Sugi Variant

Sugi Variant/P4HTM

P4HTM — 121 ClinVar variants

All ClinVar germline P4HTM variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 63 flagged for review →

5 Pathogenic · 1 Pathogenic/Likely pathogenic · 7 Likely pathogenic · 3 Conflicting · 1 Benign/Likely benign · 24 Likely benign · 80 Uncertain significance

Full P4HTM gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 63

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 1

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

Predictors lean, ClinVar uncertain 49

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

Predictors split 12

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

All P4HTM variants

Pathogenic 5

  • p.Trp220Ter Multiple submitters hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities
  • c.1074-11del Single submitter
  • p.Arg358His Single submitter P4HTM-related disorders
  • p.Gly217Ter Single submitter
  • p.Gln471Ter No assertion criteria hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities

Pathogenic/Likely pathogenic 1

  • p.Pro413Leu Multiple submitters intellectual disability

Likely pathogenic 7

  • c.1165_1166del Single submitter hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities
  • c.436+1G>T Single submitter hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities
  • p.Arg410Ser Single submitter ⚠
  • p.Glu312Lys Single submitter hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities ⚠
  • p.Leu425Pro Single submitter Poirier-Bienvenu neurodevelopmental syndrome
  • p.Thr361Ile Single submitter hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities
  • p.Asn274fs No assertion criteria hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities

Conflicting classifications of pathogenicity 3

Benign/Likely benign 1

Likely benign 24

Uncertain significance 80