PAX5 — 494 ClinVar variants

All ClinVar germline PAX5 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 218 flagged for review →

2 Pathogenic · 13 Likely pathogenic · 7 Conflicting · 27 Benign · 10 Benign/Likely benign · 193 Likely benign · 242 Uncertain significance

Full PAX5 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 218

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 2

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

Predictors lean, ClinVar uncertain 157

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 157

Predictors split 59

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

All PAX5 variants

Pathogenic 2

  • p.Arg221Trp No assertion criteria neurodevelopmental disorder
  • p.Asp53His No assertion criteria neurodevelopmental disorder

Likely pathogenic 13

  • p.Ala322fs Multiple submitters PAX5-related disorder
  • c.46+1G>A Single submitter acute lymphoblastic leukemia
  • p.Ala45fs Single submitter acute lymphoblastic leukemia
  • p.Glu205Ter Single submitter acute lymphoblastic leukemia
  • p.Gly323Ter Single submitter acute lymphoblastic leukemia
  • p.Pro130Thr Single submitter acute lymphoblastic leukemia
  • p.Pro80Arg Single submitter acute lymphoblastic leukemia
  • p.Ser134Cys Single submitter acute lymphoblastic leukemia
  • p.Ser357_Trp358insTer Single submitter acute lymphoblastic leukemia
  • p.Trp358Ter Single submitter acute lymphoblastic leukemia
  • p.Val26fs Single submitter PAX5-related disorder
  • p.Val26Gly Single submitter acute lymphoblastic leukemia
  • p.Val90fs Single submitter acute lymphoblastic leukemia

Conflicting classifications of pathogenicity 7

  • c.780+4C>T Single submitter
  • p.Ala375= Single submitter PAX5-related disorder
  • p.Gly273= Single submitter Inborn genetic diseases
  • p.Gly85Arg Single submitter leukemia, acute lymphoblastic, susceptibility to, 3 ⚠
  • p.Ile78= Single submitter Inborn genetic diseases
  • p.Ser213Leu Single submitter leukemia, acute lymphoblastic, susceptibility to, 3 ⚠
  • p.Pro321His No assertion criteria neurodevelopmental disorder

