Sugi Variant

Sugi Variant/TCOF1

TCOF1 — 1137 ClinVar variants

All ClinVar germline TCOF1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 441 flagged for review →

151 Pathogenic · 7 Pathogenic/Likely pathogenic · 70 Likely pathogenic · 70 Conflicting · 47 Benign · 64 Benign/Likely benign · 300 Likely benign · 428 Uncertain significance

Full TCOF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 441

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 2

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

Predictors agree, ClinVar conflicts 58

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

Predicted LoF vs a conflicting call 1

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 320

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 320

Predictors split 60

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

All TCOF1 variants

Pathogenic 151

Pathogenic/Likely pathogenic 7

  • p.Ala1282fs Multiple submitters TCOF1-related disorder
  • p.Arg288Ter Multiple submitters Treacher Collins syndrome 1
  • p.Asp483fs Multiple submitters Treacher Collins syndrome 1
  • p.Glu1457fs Multiple submitters Treacher Collins syndrome 1
  • p.Lys1448fs Multiple submitters Treacher Collins syndrome 1
  • p.Lys1453fs Multiple submitters Treacher Collins syndrome 1
  • p.Ser339Ter Multiple submitters Treacher Collins syndrome 1

Likely pathogenic 70

  • p.Glu268Ter Multiple submitters
  • p.Leu1130fs Multiple submitters Treacher Collins syndrome 1
  • c.109-2A>G Single submitter Treacher Collins syndrome 1
  • c.109-3del Single submitter Treacher Collins syndrome 1
  • c.2142+2T>C Single submitter Treacher Collins syndrome 1
  • c.304+1G>T Single submitter Treacher Collins syndrome 1
  • c.378+1G>A Single submitter Treacher Collins syndrome 1
  • c.640-2del Single submitter Treacher Collins syndrome 1
  • p.Ala1035fs Single submitter Treacher Collins syndrome 1
  • p.Ala184fs Single submitter Treacher Collins syndrome 1
  • p.Ala283fs Single submitter Treacher Collins syndrome 1
  • p.Ala797fs Single submitter Treacher Collins syndrome 1
  • p.Arg1018fs Single submitter Treacher Collins syndrome 1
  • p.Asp1227fs Single submitter Treacher Collins syndrome 1
  • p.Asp1452fs Single submitter
  • p.Asp247fs Single submitter Treacher Collins syndrome 1
  • p.Asp48fs Single submitter Treacher Collins syndrome 1
  • p.Gln1088fs Single submitter Emery-Dreifuss muscular dystrophy 4, autosomal dominant
  • p.Gln1252fs Single submitter Treacher Collins syndrome 1
  • p.Gln1286Ter Single submitter Treacher Collins syndrome 1
  • p.Gln1298fs Single submitter Treacher Collins syndrome 1
  • p.Gln195Ter Single submitter Treacher Collins syndrome 1
  • p.Gln467fs Single submitter Treacher Collins syndrome 1
  • p.Gln496fs Single submitter TCOF1-related disorder
  • p.Gln789fs Single submitter Treacher Collins syndrome 1
  • p.Gln789Ter Single submitter TCOF1-related disorder
  • p.Glu1193Ter Single submitter TCOF1-related disorder
  • p.Glu1375Ter Single submitter Treacher Collins syndrome 1
  • p.Gly35fs Single submitter TCOF1-related disorder
  • p.Gly685fs Single submitter Treacher Collins syndrome 1
  • p.Gly869fs Single submitter TCOF1-related disorder
  • p.Gly933fs Single submitter Treacher Collins syndrome 1
  • p.Lys1330fs Single submitter Treacher Collins syndrome 1
  • p.Lys1415Ter Single submitter Treacher Collins syndrome 1
  • p.Lys458Ter Single submitter TCOF1-related disorder
  • p.Lys732fs Single submitter Treacher Collins syndrome 1
  • p.Pro1108fs Single submitter TCOF1-related disorder
  • p.Pro1131fs Single submitter Treacher Collins syndrome 1
  • p.Pro240fs Single submitter TCOF1-related disorder
  • p.Pro43Leu Single submitter TCOF1-related disorder
  • p.Pro639fs Single submitter Treacher Collins syndrome 1
  • p.Ser1146fs Single submitter TCOF1-related disorder
  • p.Ser1268fs Single submitter TCOF1-related disorder
  • p.Ser1379fs Single submitter Treacher Collins syndrome 1
  • p.Ser1435fs Single submitter
  • p.Ser365Ter Single submitter Treacher Collins syndrome 1
  • p.Ser414fs Single submitter TCOF1-related disorder
  • p.Ser535fs Single submitter Treacher Collins syndrome 1
  • p.Ser617fs Single submitter Treacher Collins syndrome 1
  • p.Ser769Ter Single submitter TCOF1-related disorder
  • p.Ser877fs Single submitter Treacher Collins syndrome 1
  • p.Thr739fs Single submitter TCOF1-related disorder
  • p.Trp1343fs Single submitter Treacher Collins syndrome 1
  • p.Trp53Ter Single submitter Treacher Collins syndrome 1
  • p.Tyr50Cys Single submitter Treacher Collins syndrome 1 ⚠
  • p.Val212fs Single submitter
  • p.Val30Gly Single submitter Treacher Collins syndrome 1
  • p.Val466fs Single submitter Treacher Collins syndrome 1
  • c.108+1G>A No assertion criteria TCOF1-related disorder
  • p.Ala1238fs No assertion criteria Treacher Collins syndrome 1
  • p.Asn150fs No assertion criteria Treacher Collins syndrome 1
  • p.Glu1454fs No assertion criteria Treacher Collins syndrome 1
  • p.Glu340fs No assertion criteria Treacher Collins syndrome 1
  • p.Glu569Lys No assertion criteria Treacher Collins syndrome 1 ⚠
  • p.Gly1016Ser No assertion criteria Treacher Collins syndrome 1 ⚠
  • p.Gly385fs No assertion criteria TCOF1-related disorder
  • p.Gly520fs No assertion criteria TCOF1-related disorder
  • p.Lys1279fs No assertion criteria TCOF1-related disorder
  • p.Lys1476Ter No assertion criteria Treacher Collins syndrome 1
  • p.Val659fs No assertion criteria TCOF1-related disorder

