Sugi Variant

Sugi Variant/NADK2

NADK2 — 240 ClinVar variants

All ClinVar germline NADK2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 91 flagged for review →

1 Pathogenic · 1 Likely pathogenic · 5 Conflicting · 22 Benign · 1 Benign/Likely benign · 106 Likely benign · 104 Uncertain significance

Full NADK2 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 2

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

Predictors lean, ClinVar uncertain 68

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 NADK2 variants

Pathogenic 1

  • c.956+6T>C No assertion criteria progressive encephalopathy with leukodystrophy due to DECR deficiency

Likely pathogenic 1

  • p.Arg340Ter Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency

Conflicting classifications of pathogenicity 5

  • c.1013-13_1013-9del Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.389+6T>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg114Ter Single submitter NADK2-related disorders
  • p.Ile117Val Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Met409Val Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠

Benign 22

  • c.1066+167C>G Multiple submitters
  • c.1191-64T>C Multiple submitters
  • c.479-105C>T Multiple submitters
  • c.645-11A>T Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.861-57C>A Multiple submitters
  • c.957-48G>C Multiple submitters
  • c.957-73G>A Multiple submitters
  • c.-312A>G Multiple submitters
  • p.Arg211His Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg86= Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Glu146Asp Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Lys120Arg Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Pro368= Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1013-29_1013-28dup Single submitter
  • c.1067-169dup Single submitter
  • c.561-18dup Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.781+85_781+86insATGATTA Single submitter
  • c.782-193G>A Single submitter
  • c.860+8del Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.861-194dup Single submitter
  • c.957-9del Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ala16Val Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency

Benign/Likely benign 1

  • c.1013-17C>T Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency

Likely benign 106

  • c.1066+95T>C Multiple submitters
  • c.1067-56C>T Multiple submitters
  • c.301-81C>T Multiple submitters
  • c.479-92G>C Multiple submitters
  • c.560+9G>T Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.644+15C>T Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.644+16G>A Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.861-1267C>G Multiple submitters
  • c.957-101T>C Multiple submitters
  • c.957-19A>C Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ala205= Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ala274= Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg384= Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Pro177= Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1012+19A>G Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1012+9C>T Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1013-105T>A Single submitter
  • c.1013-17C>G Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1013-7T>A Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1066+11A>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1066+12A>G Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1067-11_1067-9del Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1067-134C>T Single submitter
  • c.1067-20_1067-19insTA Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1067-26G>C Single submitter
  • c.1067-4G>T Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1190+12C>G Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.1191-64T>G Single submitter
  • c.1191-6G>T Single submitter
  • c.301-17C>T Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.301-37A>G Single submitter
  • c.389+18G>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.389+9A>G Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.390-10T>A Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.390-16del Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.478+18G>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.479-11A>G Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.479-11A>T Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.479-16G>A Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.560+13G>A Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.561-15C>T Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.561-16T>A Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.644+14dup Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.644+15C>A Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.644+18T>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.645-12_645-11delinsGT Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.645-18T>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.781+13_781+14dup Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.781+16A>T Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.782-6A>G Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.782-7C>T Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.860+18A>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.860+96A>C Single submitter
  • c.861-150T>C Single submitter
  • c.861-19T>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.861-33del Single submitter
  • c.956+20G>T Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.957-14A>G Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.957-4C>T Single submitter
  • c.-296T>C Single submitter
  • c.-303G>A Single submitter
  • p.Ala22= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ala288= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ala338= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ala407= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg130= Single submitter Inborn genetic diseases
  • p.Arg141= Single submitter
  • p.Arg150= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg174= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg187= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg392= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg53= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg61His Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg67= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Asn322= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Asn324= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Asn383= Single submitter
  • p.Asp297= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Asp406= Single submitter
  • p.Asp412= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Cys3= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Glu113= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Gly180= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Gly307= Single submitter
  • p.Gly50= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.His118= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.His239= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ile293= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Leu194= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Leu308= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Leu348= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Leu352= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Leu364= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Leu365= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Leu435= Single submitter
  • p.Lys140= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Lys170= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Lys317= Single submitter
  • p.Pro195= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Pro31= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ser416= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ser426= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ser60= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Thr163= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Tyr225= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.861-1417A>G No assertion criteria NADK2-related disorder