Benign 27

Benign/Likely benign 10

Likely benign 193

  • c.1012+68C>G Multiple submitters
  • c.1013-7T>C Multiple submitters
  • c.1099+12C>T Multiple submitters
  • c.1099+13G>A Multiple submitters
  • c.1100-11G>T Multiple submitters
  • c.1100-12C>T Multiple submitters
  • c.46+8C>G Multiple submitters
  • c.780+33C>T Multiple submitters
  • c.781-16_781-15del Multiple submitters
  • c.910+9A>G Multiple submitters
  • c.*111C>T Multiple submitters
  • p.Ala266= Multiple submitters Inborn genetic diseases
  • p.Ala379= Multiple submitters Inborn genetic diseases
  • p.Ala383= Multiple submitters Inborn genetic diseases
  • p.Ala384= Multiple submitters Inborn genetic diseases
  • p.Arg104= Multiple submitters Inborn genetic diseases
  • p.Arg239= Multiple submitters Inborn genetic diseases
  • p.Arg31= Multiple submitters Inborn genetic diseases
  • p.Arg377= Multiple submitters Inborn genetic diseases
  • p.Asn210= Multiple submitters Inborn genetic diseases
  • p.Asn355= Multiple submitters Inborn genetic diseases
  • p.Asp275= Multiple submitters Inborn genetic diseases
  • p.Gly295= Multiple submitters Inborn genetic diseases
  • p.Ile289= Multiple submitters Inborn genetic diseases
  • p.Ile83= Multiple submitters Inborn genetic diseases
  • p.Leu234= Multiple submitters Inborn genetic diseases
  • p.Leu270= Multiple submitters Inborn genetic diseases
  • p.Leu274= Multiple submitters Inborn genetic diseases
  • p.Leu365= Multiple submitters Inborn genetic diseases
  • p.Pro207= Multiple submitters Inborn genetic diseases
  • p.Pro215= Multiple submitters Inborn genetic diseases
  • p.Pro258= Multiple submitters Inborn genetic diseases
  • p.Pro296= Multiple submitters Inborn genetic diseases
  • p.Pro313= Multiple submitters Inborn genetic diseases
  • p.Pro321= Multiple submitters Inborn genetic diseases
  • p.Pro330= Multiple submitters Inborn genetic diseases
  • p.Pro34= Multiple submitters Inborn genetic diseases
  • p.Pro369= Multiple submitters Inborn genetic diseases
  • p.Ser131= Multiple submitters Inborn genetic diseases
  • p.Ser213= Multiple submitters Inborn genetic diseases
  • p.Ser269= Multiple submitters Inborn genetic diseases
  • p.Ser342= Multiple submitters Inborn genetic diseases
  • p.Ser373= Multiple submitters Inborn genetic diseases
  • p.Thr108= Multiple submitters Inborn genetic diseases
  • p.Val236= Multiple submitters Inborn genetic diseases
  • p.Val319= Multiple submitters Inborn genetic diseases
  • p.Val96= Multiple submitters Inborn genetic diseases
  • c.1012+16C>T Single submitter
  • c.1012+62T>C Single submitter
  • c.1013-3C>T Single submitter
  • c.1013-5C>A Single submitter
  • c.1013-6A>G Single submitter leukemia, acute lymphoblastic, susceptibility to, 3
  • c.1099+19C>T Single submitter
  • c.1100-73G>T Single submitter
  • c.212+17G>A Single submitter
  • c.212+245A>G Single submitter
  • c.213-10T>G Single submitter
  • c.213-19C>T Single submitter
  • c.213-7G>A Single submitter
  • c.410+11C>T Single submitter
  • c.410+12G>T Single submitter
  • c.410+17T>C Single submitter
  • c.47-17T>C Single submitter
  • c.47-263A>G Single submitter
  • c.605-228A>G Single submitter
  • c.780+15G>A Single submitter
  • c.780+18C>T Single submitter
  • c.780+45C>T Single submitter
  • c.780+9C>T Single submitter
  • c.781-16C>T Single submitter
  • c.911-14C>T Single submitter
  • c.911-190GT[11] Single submitter
  • p.Ala268= Single submitter Inborn genetic diseases
  • p.Ala279= Single submitter Inborn genetic diseases
  • p.Ala282= Single submitter Inborn genetic diseases
  • p.Ala308= Single submitter Inborn genetic diseases
  • p.Ala329= Single submitter Inborn genetic diseases
  • p.Ala374= Single submitter Inborn genetic diseases
  • p.Ala376= Single submitter Inborn genetic diseases
  • p.Ala380= Single submitter Inborn genetic diseases
  • p.Ala385= Single submitter Inborn genetic diseases
  • p.Ala387= Single submitter
  • p.Ala45= Single submitter Inborn genetic diseases
  • p.Arg122= Single submitter Inborn genetic diseases
  • p.Arg38= Single submitter Inborn genetic diseases
  • p.Arg50= Single submitter Inborn genetic diseases
  • p.Arg59= Single submitter Inborn genetic diseases
  • p.Asn126= Single submitter Inborn genetic diseases
  • p.Asn136= Single submitter Inborn genetic diseases
  • p.Asn29= Single submitter Inborn genetic diseases
  • p.Asn362= Single submitter Inborn genetic diseases
  • p.Asp125= Single submitter Inborn genetic diseases
  • p.Asp127= Single submitter Inborn genetic diseases
  • p.Asp248= Single submitter Inborn genetic diseases
  • p.Asp35= Single submitter Inborn genetic diseases
  • p.Asp53= Single submitter Inborn genetic diseases
  • p.Cys124= Single submitter Inborn genetic diseases
  • p.Cys52= Single submitter Inborn genetic diseases
  • p.Gln233= Single submitter Inborn genetic diseases
  • p.Gln350= Single submitter Inborn genetic diseases
  • p.Gln39= Single submitter Inborn genetic diseases
