Sugi Variant

Sugi Variant/TRAPPC9

TRAPPC9 — 984 ClinVar variants

All ClinVar germline TRAPPC9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 330 flagged for review →

48 Pathogenic · 8 Pathogenic/Likely pathogenic · 24 Likely pathogenic · 49 Conflicting · 58 Benign · 36 Benign/Likely benign · 384 Likely benign · 377 Uncertain significance

Full TRAPPC9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 330

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 16

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

Predictors lean, ClinVar uncertain 253

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 253

Predictors split 60

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

All TRAPPC9 variants

Pathogenic 48

Pathogenic/Likely pathogenic 8

  • c.2700-2A>T Multiple submitters intellectual disability, autosomal recessive 13
  • c.3279+1G>A Multiple submitters intellectual disability, autosomal recessive 13
  • c.-204C>T Multiple submitters
  • p.Arg472Ter Multiple submitters Inborn genetic diseases
  • p.Arg51Ter Multiple submitters intellectual disability, autosomal recessive 13
  • p.Glu952Ter Multiple submitters intellectual disability, autosomal recessive 13
  • p.Lys513Ter Multiple submitters
  • p.Trp92fs Multiple submitters TRAPPC9-related disorder

Likely pathogenic 24

  • c.2811-1G>A Multiple submitters TRAPPC9-related disorder
  • c.1623-1G>A Single submitter intellectual disability, autosomal recessive 13
  • c.1768+1G>A Single submitter
  • c.1981+1G>A Single submitter intellectual disability, autosomal recessive 13
  • c.1982-1G>A Single submitter Inborn genetic diseases
  • c.2278+1G>T Single submitter
  • c.2432-1G>A Single submitter
  • c.2810+1G>A Single submitter
  • c.2964+2T>C Single submitter
  • c.731-2A>C Single submitter
  • c.-243C>T Single submitter
  • p.Ala412Thr Single submitter
  • p.Ala939fs Single submitter intellectual disability, autosomal recessive 13
  • p.Gln725Ter Single submitter intellectual disability, autosomal recessive 13
  • p.Glu773fs Single submitter TRAPPC9-related disorder
  • p.Glu996fs Single submitter congenital nervous system disorder
  • p.Ile691fs Single submitter intellectual disability, autosomal recessive 13
  • p.Lys103Ter Single submitter intellectual disability, autosomal recessive 13
  • p.Lys315fs Single submitter
  • p.Tyr643fs Single submitter intellectual disability, autosomal recessive 13
  • p.Ile349fs No assertion criteria TRAPPC9-related disorder
  • p.Lys964Glu No assertion criteria intellectual disability, autosomal recessive 13 ⚠
  • p.Ser559fs No assertion criteria intellectual disability, autosomal recessive 13
  • p.Val41fs No assertion criteria intellectual disability, autosomal recessive 13

Conflicting classifications of pathogenicity 49

Benign 58

Benign/Likely benign 36

  • c.1982-20A>C Multiple submitters
  • c.2557-13del Multiple submitters
  • c.2557-13dup Multiple submitters
  • c.2811-5C>T Multiple submitters Inborn genetic diseases
  • c.3279+4C>T Multiple submitters Inborn genetic diseases
  • c.584+19C>T Multiple submitters
  • c.-108A>G Multiple submitters Inborn genetic diseases
  • c.-11+10G>A Multiple submitters intellectual disability, autosomal recessive 13
  • c.-135A>G Multiple submitters Inborn genetic diseases
  • c.-73G>C Multiple submitters intellectual disability, autosomal recessive 13
  • p.Ala133= Multiple submitters Inborn genetic diseases
  • p.Ala405= Multiple submitters
  • p.Ala693= Multiple submitters
  • p.Arg1029= Multiple submitters
  • p.Asn1004= Multiple submitters Inborn genetic diseases
  • p.Asn66= Multiple submitters Inborn genetic diseases
  • p.Asp1023= Multiple submitters Inborn genetic diseases
  • p.Gly119= Multiple submitters Inborn genetic diseases
  • p.Gly933= Multiple submitters Inborn genetic diseases
  • p.Gly933Ser Multiple submitters Inborn genetic diseases
  • p.Ile152= Multiple submitters Inborn genetic diseases
  • p.Lys185= Multiple submitters Inborn genetic diseases
  • p.Phe1083= Multiple submitters Inborn genetic diseases
  • p.Phe486= Multiple submitters Inborn genetic diseases
  • p.Pro1130= Multiple submitters Inborn genetic diseases
  • p.Ser1097= Multiple submitters Inborn genetic diseases
  • p.Ser623= Multiple submitters Inborn genetic diseases
  • p.Thr622= Multiple submitters Inborn genetic diseases
  • p.Thr914= Multiple submitters Inborn genetic diseases
  • p.Tyr1075= Multiple submitters Inborn genetic diseases
  • p.Tyr138= Multiple submitters Inborn genetic diseases
  • p.Tyr388= Multiple submitters Inborn genetic diseases
  • p.Tyr469= Multiple submitters Inborn genetic diseases
  • p.Val1055Ile Multiple submitters Inborn genetic diseases
  • p.Val3Ile Multiple submitters Inborn genetic diseases
  • p.Val565Met Multiple submitters Inborn genetic diseases

Likely benign 384

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

Uncertain significance 377

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