Sugi Variant

Sugi Variant/PAX2

PAX2 — 655 ClinVar variants

All ClinVar germline PAX2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 216 flagged for review →

55 Pathogenic · 8 Pathogenic/Likely pathogenic · 75 Likely pathogenic · 23 Conflicting · 37 Benign · 10 Benign/Likely benign · 183 Likely benign · 264 Uncertain significance

Full PAX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 216

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 11

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

Predictors lean, ClinVar uncertain 125

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

Predictors split 80

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

All PAX2 variants

Pathogenic 55

  • c.792+2T>C Multiple submitters PAX2-Related Disorder
  • p.Arg104Ter Multiple submitters PAX2-Related Disorder
  • p.Arg115Ter Multiple submitters renal coloboma syndrome
  • p.Arg140Trp Multiple submitters PAX2-Related Disorder
  • p.Arg229Ter Multiple submitters PAX2-Related Disorder
  • p.Tyr302Ter Multiple submitters renal coloboma syndrome
  • p.Val26fs Multiple submitters renal coloboma syndrome
  • c.213-2A>G Single submitter renal coloboma syndrome
  • c.34_43+26delinsTGT Single submitter
  • c.410+1G>A Single submitter
  • c.43+1G>A Single submitter renal coloboma syndrome
  • c.43+1G>C Single submitter focal segmental glomerulosclerosis 7
  • c.497-1G>A Single submitter renal coloboma syndrome
  • c.756_792+4del Single submitter renal coloboma syndrome
  • c.*7C>A Single submitter renal coloboma syndrome
  • p.Ala111Thr Single submitter
  • p.Arg137Ter Single submitter renal coloboma syndrome
  • p.Arg40fs Single submitter
  • p.Gln144Ter Single submitter focal segmental glomerulosclerosis 7
  • p.Gln22fs Single submitter
  • p.Gln300fs Single submitter Inborn genetic diseases
  • p.Gln39fs Single submitter renal coloboma syndrome
  • p.Glu113Ter Single submitter focal segmental glomerulosclerosis 7
  • p.Glu121Ter Single submitter focal segmental glomerulosclerosis 7
  • p.Glu263Ter Single submitter PAX2-Related Disorder
  • p.Glu267Ter Single submitter renal coloboma syndrome
  • p.Glu74Ter Single submitter focal segmental glomerulosclerosis 7
  • p.Gly183fs Single submitter focal segmental glomerulosclerosis 7
  • p.Gly63Ser Single submitter
  • p.Gly76fs Single submitter focal segmental glomerulosclerosis 7
  • p.Gly81fs Single submitter focal segmental glomerulosclerosis 7
  • p.Gly85Asp Single submitter renal coloboma syndrome
  • p.Ile123fs Single submitter
  • p.Ile83delinsArgValTer Single submitter focal segmental glomerulosclerosis 7
  • p.Leu270fs Single submitter focal segmental glomerulosclerosis 7
  • p.Leu33fs Single submitter focal segmental glomerulosclerosis 7
  • p.Pro251fs Single submitter renal coloboma syndrome
  • p.Pro271fs Single submitter focal segmental glomerulosclerosis 7
  • p.Pro88Arg Single submitter focal segmental glomerulosclerosis 7
  • p.Ser131fs Single submitter coloboma
  • p.Ser262Ter Single submitter renal coloboma syndrome
  • p.Ser77fs Single submitter renal coloboma syndrome
  • p.Thr128fs Single submitter focal segmental glomerulosclerosis 7
  • p.Trp112fs Single submitter focal segmental glomerulosclerosis 7
  • p.Tyr250Ter Single submitter focal segmental glomerulosclerosis 7
  • p.Tyr318Ter Single submitter renal coloboma syndrome
  • p.Val82fs Single submitter
  • p.Arg71Thr No assertion criteria Papillorenal syndrome with macular abnormalities
  • p.Asn188fs No assertion criteria renal coloboma syndrome
  • p.Gln236Ter No assertion criteria renal coloboma syndrome
  • p.Gly189Arg No assertion criteria focal segmental glomerulosclerosis 7
  • p.Gly210fs No assertion criteria renal coloboma syndrome
  • p.Leu241fs No assertion criteria PAX2-Related Disorder
  • p.Leu44fs No assertion criteria renal coloboma syndrome
  • p.Tyr73Ter No assertion criteria inherited retinal dystrophy

Pathogenic/Likely pathogenic 8

  • c.212+1G>T Multiple submitters focal segmental glomerulosclerosis 7
  • p.Gln264fs Multiple submitters focal segmental glomerulosclerosis 7
  • p.Glu74_Thr75dup Multiple submitters focal segmental glomerulosclerosis 7
  • p.Gly162fs Multiple submitters renal coloboma syndrome
  • p.Gly76Ser Multiple submitters renal coloboma syndrome
  • p.Gly84Ser Multiple submitters PAX2-Related Disorder
  • p.Pro80Leu Multiple submitters Autosomal dominant PAX2-related disorders
  • p.Ser297Ter Multiple submitters Inborn genetic diseases

