HAX1 — 679 ClinVar variants

All ClinVar germline HAX1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 317 flagged for review →

32 Pathogenic · 8 Pathogenic/Likely pathogenic · 22 Likely pathogenic · 13 Conflicting · 5 Benign · 7 Benign/Likely benign · 240 Likely benign · 352 Uncertain significance

Full HAX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 317

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 241

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 241

Predictors split 74

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

All HAX1 variants

Pathogenic 32

Pathogenic/Likely pathogenic 8

  • c.557-1G>C Multiple submitters Kostmann syndrome
  • c.663+1G>A Multiple submitters Kostmann syndrome
  • p.Arg29Ter Multiple submitters Kostmann syndrome
  • p.Gln155fs Multiple submitters HAX1-related disorders
  • p.Glu113Ter Multiple submitters Kostmann syndrome
  • p.Glu31fs Multiple submitters HAX1-related disorders
  • p.Glu37Ter Multiple submitters HAX1-related disorder
  • p.His136fs Multiple submitters HAX1-related disorders

Likely pathogenic 22

Conflicting classifications of pathogenicity 13

Benign 5

Benign/Likely benign 7

  • c.505-16A>G Multiple submitters Kostmann syndrome
  • c.53+11G>A Multiple submitters Kostmann syndrome
  • c.53+13C>T Multiple submitters Kostmann syndrome
  • c.53+14C>T Multiple submitters Kostmann syndrome
  • p.Pro69= Multiple submitters Kostmann syndrome
  • p.Ser53= Multiple submitters hereditary sensory and autonomic neuropathy type 4
  • p.Val172Ile Multiple submitters Kostmann syndrome

