Sugi Variant

Sugi Variant/LINS1

LINS1 — 210 ClinVar variants

All ClinVar germline LINS1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 69 flagged for review →

11 Pathogenic · 1 Pathogenic/Likely pathogenic · 25 Likely pathogenic · 11 Conflicting · 38 Benign · 9 Benign/Likely benign · 37 Likely benign · 78 Uncertain significance

Full LINS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 69

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 5

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

Predictors lean, ClinVar uncertain 53

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

Predictors split 10

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

All LINS1 variants

Pathogenic 11

  • p.Gly558fs Multiple submitters intellectual disability, autosomal recessive 27
  • p.His328fs Multiple submitters intellectual disability, autosomal recessive 27
  • c.1219_1222+1del Single submitter intellectual disability
  • p.Asn487fs Single submitter intellectual disability, autosomal recessive 27
  • p.Cys239Ter Single submitter intellectual disability, autosomal recessive 27
  • p.Gln115fs Single submitter intellectual disability, autosomal recessive 27
  • p.Gln92Ter Single submitter
  • p.Glu366Ter Single submitter
  • p.Phe270fs Single submitter
  • p.Glu372fs No assertion criteria autism
  • p.His328_His329insTer No assertion criteria intellectual disability, autosomal recessive 27

Pathogenic/Likely pathogenic 1

  • p.Leu393Ter Multiple submitters intellectual disability, autosomal recessive 27

Likely pathogenic 25

  • p.Glu641fs Multiple submitters intellectual disability, autosomal recessive 27
  • p.Ser674fs Multiple submitters Inborn genetic diseases
  • c.1222+2T>C Single submitter intellectual disability, autosomal recessive 27
  • c.1394+1G>T Single submitter Inborn genetic diseases
  • c.490-1G>C Single submitter intellectual disability, autosomal recessive 27
  • c.631+1G>A Single submitter intellectual disability, autosomal recessive 27
  • p.Arg383fs Single submitter
  • p.Arg440fs Single submitter intellectual disability, autosomal recessive 27
  • p.Arg576fs Single submitter intellectual disability, autosomal recessive 27
  • p.Arg584fs Single submitter
  • p.Arg621fs Single submitter
  • p.Arg711_Ile712insTer Single submitter intellectual disability, autosomal recessive 27
  • p.Asp585fs Single submitter Inborn genetic diseases
  • p.Gln234Ter Single submitter intellectual disability, autosomal recessive 27
  • p.Gln426Ter Single submitter
  • p.Gln475fs Single submitter intellectual disability, autosomal recessive 27
  • p.Glu200fs Single submitter intellectual disability, autosomal recessive 27
  • p.Glu478Ter Single submitter intellectual disability, autosomal recessive 27
  • p.Lys186fs Single submitter intellectual disability, autosomal recessive 27
  • p.Lys729Ter Single submitter intellectual disability, autosomal recessive 27
  • p.Met82fs Single submitter
  • p.Phe520fs Single submitter
  • p.Trp535Ter Single submitter intellectual disability, autosomal recessive 27
  • p.Glu313Lys No assertion criteria intellectual disability, autosomal recessive 27 ⚠
  • p.Leu166Ter No assertion criteria intellectual disability, autosomal recessive 27

Conflicting classifications of pathogenicity 11

Benign 38

Benign/Likely benign 9

  • p.Arg240Trp Multiple submitters Inborn genetic diseases
  • p.Gln398= Multiple submitters Inborn genetic diseases
  • p.Gly707Arg Multiple submitters Inborn genetic diseases
  • p.Leu429= Multiple submitters Inborn genetic diseases
  • p.Met605Val Multiple submitters Inborn genetic diseases
  • p.Pro434= Multiple submitters Inborn genetic diseases
  • p.Ser140Thr Multiple submitters Inborn genetic diseases
  • p.Ser205= Multiple submitters Inborn genetic diseases
  • p.Tyr629= Multiple submitters Inborn genetic diseases

Likely benign 37

Uncertain significance 78