Sugi Variant

Sugi Variant/KPTN

KPTN — 226 ClinVar variants

All ClinVar germline KPTN variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 103 flagged for review →

12 Pathogenic · 3 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 10 Conflicting · 12 Benign · 6 Benign/Likely benign · 60 Likely benign · 114 Uncertain significance

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

⚑ Evidence disagreements 103

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 5

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

Predictors lean, ClinVar uncertain 73

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

Predictors split 25

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

All KPTN variants

Pathogenic 12

  • p.Ser259Ter Multiple submitters KPTN-related disorder
  • c.1183-1G>A Single submitter macrocephaly-developmental delay syndrome
  • c.394+1G>T Single submitter macrocephaly-developmental delay syndrome
  • c.397_398delAG Single submitter macrocephaly-developmental delay syndrome
  • c.599+1G>A Single submitter macrocephaly-developmental delay syndrome
  • c.599+1G>T Single submitter macrocephaly-developmental delay syndrome
  • p.Ala131fs Single submitter macrocephaly-developmental delay syndrome
  • p.Gln246Ter Single submitter macrocephaly-developmental delay syndrome
  • p.Leu219fs Single submitter macrocephaly-developmental delay syndrome
  • p.Lys262fs Single submitter macrocephaly-developmental delay syndrome
  • p.Ser223fs Single submitter macrocephaly-developmental delay syndrome
  • p.Val231fs Single submitter

Pathogenic/Likely pathogenic 3

Likely pathogenic 9

  • c.309+1G>A Single submitter macrocephaly-developmental delay syndrome
  • c.600-1G>T Single submitter macrocephaly-developmental delay syndrome
  • c.999+1G>T Single submitter macrocephaly-developmental delay syndrome
  • p.Arg252Ter Single submitter macrocephaly-developmental delay syndrome
  • p.Arg288Pro Single submitter macrocephaly-developmental delay syndrome ⚠
  • p.Glu40Ter Single submitter KPTN-related disorder
  • p.Leu258fs Single submitter
  • p.Phe191Ter Single submitter macrocephaly-developmental delay syndrome
  • p.Phe362_Ser363del Single submitter macrocephaly-developmental delay syndrome

Conflicting classifications of pathogenicity 10

Benign 12

  • c.1000-14C>T Multiple submitters macrocephaly-developmental delay syndrome
  • c.227-83T>C Multiple submitters
  • c.*2C>T Multiple submitters
  • p.Arg415= Multiple submitters macrocephaly-developmental delay syndrome
  • p.His352= Multiple submitters macrocephaly-developmental delay syndrome
  • p.Pro168= Multiple submitters macrocephaly-developmental delay syndrome
  • p.Pro302= Multiple submitters macrocephaly-developmental delay syndrome
  • c.226+11C>A Single submitter macrocephaly-developmental delay syndrome
  • c.600-5G>A Single submitter macrocephaly-developmental delay syndrome
  • c.600-6C>T Single submitter macrocephaly-developmental delay syndrome
  • c.710-14C>T Single submitter macrocephaly-developmental delay syndrome
  • p.Leu367= Single submitter macrocephaly-developmental delay syndrome

Benign/Likely benign 6

  • c.525+13G>A Multiple submitters macrocephaly-developmental delay syndrome
  • c.710-19A>C Multiple submitters macrocephaly-developmental delay syndrome
  • c.788-14T>C Multiple submitters macrocephaly-developmental delay syndrome
  • p.Gly211Arg Multiple submitters macrocephaly-developmental delay syndrome
  • p.Leu245Val Multiple submitters macrocephaly-developmental delay syndrome
  • p.Val151Ala Multiple submitters macrocephaly-developmental delay syndrome ⚠