Likely benign 240

  • c.316+12dup Multiple submitters Kostmann syndrome
  • c.316+19G>A Multiple submitters Kostmann syndrome
  • c.504+12A>G Multiple submitters Kostmann syndrome
  • c.505-14G>C Multiple submitters Kostmann syndrome
  • c.54-18A>G Multiple submitters Kostmann syndrome
  • c.556+13G>A Multiple submitters Kostmann syndrome
  • c.557-6T>C Multiple submitters Kostmann syndrome
  • p.Ala260= Multiple submitters Inborn genetic diseases
  • p.Ala97= Multiple submitters Inborn genetic diseases
  • p.Arg164= Multiple submitters Inborn genetic diseases
  • p.Arg227= Multiple submitters Kostmann syndrome
  • p.Arg274= Multiple submitters Kostmann syndrome
  • p.Arg8= Multiple submitters Inborn genetic diseases
  • p.Asp148= Multiple submitters Inborn genetic diseases
  • p.Asp176= Multiple submitters Inborn genetic diseases
  • p.Asp220= Multiple submitters Inborn genetic diseases
  • p.Asp82= Multiple submitters Inborn genetic diseases
  • p.Gln137= Multiple submitters Kostmann syndrome
  • p.Gln155= Multiple submitters Kostmann syndrome
  • p.Glu117= Multiple submitters Inborn genetic diseases
  • p.Glu121= Multiple submitters Inborn genetic diseases
  • p.Glu146Lys Multiple submitters Kostmann syndrome
  • p.Glu183= Multiple submitters Inborn genetic diseases
  • p.Glu233= Multiple submitters Inborn genetic diseases
  • p.Glu60= Multiple submitters Inborn genetic diseases
  • p.Gly12= Multiple submitters Kostmann syndrome
  • p.Gly142= Multiple submitters Kostmann syndrome
  • p.Gly143= Multiple submitters Inborn genetic diseases
  • p.Gly26= Multiple submitters Inborn genetic diseases
  • p.Gly41= Multiple submitters Kostmann syndrome
  • p.Gly96= Multiple submitters Inborn genetic diseases
  • p.His167= Multiple submitters Inborn genetic diseases
  • p.His19= Multiple submitters Inborn genetic diseases
  • p.His243= Multiple submitters Inborn genetic diseases
  • p.His56= Multiple submitters Inborn genetic diseases
  • p.His76= Multiple submitters Inborn genetic diseases
  • p.Leu119= Multiple submitters Inborn genetic diseases
  • p.Leu272= Multiple submitters Inborn genetic diseases
  • p.Leu6= Multiple submitters Kostmann syndrome
  • p.Lys215= Multiple submitters Inborn genetic diseases
  • p.Phe10= Multiple submitters Inborn genetic diseases
  • p.Phe141= Multiple submitters Inborn genetic diseases
  • p.Phe265= Multiple submitters Inborn genetic diseases
  • p.Phe75= Multiple submitters Inborn genetic diseases
  • p.Pro14= Multiple submitters Inborn genetic diseases
  • p.Pro154= Multiple submitters Kostmann syndrome
  • p.Pro165= Multiple submitters Inborn genetic diseases
  • p.Pro177= Multiple submitters Inborn genetic diseases
  • p.Pro198= Multiple submitters Inborn genetic diseases
  • p.Pro204= Multiple submitters Inborn genetic diseases
  • p.Pro256= Multiple submitters Inborn genetic diseases
  • p.Pro57= Multiple submitters Inborn genetic diseases
  • p.Ser151= Multiple submitters Inborn genetic diseases
  • p.Ser162= Multiple submitters Inborn genetic diseases
  • p.Ser189= Multiple submitters Kostmann syndrome
  • p.Ser212= Multiple submitters Inborn genetic diseases
  • p.Ser248= Multiple submitters Inborn genetic diseases
  • p.Ser266= Multiple submitters Inborn genetic diseases
  • p.Ser90= Multiple submitters Kostmann syndrome
  • p.Tyr132= Multiple submitters Inborn genetic diseases
  • p.Tyr207= Multiple submitters Inborn genetic diseases
  • p.Val230= Multiple submitters Inborn genetic diseases
  • c.316+10T>C Single submitter
  • c.316+10T>G Single submitter Kostmann syndrome
  • c.316+17_316+28del Single submitter Kostmann syndrome
  • c.316+17A>G Single submitter Kostmann syndrome
  • c.317-11C>T Single submitter Kostmann syndrome
  • c.317-17C>G Single submitter Kostmann syndrome
  • c.317-17C>T Single submitter Kostmann syndrome
  • c.317-19A>C Single submitter Kostmann syndrome
  • c.317-19A>G Single submitter Kostmann syndrome
  • c.317-33C>T Single submitter
  • c.317-41G>A Single submitter
  • c.317-9T>A Single submitter Kostmann syndrome
  • c.504+10C>A Single submitter Kostmann syndrome
  • c.504+10C>T Single submitter Kostmann syndrome
  • c.504+12A>C Single submitter Kostmann syndrome
