submitter lipoic acid synthetase deficiency
  • c.46-16T>C Single submitter lipoic acid synthetase deficiency
  • c.46-17A>G Single submitter lipoic acid synthetase deficiency
  • c.46-20A>G Single submitter lipoic acid synthetase deficiency
  • c.46-239_46-238dup Single submitter
  • c.46-7T>C Single submitter lipoic acid synthetase deficiency
  • c.550+11C>T Single submitter lipoic acid synthetase deficiency
  • c.550+12A>G Single submitter lipoic acid synthetase deficiency
  • c.550+16T>C Single submitter lipoic acid synthetase deficiency
  • c.550+20C>T Single submitter lipoic acid synthetase deficiency
  • c.550+9G>A Single submitter lipoic acid synthetase deficiency
  • c.551-16A>T Single submitter lipoic acid synthetase deficiency
  • c.551-19T>C Single submitter lipoic acid synthetase deficiency
  • c.608+13G>A Single submitter lipoic acid synthetase deficiency
  • c.608+7A>C Single submitter lipoic acid synthetase deficiency
  • c.609-13C>T Single submitter lipoic acid synthetase deficiency
  • c.609-19T>C Single submitter lipoic acid synthetase deficiency
  • c.609-6C>T Single submitter lipoic acid synthetase deficiency
  • c.737+10T>G Single submitter lipoic acid synthetase deficiency
  • c.737+11G>A Single submitter lipoic acid synthetase deficiency
  • c.737+15A>C Single submitter lipoic acid synthetase deficiency
  • c.737+20A>T Single submitter lipoic acid synthetase deficiency
  • c.737+6dup Single submitter lipoic acid synthetase deficiency
  • c.737+8C>T Single submitter lipoic acid synthetase deficiency
  • c.737+9G>A Single submitter lipoic acid synthetase deficiency
  • c.738-14C>T Single submitter lipoic acid synthetase deficiency
  • c.738-20A>G Single submitter lipoic acid synthetase deficiency
  • c.738-243A>G Single submitter
  • c.738-304_738-301del Single submitter
  • c.738-4C>T Single submitter
  • c.738-9G>A Single submitter lipoic acid synthetase deficiency
  • c.883+10T>C Single submitter lipoic acid synthetase deficiency
  • c.883+15_883+56del Single submitter lipoic acid synthetase deficiency
  • c.883+15A>T Single submitter lipoic acid synthetase deficiency
  • c.883+17A>G Single submitter lipoic acid synthetase deficiency
  • c.883+278A>G Single submitter
  • c.884-4A>G Single submitter lipoic acid synthetase deficiency
  • c.954+11C>A Single submitter lipoic acid synthetase deficiency
  • c.954+123G>A Single submitter
  • c.954+18dup Single submitter lipoic acid synthetase deficiency
  • c.954+20C>G Single submitter lipoic acid synthetase deficiency
  • c.954+20C>T Single submitter lipoic acid synthetase deficiency
  • c.954+238dup Single submitter
  • c.954+32T>A Single submitter
  • c.954+36_954+37dup Single submitter
  • c.954+8T>C Single submitter lipoic acid synthetase deficiency
  • c.954+9A>G Single submitter lipoic acid synthetase deficiency
  • c.955-11T>C Single submitter lipoic acid synthetase deficiency
  • c.955-13T>G Single submitter lipoic acid synthetase deficiency
  • c.955-4C>G Single submitter lipoic acid synthetase deficiency
  • c.955-65A>G Single submitter
  • c.955-7A>T Single submitter lipoic acid synthetase deficiency
  • c.-12C>T Single submitter
  • c.-29C>T Single submitter
  • c.-45T>C Single submitter
  • p.Ala126= Single submitter lipoic acid synthetase deficiency
  • p.Ala227= Single submitter lipoic acid synthetase deficiency
  • p.Ala235= Single submitter lipoic acid synthetase deficiency
  • p.Ala355= Single submitter lipoic acid synthetase deficiency
  • p.Ala8= Single submitter lipoic acid synthetase deficiency
