NT5C2 — 278 ClinVar variants

All ClinVar germline NT5C2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 69 flagged for review →

17 Pathogenic · 5 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 3 Conflicting · 35 Benign · 5 Benign/Likely benign · 113 Likely benign · 91 Uncertain significance

Full NT5C2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 69

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 lean, ClinVar uncertain 60

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

All NT5C2 variants

Pathogenic 17

  • p.Arg39Ter Multiple submitters hereditary spastic paraplegia 45
  • c.175+1G>A Single submitter hereditary spastic paraplegia 45
  • p.Arg29Ter Single submitter hereditary spastic paraplegia 45
  • p.Arg76fs Single submitter hereditary spastic paraplegia 45
  • p.Gln199Ter Single submitter hereditary spastic paraplegia 45
  • p.Gln542fs Single submitter hereditary spastic paraplegia 45
  • p.Leu468Pro Single submitter hereditary spastic paraplegia 45
  • p.Lys385fs Single submitter hereditary spastic paraplegia 45
  • p.Thr173fs Single submitter hereditary spastic paraplegia 45
  • p.Tyr210fs Single submitter hereditary spastic paraplegia 45
  • p.Tyr225Ter Single submitter hereditary spastic paraplegia 45
  • p.Tyr457Ter Single submitter hereditary spastic paraplegia 45
  • c.1159+2T>G No assertion criteria hereditary spastic paraplegia 45
  • c.771+573_814-298del No assertion criteria hereditary spastic paraplegia 45
  • c.989-1G>T No assertion criteria hereditary spastic paraplegia 45
  • p.Arg149Ter No assertion criteria hereditary spastic paraplegia 45
  • p.Ser409fs No assertion criteria hereditary spastic paraplegia 45

Pathogenic/Likely pathogenic 5

  • c.1449+2T>C Multiple submitters NT5C2-related disorder
  • p.Arg144Ter Multiple submitters NT5C2-related disorder
  • p.Arg367Ter Multiple submitters hereditary spastic paraplegia 45
  • p.Leu105fs Multiple submitters hereditary spastic paraplegia 45
  • p.Leu370fs Multiple submitters hereditary spastic paraplegia 45

Likely pathogenic 9

  • c.1272+1G>C Single submitter hereditary spastic paraplegia 45
  • c.175+1G>C Single submitter NT5C2-related disorder
  • c.176-2A>G Single submitter hereditary spastic paraplegia 45
  • c.539+1G>T Single submitter hereditary spastic paraplegia 45
  • c.771+1G>A Single submitter hereditary spastic paraplegia 45
  • p.Arg413fs Single submitter NT5C2-related disorder
  • p.His486Asn Single submitter hereditary spastic paraplegia 45
  • p.Val169del Single submitter
  • p.Phe369Ser No assertion criteria hereditary spastic paraplegia 45

Conflicting classifications of pathogenicity 3

  • c.176-10C>T Single submitter hereditary spastic paraplegia 45
  • c.540-4G>A Single submitter Inborn genetic diseases
  • p.Glu561del Single submitter hereditary spastic paraplegia 45

Benign 35

Benign/Likely benign 5

  • c.634-14T>G Multiple submitters hereditary spastic paraplegia 45
  • c.771+18A>T Multiple submitters hereditary spastic paraplegia 45
  • c.921+18T>G Multiple submitters hereditary spastic paraplegia 45
  • p.Lys359= Multiple submitters hereditary spastic paraplegia 45
  • p.Thr3Ala Multiple submitters hereditary spastic paraplegia 45

