Sugi Variant

Sugi Variant/NAA15

NAA15 — 668 ClinVar variants

All ClinVar germline NAA15 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 266 flagged for review →

92 Pathogenic · 10 Pathogenic/Likely pathogenic · 72 Likely pathogenic · 17 Conflicting · 33 Benign · 8 Benign/Likely benign · 134 Likely benign · 302 Uncertain significance

Full NAA15 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 266

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 vs ClinVar 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 12

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

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 197

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 197

Predictors split 54

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

All NAA15 variants

Pathogenic 92

Pathogenic/Likely pathogenic 10

  • c.1410+1G>A Multiple submitters Inborn genetic diseases
  • c.1539+1G>A Multiple submitters intellectual disability, autosomal dominant 50
  • c.1753+1G>T Multiple submitters intellectual disability, autosomal dominant 50
  • c.1947+1G>A Multiple submitters
  • c.692-2_692-1del Multiple submitters intellectual disability, autosomal dominant 50
  • p.Arg549Ter Multiple submitters NAA15-related disorder
  • p.Arg782Ter Multiple submitters intellectual disability, autosomal dominant 50
  • p.Asn614fs Multiple submitters intellectual disability, autosomal dominant 50
  • p.Glu241Ter Multiple submitters
  • p.Trp83Ter Multiple submitters intellectual disability, autosomal dominant 50

Likely pathogenic 72

  • p.Ala585Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Gln780Ter Multiple submitters NAA15-related disorder
  • p.Leu301fs Multiple submitters intellectual disability
  • c.1014+1G>A Single submitter
  • c.1257+1G>A Single submitter intellectual disability, autosomal dominant 50
  • c.1258-1G>A Single submitter
  • c.139_139+1dup Single submitter intellectual disability, autosomal dominant 50
  • c.1410+1del Single submitter
  • c.1410+1G>T Single submitter neurodevelopmental disorder
  • c.1947+1del Single submitter intellectual disability, autosomal dominant 50
  • c.2302+1G>T Single submitter
  • c.2303-2A>G Single submitter intellectual disability, autosomal dominant 50
  • c.245-2A>C Single submitter intellectual disability, autosomal dominant 50
  • c.403-1G>A Single submitter intellectual disability, autosomal dominant 50
  • c.55-2A>C Single submitter intellectual disability, autosomal dominant 50
  • c.907+1G>A Single submitter
  • p.Ala427fs Single submitter intellectual disability, autosomal dominant 50
  • p.Ala719Thr Single submitter ⚠
  • p.Arg148fs Single submitter intellectual disability, autosomal dominant 50
  • p.Arg16Gly Single submitter ⚠
  • p.Arg442_Phe443insTer Single submitter
  • p.Arg600fs Single submitter
  • p.Arg71Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Asp725fs Single submitter intellectual disability, autosomal dominant 50
  • p.Asp76_Leu77insTer Single submitter intellectual disability, autosomal dominant 50
  • p.Gln124Ter Single submitter Incidental Discovery
  • p.Gln219Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Gln251Ter Single submitter NAA15-related disorder
  • p.Gln25Pro Single submitter intellectual disability, autosomal dominant 50
  • p.Glu211Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Glu409Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Glu517Gln Single submitter intellectual disability, autosomal dominant 50
  • p.Glu591fs Single submitter intellectual disability, autosomal dominant 50
  • p.Glu67Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Glu785Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Gly249Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Gly321fs Single submitter intellectual disability, autosomal dominant 50
  • p.Gly72fs Single submitter intellectual disability, autosomal dominant 50
  • p.Gly743fs Single submitter NAA15-related disorder
  • p.His383_Tyr384insTer Single submitter intellectual disability, autosomal dominant 50
  • p.His709Pro Single submitter intellectual disability, autosomal dominant 50
  • p.Ile279_Tyr280insTer Single submitter intellectual disability, autosomal dominant 50
  • p.Ile341fs Single submitter intellectual disability, autosomal dominant 50
  • p.Ile36Thr Single submitter Inborn genetic diseases
  • p.Ile397Arg Single submitter
  • p.Leu120Pro Single submitter
  • p.Leu353Pro Single submitter
  • p.Leu373Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Leu73Phe Single submitter intellectual disability, autosomal dominant 50
  • p.Leu73Ser Single submitter neurodevelopmental disorder
  • p.Lys34fs Single submitter intellectual disability, autosomal dominant 50
  • p.Lys619Ter Single submitter
  • p.Lys649= Single submitter Inborn genetic diseases
  • p.Lys781Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Lys78fs Single submitter intellectual disability, autosomal dominant 50
  • p.Met485fs Single submitter NAA15-related disorder
  • p.Ser391fs Single submitter
  • p.Ser537Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Ser779fs Single submitter NAA15-related disorder
  • p.Thr177fs Single submitter intellectual disability, autosomal dominant 50
  • p.Trp109Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Trp83fs Single submitter intellectual disability, autosomal dominant 50
  • p.Tyr133fs Single submitter intellectual disability, autosomal dominant 50
  • p.Tyr260fs Single submitter intellectual disability, autosomal dominant 50
  • p.Tyr451fs Single submitter intellectual disability, autosomal dominant 50
  • p.Tyr495Ter Single submitter intellectual disability, autosomal dominant 50
  • p.Val720fs Single submitter intellectual disability, autosomal dominant 50
  • c.2302+1G>A No assertion criteria NAA15-related disorder
  • c.54+1_54+2del No assertion criteria
  • p.Asp364fs No assertion criteria
  • p.Glu281Ter No assertion criteria NAA15-related disorder
  • p.Leu329Ter No assertion criteria

Conflicting classifications of pathogenicity 17

Benign 33

Benign/Likely benign 8

Likely benign 134

Uncertain significance 302

Showing the top 300 by review status; the full set is in the sitemap.