OPHN1 — 553 ClinVar variants

All ClinVar germline OPHN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 224 flagged for review →

42 Pathogenic · 1 Pathogenic/Likely pathogenic · 44 Likely pathogenic · 25 Conflicting · 55 Benign · 28 Benign/Likely benign · 118 Likely benign · 240 Uncertain significance

Full OPHN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 224

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 3

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

Predictors agree, ClinVar conflicts 13

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

Predictors lean, ClinVar uncertain 150

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

Predictors split 58

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

All OPHN1 variants

Pathogenic 42

  • c.1138+1G>A Multiple submitters X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Arg497Ter Multiple submitters X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Arg597Ter Multiple submitters
  • p.Gln416Ter Multiple submitters X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.1026-2A>G Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.154+2T>C Single submitter
  • c.1834+1G>T Single submitter
  • c.2159_2171delGGGATGCTGACAG Single submitter
  • c.250+1G>T Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.312+1del Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.313_326del Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.384+1G>A Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.597+2T>C Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.702+1G>A Single submitter
  • c.932_933+3delinsTA Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Arg409Cys Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Asn422fs Single submitter
  • p.Cys321fs Single submitter
  • p.Gln166Ter Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Gln258fs Single submitter
  • p.Gln258Ter Single submitter
  • p.Glu190Ter Single submitter
  • p.Glu276Ter Single submitter
  • p.Glu381Ter Single submitter Inborn genetic diseases
  • p.His3fs Single submitter
  • p.Ile337fs Single submitter
  • p.Leu76fs Single submitter
  • p.Lys392fs Single submitter
  • p.Lys683fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Met300fs Single submitter
  • p.Phe333fs Single submitter
  • p.Phe704fs Single submitter Inborn genetic diseases
  • p.Ser571fs Single submitter
  • p.Tyr271Ter Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Tyr408Ter Single submitter
  • c.2159-1G>C No assertion criteria X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Gln349Ter No assertion criteria Seizure
  • p.Gln62Ter No assertion criteria X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Ile527fs No assertion criteria X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Lys251fs No assertion criteria X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Val215fs No assertion criteria X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Val57Asp No assertion criteria X-linked intellectual disability-cerebellar hypoplasia syndrome

Pathogenic/Likely pathogenic 1

  • p.Lys156fs Multiple submitters congenital nervous system disorder

Likely pathogenic 44

  • c.1202-1G>A Multiple submitters X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.155-2A>C Multiple submitters X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Arg243Trp Multiple submitters OPHN1-related disorder ⚠
  • p.Thr326Met Multiple submitters X-linked intellectual disability-cerebellar hypoplasia syndrome ⚠
  • c.1025+2T>C Single submitter
  • c.1105-1G>T Single submitter
  • c.1277-1G>C Single submitter
  • c.1362-2A>G Single submitter Inborn genetic diseases
  • c.1420+1G>A Single submitter
  • c.1421-2A>G Single submitter OPHN1-related disorder
  • c.1526+1G>A Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.1526+2T>G Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.154+1G>T Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.155-1G>A Single submitter
  • c.597+1del Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.598-1G>C Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.702+1G>T Single submitter OPHN1-related disorder
  • c.702+4A>G Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.702+4A>T Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Ala472fs Single submitter
  • p.Arg454Lys Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Asp679Asn Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome ⚠
  • p.Cys393Arg Single submitter
  • p.Cys749fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Gln311Ter Single submitter OPHN1-related disorder
  • p.Glu353fs Single submitter OPHN1-related disorder
  • p.Glu361fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Glu379Ter Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Glu468Ter Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Glu537fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Gly529Glu Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Ile485fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Ile771fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Leu204fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Leu249Pro Single submitter isolated cerebellar hypoplasia/agenesis
  • p.Leu314fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Lys419fs Single submitter
  • p.Pro459Thr Single submitter
  • p.Ser55Phe Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome ⚠
  • p.Ser703fs Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • p.Tyr452Ter Single submitter X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.1105-13_1109del No assertion criteria X-linked intellectual disability-cerebellar hypoplasia syndrome
  • c.934-2del No assertion criteria OPHN1-related disorder
  • p.Glu98Ter No assertion criteria X-linked intellectual disability-cerebellar hypoplasia syndrome

Conflicting classifications of pathogenicity 25

Benign 55

Benign/Likely benign 28

Likely benign 118

Uncertain significance 240