Likely pathogenic 75

  • c.213-8C>A Multiple submitters Autosomal dominant PAX2-related disorders
  • p.Gly24Val Multiple submitters focal segmental glomerulosclerosis 7
  • p.Gly25Glu Multiple submitters focal segmental glomerulosclerosis 7
  • p.Gly76Arg Multiple submitters PAX2-Related Disorder
  • p.Leu69Pro Multiple submitters congenital anomalies of kidney and urinary tract 1
  • p.Pro290fs Multiple submitters focal segmental glomerulosclerosis 7
  • p.Pro80Gln Multiple submitters focal segmental glomerulosclerosis 7
  • c.1022-1G>A Single submitter focal segmental glomerulosclerosis 7
  • c.1109-2A>G Single submitter renal coloboma syndrome
  • c.43+1G>T Single submitter focal segmental glomerulosclerosis 7
  • c.43+2dup Single submitter PAX2-Related Disorder
  • c.43+3_43+18del Single submitter PAX2-Related Disorder
  • c.43+5G>T Single submitter
  • c.44-2A>G Single submitter focal segmental glomerulosclerosis 7
  • c.617-1G>T Single submitter congenital anomalies of kidney and urinary tract 1
  • c.793-1G>A Single submitter renal coloboma syndrome
  • c.919+1G>A Single submitter focal segmental glomerulosclerosis 7
  • p.Ala120fs Single submitter focal segmental glomerulosclerosis 7
  • p.Arg140Gln Single submitter
  • p.Arg140Leu Single submitter renal coloboma syndrome
  • p.Arg31Pro Single submitter focal segmental glomerulosclerosis 7
  • p.Arg31Trp Single submitter focal segmental glomerulosclerosis 7
  • p.Arg38fs Single submitter
  • p.Arg50Gly Single submitter Inborn genetic diseases
  • p.Arg50Trp Single submitter renal coloboma syndrome
  • p.Arg59Trp Single submitter focal segmental glomerulosclerosis 7
  • p.Arg71Gly Single submitter renal coloboma syndrome
  • p.Arg71Met Single submitter focal segmental glomerulosclerosis 7
  • p.Asn106fs Single submitter renal coloboma syndrome
  • p.Asn179fs Single submitter renal coloboma syndrome
  • p.Asp125delinsGlyGlyHisLeuTer Single submitter renal coloboma syndrome
  • p.Asp35fs Single submitter
  • p.Cys52fs Single submitter renal coloboma syndrome
  • p.Gln255Ter Single submitter congenital anomalies of kidney and urinary tract 1
  • p.Gln300Ter Single submitter PAX2-Related Disorder
  • p.Gln39Ter Single submitter PAX2-Related Disorder
  • p.Gln57Ter Single submitter focal segmental glomerulosclerosis 7
  • p.Glu291Ter Single submitter renal coloboma syndrome
  • p.Gly24Arg Single submitter focal segmental glomerulosclerosis 7
  • p.Gly24Trp Single submitter renal coloboma syndrome
  • p.Gly328Val Single submitter congenital anomalies of kidney and urinary tract 1
  • p.Gly76Asp Single submitter focal segmental glomerulosclerosis 7
  • p.Gly85Cys Single submitter focal segmental glomerulosclerosis 7
  • p.His321fs Single submitter focal segmental glomerulosclerosis 7
  • p.His321Ter Single submitter focal segmental glomerulosclerosis 7
  • p.Ile165fs Single submitter renal coloboma syndrome
  • p.Ile193fs Single submitter renal hypoplasia
  • p.Ile68fs Single submitter focal segmental glomerulosclerosis 7
  • p.Ile78Met Single submitter renal coloboma syndrome
  • p.Leu33Val Single submitter focal segmental glomerulosclerosis 7
  • p.Lys281fs Single submitter renal coloboma syndrome
  • p.Phe10fs Single submitter focal segmental glomerulosclerosis 7
  • p.Pro107fs Single submitter
  • p.Pro130Arg Single submitter renal coloboma syndrome
  • p.Pro32Thr Single submitter PAX2-Related Disorder
  • p.Ser168fs Single submitter PAX2-Related Disorder
  • p.Ser282Ter Single submitter focal segmental glomerulosclerosis 7
  • p.Thr75Ile Single submitter
  • p.Tyr318fs Single submitter focal segmental glomerulosclerosis 7
  • p.Tyr73His Single submitter renal coloboma syndrome
  • p.Val244fs Single submitter focal segmental glomerulosclerosis 7
  • c.213-1_225delGGTACTACGAGACC No assertion criteria cystic kidney disease
  • c.497-1G>T No assertion criteria renal coloboma syndrome
  • p.Arg247fs No assertion criteria PAX2-Related Disorder
  • p.Arg38Lys No assertion criteria
  • p.Arg56Trp No assertion criteria focal segmental glomerulosclerosis 7
  • p.Gln145Ter No assertion criteria
  • p.Glu74fs No assertion criteria renal coloboma syndrome
  • p.Gly298fs No assertion criteria renal coloboma syndrome
  • p.Gly85Val No assertion criteria focal segmental glomerulosclerosis
  • p.Lys89Ter No assertion criteria
  • p.Pro130Ser No assertion criteria nephrotic syndrome
  • p.Ser61Ile No assertion criteria PAX2-Related Disorder
  • p.Thr92Met No assertion criteria steroid-resistant nephrotic syndrome
  • p.Val158fs No assertion criteria renal coloboma syndrome

Conflicting classifications of pathogenicity 23

Benign 37

Benign/Likely benign 10

  • c.1021+193G>A Multiple submitters focal segmental glomerulosclerosis 7
  • c.212+12G>A Multiple submitters focal segmental glomerulosclerosis 7
  • c.213-5C>T Multiple submitters focal segmental glomerulosclerosis 7
  • c.213-8C>T Multiple submitters renal coloboma syndrome
  • c.43+13G>T Multiple submitters renal coloboma syndrome
  • c.920-12G>A Multiple submitters focal segmental glomerulosclerosis 7
  • p.Gln353Pro Multiple submitters focal segmental glomerulosclerosis 7
  • p.His321= Multiple submitters renal coloboma syndrome
  • p.Leu273= Multiple submitters renal coloboma syndrome
  • p.Ser282= Multiple submitters renal coloboma syndrome

Likely benign 183

Uncertain significance 264