NIT1 — 75 ClinVar variants

All ClinVar germline NIT1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 66 flagged for review →

1 Pathogenic · 1 Likely pathogenic · 1 Conflicting · 1 Benign · 2 Likely benign · 69 Uncertain significance

Full NIT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 66

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 1

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

NIT1 p.Arg243Trp Conflicting Single submitter
brain small vessel disease 4

Predictors lean, ClinVar uncertain 56

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

Predictors split 9

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

All NIT1 variants

Pathogenic 1

p.Cys67_Ala68insTer Single submitter brain small vessel disease 4

Likely pathogenic 1

c.591+2T>G Single submitter Susceptibility to severe COVID-19

Conflicting classifications of pathogenicity 1

p.Arg243Trp Single submitter brain small vessel disease 4 ⚠

Benign 1

c.3-284A>G Single submitter

Likely benign 2

p.Glu45Lys Single submitter
p.Tyr204= Single submitter

Uncertain significance 69

p.Ala117Thr Single submitter ⚠
p.Ala236Thr Single submitter ⚠
p.Ala68Val Single submitter ⚠
p.Ala74Pro Single submitter ⚠
p.Ala79Gly Single submitter ⚠
p.Arg207Gln Single submitter ⚠
p.Arg207Trp Single submitter ⚠
p.Arg261His Single submitter ⚠
p.Arg284His Single submitter ⚠
p.Arg302Gln Single submitter ⚠
p.Arg314Cys Single submitter ⚠
p.Arg314His Single submitter
p.Arg315Gly Single submitter ⚠
p.Arg315Ser Single submitter ⚠
p.Arg35Gly Single submitter ⚠
p.Arg72Gln Single submitter ⚠
p.Asn179Ser Single submitter ⚠
p.Asp297Glu Single submitter
p.Cys120Arg Single submitter
p.Cys145Arg Single submitter ⚠
p.Cys292Tyr Single submitter ⚠
p.Cys52Ser Single submitter ⚠
p.Gln134Arg Single submitter ⚠
p.Gln258His Single submitter ⚠
p.Glu168Asp Single submitter ⚠
p.Glu177Gln Single submitter ⚠
p.Glu248Lys Single submitter ⚠
p.Glu73Gly Single submitter ⚠
p.Gly323Asp Single submitter ⚠
p.His100Tyr Single submitter ⚠
p.His10Gln Single submitter ⚠
p.His307Arg Single submitter ⚠
p.Ile247Val Single submitter ⚠
p.Ile39Ser Single submitter ⚠
p.Leu122Phe Single submitter ⚠
p.Leu16Val Single submitter ⚠
p.Leu200Ile Single submitter ⚠
p.Leu223Phe Single submitter ⚠
p.Leu25Phe Single submitter ⚠
p.Leu28Phe Single submitter ⚠
p.Lys152Arg Single submitter ⚠
p.Lys265Glu Single submitter ⚠
p.Met175Thr Single submitter ⚠
p.Met273Ile Single submitter ⚠
p.Met37Ile Single submitter
p.Pro170Ser Single submitter ⚠
p.Pro183Leu Single submitter ⚠
p.Pro235Ser Single submitter ⚠
p.Pro23Ser Single submitter ⚠
p.Pro32Leu Single submitter ⚠
p.Pro34Leu Single submitter ⚠
p.Ser180Phe Single submitter ⚠
p.Ser227Leu Single submitter ⚠
p.Ser231Cys Single submitter ⚠
p.Ser272Gly Single submitter ⚠
p.Ser286Pro Single submitter ⚠
p.Ser286Thr Single submitter ⚠
p.Ser40Pro Single submitter ⚠
p.Thr158Ala Single submitter ⚠
p.Thr224Asn Single submitter ⚠
p.Thr233Ile Single submitter ⚠
p.Thr280Arg Single submitter ⚠
p.Thr55Ile Single submitter ⚠
p.Thr98Met Single submitter ⚠
p.Tyr225Cys Single submitter ⚠
p.Val167Gly Single submitter ⚠
p.Val275Leu Single submitter ⚠
p.Val281Glu Single submitter ⚠
p.Val51Met Single submitter ⚠