  • c.504+12A>T Single submitter Kostmann syndrome
  • c.504+15T>C Single submitter Kostmann syndrome
  • c.504+19C>T Single submitter Kostmann syndrome
  • c.504+7A>G Single submitter Kostmann syndrome
  • c.504+7dup Single submitter Kostmann syndrome
  • c.504+9C>G Single submitter Kostmann syndrome
  • c.505-13G>T Single submitter Kostmann syndrome
  • c.505-14G>T Single submitter Kostmann syndrome
  • c.505-20T>C Single submitter Kostmann syndrome
  • c.505-9C>T Single submitter Kostmann syndrome
  • c.53+16G>A Single submitter Kostmann syndrome
  • c.53+19C>T Single submitter Kostmann syndrome
  • c.53+3GA[3] Single submitter Kostmann syndrome
  • c.53+6_53+7insT Single submitter Kostmann syndrome
  • c.53+7G>A Single submitter Kostmann syndrome
  • c.53+9A>C Single submitter Kostmann syndrome
  • c.54-12C>T Single submitter Kostmann syndrome
  • c.54-14G>A Single submitter Kostmann syndrome
  • c.54-15T>G Single submitter Kostmann syndrome
  • c.54-20C>G Single submitter Kostmann syndrome
  • c.54-4T>A Single submitter Kostmann syndrome
  • c.54-4T>G Single submitter Kostmann syndrome
  • c.54-5C>T Single submitter Kostmann syndrome
  • c.54-6T>C Single submitter Kostmann syndrome
  • c.54-8A>G Single submitter Kostmann syndrome
  • c.54-9del Single submitter Kostmann syndrome
  • c.556+11A>G Single submitter Kostmann syndrome
  • c.556+15A>C Single submitter Kostmann syndrome
  • c.556+15A>G Single submitter Kostmann syndrome
  • c.556+17G>T Single submitter Kostmann syndrome
  • c.556+9G>A Single submitter Kostmann syndrome
  • c.557-11T>C Single submitter Kostmann syndrome
  • c.557-16C>T Single submitter Kostmann syndrome
  • c.557-18A>G Single submitter Kostmann syndrome
  • c.557-19C>T Single submitter Kostmann syndrome
  • c.557-5T>C Single submitter Kostmann syndrome
  • c.557-7C>T Single submitter Kostmann syndrome
  • c.557-8del Single submitter
  • c.557-8T>C Single submitter Kostmann syndrome
  • c.557-9C>A Single submitter Kostmann syndrome
  • c.663+14_663+17del Single submitter Kostmann syndrome
  • c.663+18G>C Single submitter Kostmann syndrome
  • c.663+20dup Single submitter Kostmann syndrome
  • c.664-10C>T Single submitter Kostmann syndrome
  • c.664-13C>T Single submitter Kostmann syndrome
  • c.664-4G>A Single submitter Kostmann syndrome
  • c.664-5T>G Single submitter Kostmann syndrome
  • c.664-6T>C Single submitter Kostmann syndrome
  • c.664-8C>G Single submitter Kostmann syndrome
  • c.664-8C>T Single submitter Kostmann syndrome
  • c.664-9T>C Single submitter Kostmann syndrome
  • c.754+12G>A Single submitter Kostmann syndrome
  • c.754+16_754+17del Single submitter Kostmann syndrome
  • c.754+16A>G Single submitter Kostmann syndrome
  • c.754+17A>G Single submitter Kostmann syndrome
  • c.754+18G>T Single submitter Kostmann syndrome
  • c.754+19G>C Single submitter Kostmann syndrome
  • c.754+7T>G Single submitter Kostmann syndrome
  • c.754+8A>C Single submitter Kostmann syndrome
  • c.755-12T>A Single submitter Kostmann syndrome
  • c.755-13C>T Single submitter Kostmann syndrome
  • c.755-17A>G Single submitter Kostmann syndrome
  • c.755-19G>A Single submitter Kostmann syndrome
  • c.755-19G>T Single submitter Kostmann syndrome
  • c.755-4T>C Single submitter Kostmann syndrome
  • c.755-5C>G Single submitter Kostmann syndrome
  • c.755-5C>T Single submitter Kostmann syndrome
  • c.755-6C>T Single submitter Kostmann syndrome
  • c.-5C>T Single submitter
  • p.Ala149Gly Single submitter Inborn genetic diseases
  • p.Ala157= Single submitter Kostmann syndrome
  • p.Ala264= Single submitter Inborn genetic diseases
  • p.Arg120Gln Single submitter Inborn genetic diseases
  • p.Arg139= Single submitter Inborn genetic diseases
  • p.Arg17= Single submitter Inborn genetic diseases
  • p.Arg226= Single submitter Kostmann syndrome
  • p.Arg235= Single submitter Kostmann syndrome
  • p.Arg277= Single submitter Kostmann syndrome
  • p.Arg279= Single submitter Kostmann syndrome
  • p.Asn48= Single submitter Inborn genetic diseases
  • p.Asn89= Single submitter Inborn genetic diseases
  • p.Asp127= Single submitter Kostmann syndrome
  • p.Asp171= Single submitter Kostmann syndrome