Likely benign 60

  • c.1183-9del Multiple submitters macrocephaly-developmental delay syndrome
  • c.599+17A>C Multiple submitters macrocephaly-developmental delay syndrome
  • p.Asp424= Multiple submitters
  • p.Gly34= Multiple submitters macrocephaly-developmental delay syndrome
  • p.Gly389= Multiple submitters macrocephaly-developmental delay syndrome
  • p.Leu179= Multiple submitters macrocephaly-developmental delay syndrome
  • p.Ser259= Multiple submitters macrocephaly-developmental delay syndrome
  • p.Tyr29= Multiple submitters macrocephaly-developmental delay syndrome
  • c.1000-19T>C Single submitter macrocephaly-developmental delay syndrome
  • c.1182+8C>T Single submitter
  • c.227-6T>C Single submitter macrocephaly-developmental delay syndrome
  • c.227-9C>T Single submitter macrocephaly-developmental delay syndrome
  • c.309+12C>A Single submitter
  • c.309+8G>T Single submitter macrocephaly-developmental delay syndrome
  • c.394+12G>A Single submitter macrocephaly-developmental delay syndrome
  • c.394+17C>T Single submitter macrocephaly-developmental delay syndrome
  • c.394+18G>A Single submitter macrocephaly-developmental delay syndrome
  • c.449+16G>A Single submitter macrocephaly-developmental delay syndrome
  • c.449+7G>T Single submitter
  • c.450-478A>G Single submitter
  • c.526-11G>C Single submitter macrocephaly-developmental delay syndrome
  • c.600-17A>G Single submitter macrocephaly-developmental delay syndrome
  • c.600-8C>T Single submitter
  • c.709+10G>T Single submitter macrocephaly-developmental delay syndrome
  • c.709+9C>T Single submitter macrocephaly-developmental delay syndrome
  • c.710-12C>G Single submitter macrocephaly-developmental delay syndrome
  • c.710-4G>A Single submitter macrocephaly-developmental delay syndrome
  • c.788-5T>C Single submitter macrocephaly-developmental delay syndrome
  • c.863+13GA[4] Single submitter macrocephaly-developmental delay syndrome
  • p.Ala149= Single submitter macrocephaly-developmental delay syndrome
  • p.Ala435= Single submitter macrocephaly-developmental delay syndrome
  • p.Ala78= Single submitter macrocephaly-developmental delay syndrome
  • p.Arg293= Single submitter
  • p.Arg416= Single submitter
  • p.Glu344= Single submitter macrocephaly-developmental delay syndrome
  • p.Gly421= Single submitter macrocephaly-developmental delay syndrome
  • p.Gly425Arg Single submitter Inborn genetic diseases
  • p.Gly427= Single submitter macrocephaly-developmental delay syndrome
  • p.His355Tyr Single submitter macrocephaly-developmental delay syndrome
  • p.His371= Single submitter macrocephaly-developmental delay syndrome
  • p.Leu163= Single submitter macrocephaly-developmental delay syndrome
  • p.Leu258= Single submitter macrocephaly-developmental delay syndrome
  • p.Leu276= Single submitter macrocephaly-developmental delay syndrome
  • p.Leu327= Single submitter
  • p.Leu357= Single submitter
  • p.Leu42= Single submitter macrocephaly-developmental delay syndrome
  • p.Pro13= Single submitter macrocephaly-developmental delay syndrome
  • p.Pro143= Single submitter macrocephaly-developmental delay syndrome
  • p.Pro186= Single submitter macrocephaly-developmental delay syndrome
  • p.Ser23= Single submitter
  • p.Ser274= Single submitter macrocephaly-developmental delay syndrome
  • p.Ser309= Single submitter macrocephaly-developmental delay syndrome
  • p.Ser345= Single submitter macrocephaly-developmental delay syndrome
  • p.Thr195= Single submitter macrocephaly-developmental delay syndrome
  • p.Thr20= Single submitter
  • p.Thr316= Single submitter macrocephaly-developmental delay syndrome
  • p.Val28= Single submitter macrocephaly-developmental delay syndrome
  • p.Val310= Single submitter macrocephaly-developmental delay syndrome
  • p.Val65= Single submitter macrocephaly-developmental delay syndrome
  • p.Thr45= No assertion criteria KPTN-related disorder

Uncertain significance 114