Conflicting classifications of pathogenicity 70

Benign 47

Benign/Likely benign 64

  • c.1083+12G>A Multiple submitters Treacher Collins syndrome 1
  • c.109-13T>C Multiple submitters Treacher Collins syndrome 1
  • c.1278+14G>A Multiple submitters Treacher Collins syndrome 1
  • c.1488+16G>A Multiple submitters Treacher Collins syndrome 1
  • c.1704+16G>A Multiple submitters Treacher Collins syndrome 1
  • c.1704+9C>T Multiple submitters Treacher Collins syndrome 1
  • c.2859+3389G>T Multiple submitters Treacher Collins syndrome 1
  • c.3047-20C>T Multiple submitters Treacher Collins syndrome 1
  • c.3518-3C>T Multiple submitters Treacher Collins syndrome 1
  • c.3604-14A>G Multiple submitters Treacher Collins syndrome 1
  • c.3604-3C>T Multiple submitters Treacher Collins syndrome 1
  • c.378+16T>C Multiple submitters Treacher Collins syndrome 1
  • c.3784+8A>G Multiple submitters Treacher Collins syndrome 1
  • c.4345+11G>A Multiple submitters Treacher Collins syndrome 1
  • p.Ala1198= Multiple submitters Treacher Collins syndrome 1
  • p.Ala1238Thr Multiple submitters Treacher Collins syndrome 1
  • p.Ala1391Val Multiple submitters Treacher Collins syndrome 1
  • p.Ala193= Multiple submitters Treacher Collins syndrome 1
  • p.Ala374Ser Multiple submitters Treacher Collins syndrome 1
  • p.Ala41Val Multiple submitters Treacher Collins syndrome 1
  • p.Ala427= Multiple submitters Treacher Collins syndrome 1
  • p.Ala433= Multiple submitters Treacher Collins syndrome 1
  • p.Ala464Thr Multiple submitters Inborn genetic diseases
  • p.Ala623Thr Multiple submitters Treacher Collins syndrome 1
  • p.Ala799Ser Multiple submitters Treacher Collins syndrome 1
  • p.Ala911Ser Multiple submitters
  • p.Ala948Ser Multiple submitters Treacher Collins syndrome 1
  • p.Arg667Gln Multiple submitters Treacher Collins syndrome 1
  • p.Asp1416= Multiple submitters Treacher Collins syndrome 1
  • p.Asp557= Multiple submitters Treacher Collins syndrome 1
  • p.Gln1113= Multiple submitters Treacher Collins syndrome 1
  • p.Glu1056= Multiple submitters Treacher Collins syndrome 1
  • p.Glu1471= Multiple submitters Treacher Collins syndrome 1
  • p.Glu175= Multiple submitters Treacher Collins syndrome 1
  • p.Gly276_Glu281del Multiple submitters Treacher Collins syndrome 1
  • p.Gly276Glu Multiple submitters Treacher Collins syndrome 1
  • p.Gly333= Multiple submitters Treacher Collins syndrome 1
  • p.Gly530= Multiple submitters Treacher Collins syndrome 1
  • p.Gly587= Multiple submitters Treacher Collins syndrome 1
  • p.His1170= Multiple submitters Treacher Collins syndrome 1
  • p.Ile575Val Multiple submitters Inborn genetic diseases
  • p.Leu572= Multiple submitters Treacher Collins syndrome 1
  • p.Lys1341= Multiple submitters Treacher Collins syndrome 1
  • p.Lys1367Gln Multiple submitters Treacher Collins syndrome 1
  • p.Lys1445del Multiple submitters Treacher Collins syndrome 1
  • p.Met1208Lys Multiple submitters Treacher Collins syndrome 1
  • p.Met512Thr Multiple submitters Treacher Collins syndrome 1
  • p.Pro434Ser Multiple submitters Inborn genetic diseases
  • p.Pro516Leu Multiple submitters Treacher Collins syndrome 1
  • p.Pro730Ser Multiple submitters Treacher Collins syndrome 1
  • p.Pro778Ser Multiple submitters Inborn genetic diseases
  • p.Pro921Leu Multiple submitters Treacher Collins syndrome 1
  • p.Ser1142= Multiple submitters Treacher Collins syndrome 1
  • p.Ser1146Arg Multiple submitters Treacher Collins syndrome 1
  • p.Ser178= Multiple submitters Treacher Collins syndrome 1
  • p.Ser343Asn Multiple submitters Treacher Collins syndrome 1 ⚠
  • p.Ser410Leu Multiple submitters Treacher Collins syndrome 1 ⚠
  • p.Ser696Arg Multiple submitters Treacher Collins syndrome 1 ⚠
  • p.Ser717= Multiple submitters Treacher Collins syndrome 1
  • p.Ser990= Multiple submitters Treacher Collins syndrome 1
  • p.Thr1180Ser Multiple submitters Treacher Collins syndrome 1
  • p.Thr1182= Multiple submitters Treacher Collins syndrome 1
  • p.Thr168Met Multiple submitters Treacher Collins syndrome 1
  • p.Thr210= Multiple submitters Treacher Collins syndrome 1

Likely benign 300

Uncertain significance 428

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