  • p.Asp184= Single submitter Kostmann syndrome
  • p.Asp246= Single submitter Inborn genetic diseases
  • p.Asp262= Single submitter Kostmann syndrome
  • p.Asp32= Single submitter Kostmann syndrome
  • p.Asp33= Single submitter Kostmann syndrome
  • p.Asp33Glu Single submitter Inborn genetic diseases
  • p.Asp5= Single submitter Inborn genetic diseases
  • p.Asp77= Single submitter Kostmann syndrome
  • p.Asp87= Single submitter Inborn genetic diseases
  • p.Gln155Lys Single submitter Inborn genetic diseases
  • p.Gln163= Single submitter Inborn genetic diseases
  • p.Gln203= Single submitter Inborn genetic diseases
  • p.Glu152= Single submitter Kostmann syndrome
  • p.Glu194= Single submitter Kostmann syndrome
  • p.Glu225= Single submitter Inborn genetic diseases
  • p.Glu35= Single submitter Inborn genetic diseases
  • p.Glu36= Single submitter Kostmann syndrome
  • p.Glu59= Single submitter Inborn genetic diseases
  • p.Gly122= Single submitter Inborn genetic diseases
  • p.Gly234= Single submitter Kostmann syndrome
  • p.Gly251Asp Single submitter Inborn genetic diseases
  • p.Gly273= Single submitter Kostmann syndrome
  • p.Gly42= Single submitter Inborn genetic diseases
  • p.Gly42Ala Single submitter Inborn genetic diseases
  • p.Gly62= Single submitter Kostmann syndrome
  • p.Gly70= Single submitter Inborn genetic diseases
  • p.Gly72= Single submitter Kostmann syndrome
  • p.Gly9= Single submitter Kostmann syndrome
  • p.His103Arg Single submitter Inborn genetic diseases
  • p.His243Gln Single submitter Inborn genetic diseases
  • p.Ile140= Single submitter Kostmann syndrome
  • p.Ile211= Single submitter Kostmann syndrome
  • p.Ile211Val Single submitter Inborn genetic diseases
  • p.Ile222= Single submitter Kostmann syndrome
  • p.Leu130= Single submitter Inborn genetic diseases
  • p.Leu187= Single submitter Inborn genetic diseases
  • p.Leu196= Single submitter Inborn genetic diseases
  • p.Leu261= Single submitter Inborn genetic diseases
  • p.Leu268= Single submitter Kostmann syndrome
  • p.Leu270= Single submitter Inborn genetic diseases
  • p.Leu3= Single submitter Kostmann syndrome
  • p.Lys131= Single submitter Kostmann syndrome
  • p.Lys218= Single submitter Kostmann syndrome
  • p.Met175Val Single submitter Inborn genetic diseases
  • p.Phe11= Single submitter Inborn genetic diseases
  • p.Phe13= Single submitter Inborn genetic diseases
  • p.Phe169= Single submitter Kostmann syndrome
  • p.Phe208= Single submitter Inborn genetic diseases
  • p.Phe276= Single submitter Inborn genetic diseases
  • p.Phe4= Single submitter Kostmann syndrome
  • p.Phe63= Single submitter Kostmann syndrome
  • p.Phe7= Single submitter Kostmann syndrome
  • p.Phe79= Single submitter Inborn genetic diseases
  • p.Phe92= Single submitter Kostmann syndrome
  • p.Pro133= Single submitter Kostmann syndrome
  • p.Pro138= Single submitter Kostmann syndrome
  • p.Pro16= Single submitter Inborn genetic diseases
  • p.Pro202= Single submitter Kostmann syndrome
  • p.Pro219= Single submitter Kostmann syndrome
  • p.Pro253= Single submitter Inborn genetic diseases
  • p.Pro258= Single submitter Inborn genetic diseases
  • p.Pro49= Single submitter Kostmann syndrome
  • p.Pro54= Single submitter Kostmann syndrome
  • p.Pro58= Single submitter Kostmann syndrome
  • p.Ser102= Single submitter Inborn genetic diseases
  • p.Ser128= Single submitter Inborn genetic diseases
  • p.Ser192= Single submitter Inborn genetic diseases
  • p.Ser206= Single submitter Inborn genetic diseases
  • p.Ser210= Single submitter Inborn genetic diseases
  • p.Ser247= Single submitter Kostmann syndrome
  • p.Ser43= Single submitter Kostmann syndrome
  • p.Ser93= Single submitter Kostmann syndrome
  • p.Thr114= Single submitter Inborn genetic diseases
  • p.Thr181= Single submitter Kostmann syndrome
  • p.Thr228= Single submitter Kostmann syndrome
  • p.Thr239= Single submitter Kostmann syndrome
  • p.Thr241= Single submitter Inborn genetic diseases
  • p.Thr28= Single submitter Kostmann syndrome
  • p.Val172= Single submitter Kostmann syndrome
  • p.Val85= Single submitter Inborn genetic diseases

Uncertain significance 352

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