  • p.Ala9= Single submitter lipoic acid synthetase deficiency
  • p.Arg110= Single submitter lipoic acid synthetase deficiency
  • p.Arg56= Single submitter lipoic acid synthetase deficiency
  • p.Arg98= Single submitter lipoic acid synthetase deficiency
  • p.Asp135= Single submitter lipoic acid synthetase deficiency
  • p.Asp300= Single submitter lipoic acid synthetase deficiency
  • p.Asp371= Single submitter lipoic acid synthetase deficiency
  • p.Asp47= Single submitter lipoic acid synthetase deficiency
  • p.Asp7= Single submitter lipoic acid synthetase deficiency
  • p.Gln308= Single submitter lipoic acid synthetase deficiency
  • p.Gln40= Single submitter lipoic acid synthetase deficiency
  • p.Gln46= Single submitter lipoic acid synthetase deficiency
  • p.Glu321= Single submitter lipoic acid synthetase deficiency
  • p.Gly140= Single submitter lipoic acid synthetase deficiency
  • p.Gly18= Single submitter lipoic acid synthetase deficiency
  • p.Gly283= Single submitter lipoic acid synthetase deficiency
  • p.Gly356= Single submitter lipoic acid synthetase deficiency
  • p.His341= Single submitter lipoic acid synthetase deficiency
  • p.Ile114= Single submitter lipoic acid synthetase deficiency
  • p.Ile278= Single submitter lipoic acid synthetase deficiency
  • p.Leu155= Single submitter lipoic acid synthetase deficiency
  • p.Leu177= Single submitter lipoic acid synthetase deficiency
  • p.Leu200= Single submitter lipoic acid synthetase deficiency
  • p.Leu280= Single submitter lipoic acid synthetase deficiency
  • p.Leu306= Single submitter lipoic acid synthetase deficiency
  • p.Leu31= Single submitter lipoic acid synthetase deficiency
  • p.Leu338= Single submitter lipoic acid synthetase deficiency
  • p.Leu372= Single submitter lipoic acid synthetase deficiency
  • p.Leu66= Single submitter lipoic acid synthetase deficiency
  • p.Leu97= Single submitter lipoic acid synthetase deficiency
  • p.Lys263= Single submitter lipoic acid synthetase deficiency
  • p.Lys267= Single submitter lipoic acid synthetase deficiency
  • p.Lys333= Single submitter lipoic acid synthetase deficiency
  • p.Lys35= Single submitter lipoic acid synthetase deficiency
  • p.Lys366= Single submitter lipoic acid synthetase deficiency
  • p.Phe48= Single submitter lipoic acid synthetase deficiency
  • p.Pro154= Single submitter lipoic acid synthetase deficiency
  • p.Pro205= Single submitter lipoic acid synthetase deficiency
  • p.Pro27= Single submitter lipoic acid synthetase deficiency
  • p.Pro325= Single submitter lipoic acid synthetase deficiency
  • p.Pro347= Single submitter lipoic acid synthetase deficiency
  • p.Pro77= Single submitter lipoic acid synthetase deficiency
  • p.Pro78= Single submitter lipoic acid synthetase deficiency
  • p.Ser23= Single submitter lipoic acid synthetase deficiency
  • p.Ter373= Single submitter lipoic acid synthetase deficiency
  • p.Thr136= Single submitter
  • p.Thr196= Single submitter lipoic acid synthetase deficiency
  • p.Tyr199= Single submitter lipoic acid synthetase deficiency
  • p.Tyr330= Single submitter lipoic acid synthetase deficiency
  • p.Tyr62= Single submitter lipoic acid synthetase deficiency
  • p.Val105= Single submitter lipoic acid synthetase deficiency
  • p.Val238= Single submitter lipoic acid synthetase deficiency
  • p.Val241= Single submitter lipoic acid synthetase deficiency
  • p.Val289= Single submitter lipoic acid synthetase deficiency
  • p.Val49= Single submitter lipoic acid synthetase deficiency
  • c.608+9T>G No assertion criteria LIAS-related disorder

Uncertain significance 182