Sugi Variant

Sugi Variant/PRUNE1

PRUNE1 — 136 ClinVar variants

All ClinVar germline PRUNE1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 42 flagged for review →

14 Pathogenic · 4 Pathogenic/Likely pathogenic · 8 Likely pathogenic · 2 Conflicting · 10 Benign · 2 Benign/Likely benign · 53 Likely benign · 43 Uncertain significance

Full PRUNE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 42

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 1

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

Predictors lean, ClinVar uncertain 16

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

Predictors split 25

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

All PRUNE1 variants

Pathogenic 14

  • c.132+2T>C Multiple submitters neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Ala149fs Single submitter neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Ala221fs Single submitter Inborn genetic diseases
  • p.Arg297Trp Single submitter neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Asp3fs Single submitter Inborn genetic diseases
  • p.Gln238Ter Single submitter
  • p.Glu131fs Single submitter neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Tyr242fs Single submitter
  • p.Tyr254Ter Single submitter neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Tyr95Ter Single submitter
  • p.Cys180Ter No assertion criteria neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Leu172Pro No assertion criteria neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Leu18fs No assertion criteria neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Pro54Thr No assertion criteria neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies

Pathogenic/Likely pathogenic 4

  • p.Arg128Gln Multiple submitters neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies ⚠
  • p.Arg66Ter Multiple submitters neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Asp106Asn Multiple submitters neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Asp30Asn Multiple submitters neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies

Likely pathogenic 8

  • c.39+1G>T Single submitter
  • c.521-2A>G Single submitter neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
  • p.Gly174Ter Single submitter Abnormal brain morphology
  • p.His127Arg Single submitter
  • p.Leu270Pro Single submitter
  • p.Ala160fs No assertion criteria
  • p.Arg128Ter No assertion criteria PRUNE1-related disorder
  • p.Met1Ile No assertion criteria neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies

Conflicting classifications of pathogenicity 2

  • p.Ile214Val Single submitter ⚠
  • p.Tyr339Cys Single submitter neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies ⚠

Benign 10

Benign/Likely benign 2

Likely benign 53

Uncertain significance 43