  • p.Gln57= Single submitter Inborn genetic diseases
  • p.Glu101= Single submitter Inborn genetic diseases
  • p.Glu113= Single submitter Inborn genetic diseases
  • p.Glu121= Single submitter Inborn genetic diseases
  • p.Glu254= Single submitter Inborn genetic diseases
  • p.Glu263= Single submitter Inborn genetic diseases
  • p.Glu340= Single submitter Inborn genetic diseases
  • p.Gly18= Single submitter Inborn genetic diseases
  • p.Gly211= Single submitter Inborn genetic diseases
  • p.Gly216= Single submitter Inborn genetic diseases
  • p.Gly226= Single submitter Inborn genetic diseases
  • p.Gly24= Single submitter Inborn genetic diseases
  • p.Gly25= Single submitter Inborn genetic diseases
  • p.Gly272= Single submitter Inborn genetic diseases
  • p.Gly290= Single submitter Inborn genetic diseases
  • p.Gly30= Single submitter Inborn genetic diseases
  • p.Gly314= Single submitter Inborn genetic diseases
  • p.Gly334= Single submitter Inborn genetic diseases
  • p.Gly338= Single submitter Inborn genetic diseases
  • p.Gly367= Single submitter Inborn genetic diseases
  • p.Gly76= Single submitter Inborn genetic diseases
  • p.Gly81= Single submitter Inborn genetic diseases
  • p.Gly85= Single submitter Inborn genetic diseases
  • p.His17= Single submitter Inborn genetic diseases
  • p.His348= Single submitter Inborn genetic diseases
  • p.Ile99= Single submitter Inborn genetic diseases
  • p.Leu118= Single submitter Inborn genetic diseases
  • p.Leu237= Single submitter Inborn genetic diseases
  • p.Leu312= Single submitter Inborn genetic diseases
  • p.Leu33= Single submitter Inborn genetic diseases
  • p.Leu332= Single submitter Inborn genetic diseases
  • p.Leu44= Single submitter Inborn genetic diseases
  • p.Leu58= Single submitter Inborn genetic diseases
  • p.Leu69= Single submitter Inborn genetic diseases
  • p.Lys257= Single submitter Inborn genetic diseases
  • p.Lys278= Single submitter Inborn genetic diseases
  • p.Phe27= Single submitter Inborn genetic diseases
  • p.Phe360= Single submitter Inborn genetic diseases
  • p.Pro209= Single submitter Inborn genetic diseases
  • p.Pro255= Single submitter Inborn genetic diseases
  • p.Pro286= Single submitter Inborn genetic diseases
  • p.Pro316= Single submitter Inborn genetic diseases
  • p.Pro317= Single submitter Inborn genetic diseases
  • p.Pro320= Single submitter Inborn genetic diseases
  • p.Pro321Ala Single submitter Inborn genetic diseases
  • p.Pro363= Single submitter Inborn genetic diseases
  • p.Pro382= Single submitter Inborn genetic diseases
  • p.Pro51= Single submitter Inborn genetic diseases
  • p.Pro8= Single submitter Inborn genetic diseases
  • p.Pro80= Single submitter Inborn genetic diseases
  • p.Pro88= Single submitter Inborn genetic diseases
  • p.Pro93= Single submitter Inborn genetic diseases
  • p.Ser283= Single submitter Inborn genetic diseases
  • p.Ser291= Single submitter Inborn genetic diseases
  • p.Ser298= Single submitter Inborn genetic diseases
  • p.Ser326= Single submitter Inborn genetic diseases
  • p.Ser328= Single submitter Inborn genetic diseases
  • p.Ser353= Single submitter Inborn genetic diseases
  • p.Ser368= Single submitter Inborn genetic diseases
  • p.Ser55= Single submitter Inborn genetic diseases
  • p.Ser77= Single submitter Inborn genetic diseases
  • p.Thr128= Single submitter Inborn genetic diseases
  • p.Thr251= Single submitter Inborn genetic diseases
  • p.Thr252= Single submitter Inborn genetic diseases
  • p.Thr253= Single submitter Inborn genetic diseases
  • p.Thr262= Single submitter Inborn genetic diseases
  • p.Thr310= Single submitter Inborn genetic diseases
  • p.Thr311= Single submitter Inborn genetic diseases
  • p.Thr331= Single submitter Inborn genetic diseases
  • p.Thr386= Single submitter Inborn genetic diseases
  • p.Thr75= Single submitter Inborn genetic diseases
  • p.Thr92= Single submitter Inborn genetic diseases
  • p.Tyr246= Single submitter Inborn genetic diseases
  • p.Tyr264= Single submitter Inborn genetic diseases
  • p.Tyr299= Single submitter Inborn genetic diseases
  • p.Tyr346= Single submitter
  • p.Tyr7= Single submitter Inborn genetic diseases
  • p.Tyr73= Single submitter Inborn genetic diseases
  • p.Val129= Single submitter Inborn genetic diseases
  • p.Val132= Single submitter Inborn genetic diseases
  • p.Val20= Single submitter Inborn genetic diseases
  • p.Val240= Single submitter Inborn genetic diseases
  • p.Val302= Single submitter Inborn genetic diseases
  • p.Val336= Single submitter Inborn genetic diseases
  • p.Val36= Single submitter Inborn genetic diseases
  • p.Val37= Single submitter Inborn genetic diseases
  • p.Val42= Single submitter Inborn genetic diseases
  • p.Val49= Single submitter Inborn genetic diseases
  • p.Val82= Single submitter Inborn genetic diseases
  • p.Val90= Single submitter Inborn genetic diseases
  • c.780+10G>A No assertion criteria
  • c.*16G>A No assertion criteria PAX5-related disorder

Uncertain significance 242