Sugi Variant

Sugi Variant/TPP1

TPP1 — 1211 ClinVar variants

All ClinVar germline TPP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 423 flagged for review →

89 Pathogenic · 41 Pathogenic/Likely pathogenic · 79 Likely pathogenic · 63 Conflicting · 22 Benign · 25 Benign/Likely benign · 449 Likely benign · 443 Uncertain significance

Full TPP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 423

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 5

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

Predictors agree, ClinVar conflicts 36

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

Predictors lean, ClinVar uncertain 271

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 271

Predictors split 111

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

All TPP1 variants

Pathogenic 89

Pathogenic/Likely pathogenic 41

  • c.1075+2T>C Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • c.1076-2A>G Multiple submitters TPP1-related disorder
  • c.1363_1425+9del Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.1551+1G>A Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.1551+1G>C Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • c.1551+1G>T Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.380+5G>A Multiple submitters neuronal ceroid lipofuscinosis
  • c.509-1G>T Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.90del Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Arg127Gln Multiple submitters neuronal ceroid lipofuscinosis ⚠
  • p.Arg206His Multiple submitters neuronal ceroid lipofuscinosis 2 ⚠
  • p.Arg339Trp Multiple submitters TPP1-related disorder
  • p.Arg350Trp Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Arg447His Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • p.Arg497fs Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • p.Asn286Ser Multiple submitters TPP1-related disorder ⚠
  • p.Cys365Arg Multiple submitters TPP1-related disorder
  • p.Gln109Ter Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Gln161Ter Multiple submitters neuronal ceroid lipofuscinosis
  • p.Gln263Ter Multiple submitters neuronal ceroid lipofuscinosis
  • p.Gln278Arg Multiple submitters neuronal ceroid lipofuscinosis
  • p.Gln338Glu Multiple submitters neuronal ceroid lipofuscinosis 2 ⚠
  • p.Gln509Ter Multiple submitters TPP1-related disorder
  • p.Gln75= Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • p.Glu343Lys Multiple submitters neuronal ceroid lipofuscinosis
  • p.Glu44Ter Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Gly389Glu Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Gly473Arg Multiple submitters TPP1-related disorder
  • p.Gly501fs Multiple submitters Inborn genetic diseases
  • p.Gly77Arg Multiple submitters TPP1-related disorder ⚠
  • p.His491fs Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Leu49fs Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • p.Leu500fs Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Pro202Leu Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Ser113fs Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • p.Ser475Leu Multiple submitters neuronal ceroid lipofuscinosis
  • p.Ser62fs Multiple submitters neuronal ceroid lipofuscinosis
  • p.Thr148fs Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Val466fs Multiple submitters neuronal ceroid lipofuscinosis
  • p.Val466Gly Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Val518Ter Multiple submitters

Likely pathogenic 79

Conflicting classifications of pathogenicity 63

Benign 22

  • c.1075+28T>C Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • c.1075+42C>T Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • c.1146-107C>G Multiple submitters
  • c.1426-78T>C Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.381-10dup Multiple submitters neuronal ceroid lipofuscinosis
  • c.508+26T>A Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • c.508+31G>A Multiple submitters
  • c.687+32T>C Multiple submitters autosomal recessive spinocerebellar ataxia 7
  • c.688-45G>A Multiple submitters
  • c.887-6del Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.887-7_887-6del Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.-122T>C Multiple submitters
  • c.-238T>C Multiple submitters
  • c.*1118G>C Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.*1588C>T Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.*1628G>A Multiple submitters neuronal ceroid lipofuscinosis 2
  • c.*71G>A Multiple submitters neuronal ceroid lipofuscinosis 2
  • p.Glu147= Multiple submitters Inborn genetic diseases
  • p.Gly514= Multiple submitters Inborn genetic diseases
  • c.90-12dup Single submitter
  • c.-40T>C Single submitter
  • c.*241T>C Single submitter neuronal ceroid lipofuscinosis 2

Benign/Likely benign 25

Likely benign 449

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

Uncertain significance 443

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