Sugi Variant

Sugi Variant/CNKSR2

CNKSR2 — 271 ClinVar variants

All ClinVar germline CNKSR2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 158 flagged for review →

35 Pathogenic · 2 Pathogenic/Likely pathogenic · 18 Likely pathogenic · 7 Conflicting · 7 Benign · 3 Benign/Likely benign · 30 Likely benign · 169 Uncertain significance

Full CNKSR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 158

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 95

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

Predictors split 61

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

All CNKSR2 variants

Pathogenic 35

  • p.Arg663fs Multiple submitters intellectual disability, X-linked, syndromic, Houge type
  • p.Arg676fs Multiple submitters
  • p.Arg712Ter Multiple submitters intellectual disability, X-linked, syndromic, Houge type
  • c.1905-2A>G Single submitter
  • c.1977-1G>A Single submitter intellectual disability
  • c.2145+1G>A Single submitter
  • c.2693-43_2703del Single submitter
  • c.742-1G>A Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Arg283Ter Single submitter
  • p.Arg427fs Single submitter
  • p.Arg428Ter Single submitter
  • p.Arg562Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Asn551fs Single submitter
  • p.Gln100Ter Single submitter
  • p.Gln162Ter Single submitter
  • p.Gln63Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Gln681Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Glu675fs Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Gly751fs Single submitter Inborn genetic diseases
  • p.His782fs Single submitter
  • p.Ile39fs Single submitter
  • p.Lys183fs Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Lys579Ter Single submitter
  • p.Met517fs Single submitter Inborn genetic diseases
  • p.Pro554fs Single submitter
  • p.Ser192fs Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Ser779Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Thr433fs Single submitter
  • p.Trp141Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Trp578Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Trp660Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Tyr635fs Single submitter
  • p.Tyr783Ter Single submitter
  • p.Asp152fs No assertion criteria intellectual disability, X-linked, syndromic, Houge type
  • p.Leu412Ter No assertion criteria intellectual disability, X-linked, syndromic, Houge type

Pathogenic/Likely pathogenic 2

  • p.Arg400Ter Multiple submitters intellectual disability, X-linked, syndromic, Houge type
  • p.Arg729Ter Multiple submitters intellectual disability, X-linked, syndromic, Houge type

Likely pathogenic 18

  • p.Arg438Ter Multiple submitters intellectual disability, X-linked, syndromic, Houge type
  • c.1394-13_1423del Single submitter intellectual disability, X-linked, syndromic, Houge type
  • c.1657+1G>A Single submitter intellectual disability, X-linked, syndromic, Houge type
  • c.228+1G>A Single submitter intellectual disability
  • p.Arg252Trp Single submitter ⚠
  • p.Arg364Gly Single submitter intellectual disability, X-linked, syndromic, Houge type ⚠
  • p.Gln522Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Gln539Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Ile625fs Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Leu789fs Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Ser696Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Ser767Phe Single submitter neurodevelopmental disorder
  • p.Thr507fs Single submitter
  • p.Trp19Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Trp605Ter Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Val57fs Single submitter intellectual disability, X-linked, syndromic, Houge type
  • c.1303+1G>C No assertion criteria X-linked recessive seizure and neurodevelopmental deficit
  • c.1905-1G>A No assertion criteria CNKSR2-related disorder

Conflicting classifications of pathogenicity 7

Benign 7

  • p.Asp995Asn Multiple submitters
  • p.Cys175= Multiple submitters
  • p.Gln217= Multiple submitters
  • p.Leu817= Multiple submitters
  • p.Leu976= Multiple submitters intellectual disability, X-linked, syndromic, Houge type
  • c.1657+20C>T Single submitter intellectual disability, X-linked, syndromic, Houge type
  • p.Glu886del Single submitter Inborn genetic diseases

Benign/Likely benign 3

Likely benign 30

Uncertain significance 169