Uncertain significance 104

  • c.1190+6C>T Multiple submitters Inborn genetic diseases
  • p.Arg130Trp Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg137Cys Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg137His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg150Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg197Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg250Thr Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg261Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Arg34Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Asn336Asp Multiple submitters Inborn genetic diseases ⚠
  • p.Asp259Glu Multiple submitters Inborn genetic diseases ⚠
  • p.Gln207Lys Multiple submitters Inborn genetic diseases ⚠
  • p.Gln241Arg Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Gln268Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Glu204Gly Multiple submitters Inborn genetic diseases ⚠
  • p.Glu432Asp Multiple submitters Inborn genetic diseases ⚠
  • p.His258Arg Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ile117Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Ile280Thr Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ile424Val Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Leu224Phe Multiple submitters Inborn genetic diseases ⚠
  • p.Met1Val Multiple submitters progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Pro368Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Val196Ile Multiple submitters Inborn genetic diseases ⚠
  • c.1012+3G>A Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.561-3T>C Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • c.645-3A>G Single submitter Inborn genetic diseases
  • c.782-5T>C Single submitter Inborn genetic diseases
  • p.Ala102Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala205Thr Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ala22Glu Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ala257Thr Single submitter Inborn genetic diseases ⚠
  • p.Arg150Gly Single submitter Inborn genetic diseases ⚠
  • p.Arg150Ter Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg187Trp Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg211Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg24Gly Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg340Gln Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg378Gln Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg390Cys Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg392His Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Arg392Pro Single submitter Inborn genetic diseases ⚠
  • p.Arg401His Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg436Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg5Gly Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Arg61Gly Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Asn249Ser Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Asn309Thr Single submitter Inborn genetic diseases ⚠
  • p.Asn322Ser Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Asn349Lys Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Asn358Ser Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Asn430Ser Single submitter Inborn genetic diseases ⚠
  • p.Asp153Val Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Asp296Asn Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Asp333Gly Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Asp412Gly Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Cys404Gly Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Cys408Tyr Single submitter Inborn genetic diseases ⚠
  • p.Gln207Arg Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Gln247Ter Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Gln268His Single submitter Inborn genetic diseases ⚠
  • p.Glu132Lys Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Glu292Asp Single submitter Inborn genetic diseases ⚠
  • p.Glu332Asp Single submitter Inborn genetic diseases ⚠
  • p.Glu354Asp Single submitter Inborn genetic diseases ⚠
  • p.Glu369Gly Single submitter Inborn genetic diseases ⚠
  • p.Glu370Gly Single submitter Inborn genetic diseases ⚠
  • p.Gly133Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly190Val Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Gly57Arg Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.His115Asn Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.His115Gln Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ile125Val Single submitter Inborn genetic diseases ⚠
  • p.Ile231Thr Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ile254Val Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ile280Phe Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ile337= Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ile424Leu Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Leu129Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu129Ser Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Leu224Ile Single submitter ⚠
  • p.Leu335Ile Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Leu374Arg Single submitter Inborn genetic diseases ⚠
  • p.Leu37Pro Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Met164Ile Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Met164Thr Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Pro235Ser Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Pro35Ser Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Pro68Ser Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ser201fs Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ser262fs Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Ser283Arg Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ser286Cys Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Ser426Leu Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Thr229Ser Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Thr437Ile Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Trp216Ter Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency
  • p.Tyr144His Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Tyr210Phe Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠
  • p.Tyr225His Single submitter Inborn genetic diseases ⚠
  • p.Val136Phe Single submitter Inborn genetic diseases ⚠
  • p.Val155Ile Single submitter Inborn genetic diseases ⚠
  • p.Val326Ile Single submitter Inborn genetic diseases ⚠
  • p.Val410Ala Single submitter progressive encephalopathy with leukodystrophy due to DECR deficiency ⚠