Sugi Variant

Sugi Variant/KANSL1

KANSL1 — 1436 ClinVar variants

All ClinVar germline KANSL1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 605 flagged for review →

73 Pathogenic · 9 Pathogenic/Likely pathogenic · 43 Likely pathogenic · 131 Conflicting · 120 Benign · 58 Benign/Likely benign · 461 Likely benign · 541 Uncertain significance

Full KANSL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 605

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 1

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

Predictors agree, ClinVar conflicts 95

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

Predicted LoF vs a conflicting call 8

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 388

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 388

Predictors split 113

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

All KANSL1 variants

Pathogenic 73

Pathogenic/Likely pathogenic 9

Likely pathogenic 43

Conflicting classifications of pathogenicity 131

Benign 120

Benign/Likely benign 58

  • c.1289+18A>G Multiple submitters Koolen-de Vries syndrome
  • c.1653-10C>G Multiple submitters Koolen-de Vries syndrome
  • c.1653-11C>T Multiple submitters Koolen-de Vries syndrome
  • c.3091-18C>G Multiple submitters Koolen-de Vries syndrome
  • p.Ala475Thr Multiple submitters Koolen-de Vries syndrome
  • p.Ala765Val Multiple submitters Koolen-de Vries syndrome
  • p.Ala919Thr Multiple submitters Koolen-de Vries syndrome
  • p.Arg283= Multiple submitters Koolen-de Vries syndrome
  • p.Arg619= Multiple submitters Koolen-de Vries syndrome
  • p.Arg619Trp Multiple submitters Koolen-de Vries syndrome
  • p.Arg720His Multiple submitters Inborn genetic diseases
  • p.Arg876= Multiple submitters Koolen-de Vries syndrome
  • p.Asn207Ser Multiple submitters Koolen-de Vries syndrome
  • p.Asn225Asp Multiple submitters Koolen-de Vries syndrome
  • p.Asn230Asp Multiple submitters Inborn genetic diseases
  • p.Asn334Asp Multiple submitters Koolen-de Vries syndrome
  • p.Asn369Ser Multiple submitters Koolen-de Vries syndrome
  • p.Asn906Lys Multiple submitters Inborn genetic diseases
  • p.Asp10= Multiple submitters Koolen-de Vries syndrome
  • p.Asp1028His Multiple submitters Inborn genetic diseases
  • p.Asp563= Multiple submitters Koolen-de Vries syndrome
  • p.Asp744His Multiple submitters Koolen-de Vries syndrome
  • p.Asp831Glu Multiple submitters Koolen-de Vries syndrome
  • p.Gln1057Arg Multiple submitters Koolen-de Vries syndrome
  • p.Gln243= Multiple submitters Koolen-de Vries syndrome
  • p.Gln243Lys Multiple submitters Inborn genetic diseases
  • p.Gln99= Multiple submitters Koolen-de Vries syndrome
  • p.Gln99Arg Multiple submitters Inborn genetic diseases
  • p.Glu905del Multiple submitters Koolen-de Vries syndrome
  • p.Gly191Cys Multiple submitters dystonia, early-onset, and/or spastic paraplegia
  • p.Gly203Trp Multiple submitters Koolen-de Vries syndrome
  • p.Gly900Arg Multiple submitters Koolen-de Vries syndrome
  • p.His212Arg Multiple submitters Inborn genetic diseases
  • p.Ile317Val Multiple submitters Inborn genetic diseases
  • p.Leu138= Multiple submitters Koolen-de Vries syndrome
  • p.Leu552Ile Multiple submitters Inborn genetic diseases
  • p.Leu703= Multiple submitters Koolen-de Vries syndrome
  • p.Leu895Val Multiple submitters Inborn genetic diseases
  • p.Leu96= Multiple submitters Koolen-de Vries syndrome
  • p.Lys104Thr Multiple submitters Koolen-de Vries syndrome ⚠
  • p.Lys159Asn Multiple submitters Koolen-de Vries syndrome ⚠
  • p.Lys267Arg Multiple submitters Koolen-de Vries syndrome
  • p.Lys372= Multiple submitters Koolen-de Vries syndrome
  • p.Met805Thr Multiple submitters Inborn genetic diseases
  • p.Pro1102= Multiple submitters Koolen-de Vries syndrome
  • p.Pro240Leu Multiple submitters Koolen-de Vries syndrome
  • p.Pro525Arg Multiple submitters Koolen-de Vries syndrome
  • p.Pro646= Multiple submitters Koolen-de Vries syndrome
  • p.Pro777= Multiple submitters Koolen-de Vries syndrome
  • p.Ser227Asn Multiple submitters Inborn genetic diseases
  • p.Ser236Pro Multiple submitters Koolen-de Vries syndrome
  • p.Ser375Leu Multiple submitters Inborn genetic diseases
  • p.Ser827= Multiple submitters Koolen-de Vries syndrome
  • p.Thr1018Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Thr166= Multiple submitters Koolen-de Vries syndrome
  • p.Thr221Ile Multiple submitters Koolen-de Vries syndrome
  • p.Val580Ile Multiple submitters Koolen-de Vries syndrome
  • p.Val611Ile Multiple submitters Koolen-de Vries syndrome

Likely benign 461

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

Uncertain significance 541

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