Sugi Variant

Sugi Variant/CLTC

CLTC — 1172 ClinVar variants

All ClinVar germline CLTC variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 449 flagged for review →

63 Pathogenic · 5 Pathogenic/Likely pathogenic · 57 Likely pathogenic · 13 Conflicting · 33 Benign · 8 Benign/Likely benign · 480 Likely benign · 513 Uncertain significance

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

⚑ Evidence disagreements 449

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 267

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 267

Predictors split 176

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 176

All CLTC variants

Pathogenic 63

Pathogenic/Likely pathogenic 5

  • p.Glu1564fs Multiple submitters intellectual disability, autosomal dominant 56
  • p.Pro890Leu Multiple submitters intellectual disability, autosomal dominant 56
  • p.Ser1524fs Multiple submitters intellectual disability, autosomal dominant 56
  • p.Tyr1574Ter Multiple submitters intellectual disability, autosomal dominant 56
  • p.Tyr803Ter Multiple submitters

Likely pathogenic 57

  • p.Arg1165Ter Multiple submitters intellectual disability, autosomal dominant 56
  • p.Arg1311Ter Multiple submitters intellectual disability, autosomal dominant 56
  • c.1947+3A>G Single submitter
  • c.250+14_250+15del Single submitter
  • c.250+3A>G Single submitter intellectual disability, autosomal dominant 56
  • c.2562-1G>C Single submitter intellectual disability, autosomal dominant 56
  • c.2562-2A>G Single submitter intellectual disability, autosomal dominant 56
  • c.3065+1G>A Single submitter
  • c.3066-2A>G Single submitter
  • c.3442+1G>T Single submitter
  • c.4042-1G>C Single submitter
  • c.4324-8T>G Single submitter intellectual disability, autosomal dominant 56
  • c.4606-1G>A Single submitter Inborn genetic diseases
  • c.4904-1G>A Single submitter Inborn genetic diseases
  • c.519+2T>A Single submitter
  • c.796-1G>A Single submitter
  • p.Ala1112fs Single submitter intellectual disability, autosomal dominant 56
  • p.Ala1269Pro Single submitter intellectual disability, autosomal dominant 56
  • p.Ala71fs Single submitter intellectual disability, autosomal dominant 56
  • p.Ala735Val Single submitter Inborn genetic diseases
  • p.Arg1481fs Single submitter intellectual disability, autosomal dominant 56
  • p.Asn678fs Single submitter intellectual disability, autosomal dominant 56
  • p.Asp1366fs Single submitter intellectual disability, autosomal dominant 56
  • p.Asp1476Asn Single submitter
  • p.Gln1291Ter Single submitter intellectual disability, autosomal dominant 56
  • p.Gln1638Ter Single submitter intellectual disability, autosomal dominant 56
  • p.Gln1652fs Single submitter
  • p.Gln173Arg Single submitter intellectual disability, autosomal dominant 56 ⚠
  • p.Glu1123fs Single submitter neurodevelopmental disorder
  • p.Glu1172fs Single submitter
  • p.Glu1310Lys Single submitter intellectual disability, autosomal dominant 56
  • p.Glu1413Ter Single submitter
  • p.Glu1503Ter Single submitter intellectual disability, autosomal dominant 56
  • p.Glu850fs Single submitter intellectual disability, autosomal dominant 56
  • p.Gly1202del Single submitter Inborn genetic diseases
  • p.Ile1129_Lys1130delinsLysLeuTer Single submitter
  • p.Ile114fs Single submitter Neurodevelopmental abnormality
  • p.Ile1632fs Single submitter Global developmental delay
  • p.Ile699fs Single submitter intellectual disability, autosomal dominant 56
  • p.Leu116fs Single submitter intellectual disability, autosomal dominant 56
  • p.Leu1217del Single submitter intellectual disability, autosomal dominant 56
  • p.Leu1480Pro Single submitter
  • p.Leu585fs Single submitter intellectual disability, autosomal dominant 56
  • p.Lys1535fs Single submitter intellectual disability, autosomal dominant 56
  • p.Lys1621fs Single submitter Inborn genetic diseases
  • p.Lys487fs Single submitter
  • p.Phe1471del Single submitter intellectual disability, autosomal dominant 56
  • p.Phe37fs Single submitter intellectual disability, autosomal dominant 56
  • p.Ser1080Ter Single submitter intellectual disability, autosomal dominant 56
  • p.Ser1494fs Single submitter
  • p.Ser694_Leu698del Single submitter Inborn genetic diseases
  • p.Trp113Ter Single submitter intellectual disability, autosomal dominant 56
  • p.Tyr608Ter Single submitter intellectual disability, autosomal dominant 56
  • p.Ala1052Asp No assertion criteria
  • p.Arg1204fs No assertion criteria intellectual disability, autosomal dominant 56
  • p.Glu133Ter No assertion criteria CLTC-related disorder
  • p.Met1302fs No assertion criteria intellectual disability, autosomal dominant 56

Conflicting classifications of pathogenicity 13

Benign 33

Benign/Likely benign 8

Likely benign 480

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

Uncertain significance 513

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