PHEX — 1390 ClinVar variants

All ClinVar germline PHEX variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 248 flagged for review →

591 Pathogenic · 62 Pathogenic/Likely pathogenic · 133 Likely pathogenic · 65 Conflicting · 93 Benign · 35 Benign/Likely benign · 141 Likely benign · 270 Uncertain significance

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

⚑ Evidence disagreements 248

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 6

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

Predictors agree, ClinVar conflicts 32

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

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 145

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

Predictors split 64

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

All PHEX variants

Pathogenic 591

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

Pathogenic/Likely pathogenic 62

  • c.118+1G>A Multiple submitters PHEX-related disorder
  • c.1302+1G>T Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.1482+1G>A Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.1482+2T>A Multiple submitters PHEX-related disorder
  • c.1482+3A>C Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.1586+5G>A Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.1645+1G>A Multiple submitters PHEX-related disorder
  • c.1700+5G>A Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.188-1G>C Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.1900-1G>A Multiple submitters
  • c.1965+1G>A Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.1966-1G>C Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.1966-1G>T Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.2070+1G>A Multiple submitters
  • c.349+1G>C Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.664-1G>A Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.732+1G>A Multiple submitters PHEX-related disorder
  • c.732+1G>T Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.733-1G>A Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.733-1G>C Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.933+1G>T Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.934-2A>G Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Ala469Glu Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Ala573Asp Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Ala653Asp Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Ala84Pro Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Arg567Pro Multiple submitters PHEX-related disorder ⚠
  • p.Asn723_Phe724insTer Multiple submitters
  • p.Asp349Gly Multiple submitters X-linked dominant hypophosphatemic rickets ⚠
  • p.Asp646His Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Cys693Ser Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Cys693Tyr Multiple submitters PHEX-related disorder
  • p.Cys733Phe Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Cys733Tyr Multiple submitters
  • p.Cys85Phe Multiple submitters PHEX-related disorder ⚠
  • p.Cys85Ser Multiple submitters X-linked dominant hypophosphatemic rickets ⚠
  • p.Gln197= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Gln706fs Multiple submitters
  • p.Gln714Ter Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Gln728Ter Multiple submitters PHEX-related disorder
  • p.Gly553Glu Multiple submitters
  • p.Gly572Asp Multiple submitters PHEX-related disorder
  • p.Gly572Ser Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Gly572Val Multiple submitters
  • p.Gly575Glu Multiple submitters PHEX-related disorder
  • p.Gly579Arg Multiple submitters PHEX-related disorder
  • p.Gly667Ter Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.His584Tyr Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Leu275Pro Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Leu650Pro Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Lys221= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Lys320del Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Met296fs Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Phe731fs Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Ser141Phe Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Thr509Pro Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Trp167Ter Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Trp520Ter Multiple submitters Hypophosphataemia or rickets
  • p.Trp88Ter Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Tyr346Cys Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Tyr625Ter Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Tyr657Cys Multiple submitters hypophosphatemic rickets

Likely pathogenic 133

Conflicting classifications of pathogenicity 65

Benign 93

Benign/Likely benign 35

  • c.1404+28dup Multiple submitters
  • c.1405-4del Multiple submitters
  • c.1482+16A>C Multiple submitters
  • c.1483-7T>C Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.1645+8C>T Multiple submitters
  • c.1769-20C>T Multiple submitters
  • c.187+9_187+10del Multiple submitters
  • c.663+8G>A Multiple submitters
  • c.849+3A>G Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.-108A>G Multiple submitters X-linked dominant hypophosphatemic rickets
  • c.*218A>C Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Ala147= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Arg127Gln Multiple submitters
  • p.Asn301= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Asn301His Multiple submitters ⚠
  • p.Asp211Asn Multiple submitters X-linked dominant hypophosphatemic rickets ⚠
  • p.Asp332= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Gln133= Multiple submitters
  • p.Glu96= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Gly28Ser Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.His487= Multiple submitters
  • p.Leu160= Multiple submitters
  • p.Lys280= Multiple submitters
  • p.Phe83= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Pro168= Multiple submitters
  • p.Pro479= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Ser163= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Ser336= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Thr129= Multiple submitters
  • p.Thr35= Multiple submitters
  • p.Thr461= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Thr679= Multiple submitters
  • p.Val169Met Multiple submitters
  • p.Val179= Multiple submitters X-linked dominant hypophosphatemic rickets
  • p.Val27= Multiple submitters X-linked dominant hypophosphatemic rickets

Likely benign 141

Uncertain significance 270