Sugi Variant

Sugi Variant/TRAPPC12

TRAPPC12 — 364 ClinVar variants

All ClinVar germline TRAPPC12 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 193 flagged for review →

12 Pathogenic · 1 Pathogenic/Likely pathogenic · 16 Likely pathogenic · 8 Conflicting · 24 Benign · 8 Benign/Likely benign · 90 Likely benign · 205 Uncertain significance

Full TRAPPC12 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 193

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 agree, ClinVar conflicts 7

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

Predictors lean, ClinVar uncertain 146

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

Predictors split 40

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

All TRAPPC12 variants

Pathogenic 12

  • c.1677+5G>A Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • c.1776+16C>A Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • c.1966-1G>A Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Gln149Ter Single submitter Inborn genetic diseases
  • p.Gln327Ter Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Gln32fs Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Glu121fs Single submitter Progressive childhood encephalopathy
  • p.Gly128fs Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Leu58fs Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Lys608Ter Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Phe227fs Single submitter Inborn genetic diseases
  • p.Ser376Ter Single submitter

Pathogenic/Likely pathogenic 1

  • p.Ala627Val Multiple submitters early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome

Likely pathogenic 16

  • p.Glu49fs Multiple submitters early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • c.1164+1G>T Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • c.1530+1G>A Single submitter Inborn genetic diseases
  • c.1604-1G>T Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • c.1678-2A>G Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • c.1965+4A>G Single submitter
  • c.1966-2A>G Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Arg402fs Single submitter TRAPPC12-related disorder
  • p.Asp84fs Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Gln284Ter Single submitter TRAPPC12-related disorder
  • p.Gly241fs Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Leu591fs Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Leu616fs Single submitter
  • p.Met66fs Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Pro19fs Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Glu121Ter No assertion criteria Severe hydrocephalus

Conflicting classifications of pathogenicity 8

  • p.Ala145Thr Single submitter Inborn genetic diseases ⚠
  • p.Arg266Ter Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Glu121Lys Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome ⚠
  • p.Glu9Gln Single submitter Inborn genetic diseases ⚠
  • p.Gly172Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly587Ser Single submitter ⚠
  • p.Ile482Thr Single submitter ⚠
  • p.Ser570Leu Single submitter Inborn genetic diseases ⚠

Benign 24

  • c.1164+3A>G Multiple submitters
  • c.1603+12G>A Multiple submitters
  • c.1777-15A>C Multiple submitters
  • c.1878-19A>T Multiple submitters
  • p.Ala144= Multiple submitters early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Asp173= Multiple submitters
  • p.Glu449= Multiple submitters
  • p.Gly415Glu Multiple submitters ⚠
  • p.Leu591= Multiple submitters early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Phe209= Multiple submitters
  • p.Phe227= Multiple submitters early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Phe727= Multiple submitters early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Pro245Ser Multiple submitters
  • p.Ser301Gly Multiple submitters early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • p.Ser414= Multiple submitters
  • p.Tyr461= Multiple submitters
  • p.Val719= Multiple submitters
  • c.1047+72_1047+73delinsCA Single submitter early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
  • c.1603+15C>G Single submitter
  • p.Ala59Thr Single submitter
  • p.Gln633= Single submitter
  • p.Pro312= Single submitter
  • p.Ser479= Single submitter
  • p.Val331= Single submitter

Benign/Likely benign 8

Likely benign 90

Uncertain significance 205