Likely benign 113

  • c.102-4A>G Multiple submitters hereditary spastic paraplegia 45
  • c.176-15C>T Multiple submitters hereditary spastic paraplegia 45
  • c.634-16T>C Multiple submitters hereditary spastic paraplegia 45
  • c.772-20T>C Multiple submitters hereditary spastic paraplegia 45
  • c.772-9T>A Multiple submitters hereditary spastic paraplegia 45
  • c.814-50C>T Multiple submitters
  • c.-24-99G>A Multiple submitters
  • p.Arg363= Multiple submitters hereditary spastic paraplegia 45
  • p.Glu554= Multiple submitters hereditary spastic paraplegia 45
  • p.Glu557= Multiple submitters hereditary spastic paraplegia 45
  • p.His352= Multiple submitters hereditary spastic paraplegia 45
  • p.Ile325= Multiple submitters
  • p.Leu375= Multiple submitters hereditary spastic paraplegia 45
  • p.Leu469= Multiple submitters hereditary spastic paraplegia 45
  • p.Phe441= Multiple submitters hereditary spastic paraplegia 45
  • p.Ser67= Multiple submitters hereditary spastic paraplegia 45
  • p.Ter562= Multiple submitters hereditary spastic paraplegia 45
  • p.Thr334= Multiple submitters hereditary spastic paraplegia 45
  • p.Tyr255= Multiple submitters hereditary spastic paraplegia 45
  • c.101+16A>G Single submitter hereditary spastic paraplegia 45
  • c.1159+137del Single submitter
  • c.1159+16A>G Single submitter hereditary spastic paraplegia 45
  • c.1160-13A>C Single submitter hereditary spastic paraplegia 45
  • c.1160-14C>T Single submitter
  • c.1160-18C>T Single submitter hereditary spastic paraplegia 45
  • c.1160-20T>C Single submitter hereditary spastic paraplegia 45
  • c.1160-4C>T Single submitter hereditary spastic paraplegia 45
  • c.1211+16A>G Single submitter hereditary spastic paraplegia 45
  • c.1211+197G>A Single submitter
  • c.1211+8T>A Single submitter hereditary spastic paraplegia 45
  • c.1212-13_1212-12del Single submitter hereditary spastic paraplegia 45
  • c.1212-13_1212-9del Single submitter hereditary spastic paraplegia 45
  • c.1212-142C>T Single submitter
  • c.1212-21_1212-19dup Single submitter hereditary spastic paraplegia 45
  • c.1212-8_1212-6dup Single submitter hereditary spastic paraplegia 45
  • c.1273-4T>C Single submitter hereditary spastic paraplegia 45
  • c.1273-7_1273-4del Single submitter hereditary spastic paraplegia 45
  • c.1273-7_1273-4dup Single submitter hereditary spastic paraplegia 45
  • c.1273-9_1273-8del Single submitter hereditary spastic paraplegia 45
  • c.1449+13T>A Single submitter hereditary spastic paraplegia 45
  • c.1449+18T>A Single submitter hereditary spastic paraplegia 45
  • c.1450-16G>C Single submitter hereditary spastic paraplegia 45
  • c.1450-8C>G Single submitter hereditary spastic paraplegia 45
  • c.175+19T>C Single submitter hereditary spastic paraplegia 45
  • c.176-19A>G Single submitter hereditary spastic paraplegia 45
  • c.293+13G>T Single submitter hereditary spastic paraplegia 45
  • c.389+10G>C Single submitter
  • c.389+15C>T Single submitter hereditary spastic paraplegia 45
  • c.389+328T>G Single submitter
  • c.390-118C>T Single submitter
  • c.390-15A>C Single submitter hereditary spastic paraplegia 45
  • c.481+11T>C Single submitter hereditary spastic paraplegia 45
  • c.481+59T>C Single submitter
  • c.481+8C>T Single submitter hereditary spastic paraplegia 45
  • c.539+15T>C Single submitter hereditary spastic paraplegia 45
  • c.633+14G>A Single submitter
  • c.634-14T>C Single submitter
  • c.634-151G>A Single submitter
  • c.634-19T>C Single submitter hereditary spastic paraplegia 45
  • c.634-25_634-19dup Single submitter hereditary spastic paraplegia 45
  • c.634-6C>T Single submitter hereditary spastic paraplegia 45
  • c.634-89G>A Single submitter
  • c.687+14G>A Single submitter hereditary spastic paraplegia 45
  • c.687+169_687+170insT Single submitter
  • c.813+14C>T Single submitter hereditary spastic paraplegia 45
  • c.813+18A>G Single submitter hereditary spastic paraplegia 45
  • c.813+19T>C Single submitter hereditary spastic paraplegia 45
  • c.814-10C>T Single submitter hereditary spastic paraplegia 45
  • c.814-20T>A Single submitter hereditary spastic paraplegia 45
  • c.814-232A>C Single submitter
  • c.814-9C>T Single submitter
  • c.-24-17A>G Single submitter
  • p.Ala166= Single submitter hereditary spastic paraplegia 45
  • p.Ala451= Single submitter hereditary spastic paraplegia 45
  • p.Ala463= Single submitter
  • p.Ala540= Single submitter hereditary spastic paraplegia 45
  • p.Asp113= Single submitter hereditary spastic paraplegia 45
  • p.Asp146= Single submitter hereditary spastic paraplegia 45
  • p.Asp206= Single submitter hereditary spastic paraplegia 45
  • p.Gln136Arg Single submitter hereditary spastic paraplegia 45
  • p.Gln542= Single submitter hereditary spastic paraplegia 45
  • p.Glu412= Single submitter hereditary spastic paraplegia 45
  • p.Glu491= Single submitter hereditary spastic paraplegia 45
  • p.Glu556= Single submitter hereditary spastic paraplegia 45
  • p.Glu558= Single submitter hereditary spastic paraplegia 45
  • p.Glu559= Single submitter hereditary spastic paraplegia 45
  • p.Gly273= Single submitter hereditary spastic paraplegia 45
  • p.His123= Single submitter hereditary spastic paraplegia 45
  • p.His494= Single submitter hereditary spastic paraplegia 45
  • p.His548= Single submitter hereditary spastic paraplegia 45
  • p.Ile314= Single submitter hereditary spastic paraplegia 45
  • p.Leu100= Single submitter hereditary spastic paraplegia 45
  • p.Leu110= Single submitter hereditary spastic paraplegia 45
  • p.Leu287= Single submitter hereditary spastic paraplegia 45
  • p.Leu321= Single submitter hereditary spastic paraplegia 45
  • p.Leu347= Single submitter hereditary spastic paraplegia 45
  • p.Leu524= Single submitter hereditary spastic paraplegia 45
  • p.Phe191= Single submitter
  • p.Phe283= Single submitter
  • p.Pro270= Single submitter hereditary spastic paraplegia 45
  • p.Ser408= Single submitter hereditary spastic paraplegia 45
  • p.Ser88= Single submitter hereditary spastic paraplegia 45
  • p.Thr155= Single submitter hereditary spastic paraplegia 45
  • p.Thr162= Single submitter hereditary spastic paraplegia 45
  • p.Thr179= Single submitter hereditary spastic paraplegia 45
  • p.Thr383= Single submitter hereditary spastic paraplegia 45
  • p.Thr489= Single submitter hereditary spastic paraplegia 45
  • p.Thr73= Single submitter hereditary spastic paraplegia 45
  • p.Tyr348= Single submitter hereditary spastic paraplegia 45
  • p.Tyr471= Single submitter hereditary spastic paraplegia 45
  • p.Val112= Single submitter hereditary spastic paraplegia 45
  • p.Val219Ala Single submitter hereditary spastic paraplegia 45
  • p.Val512= No assertion criteria NT5C2-related disorder

Uncertain significance 91