JAGN1 — 161 ClinVar variants

All ClinVar germline JAGN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 81 flagged for review →

2 Pathogenic · 2 Likely pathogenic · 11 Conflicting · 3 Benign · 10 Benign/Likely benign · 48 Likely benign · 85 Uncertain significance

Full JAGN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 81

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 42

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

Predictors split 37

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

All JAGN1 variants

Pathogenic 2

Likely pathogenic 2

  • p.Ser111fs Single submitter
  • p.Glu121Ter No assertion criteria autosomal recessive severe congenital neutropenia due to JAGN1 deficiency

Conflicting classifications of pathogenicity 11

  • c.89+4T>C Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Arg20Gln Single submitter severe congenital neutropenia ⚠
  • p.Gln18Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu21Asp Single submitter severe congenital neutropenia ⚠
  • p.Gly118= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Gly14Ser Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.His19Arg Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.His44Tyr Single submitter severe congenital neutropenia ⚠
  • p.Met1Ile Single submitter JAGN1-related disorder
  • p.Ser166= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Thr12_Gly14del Single submitter severe congenital neutropenia

Benign 3

Benign/Likely benign 10

  • c.90-19C>T Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.90-20C>T Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.*9T>C Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ala135Thr Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ile105= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ile112= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ile82Val Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Met1Val Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Pro7= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Thr32= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency

Likely benign 48

  • p.Ala69= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.His19= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Leu109= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Leu63= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Lys34= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ser30= Multiple submitters Inborn genetic diseases
  • p.Tyr42= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Val46= Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.89+15G>T Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.89+20G>T Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.90-13C>G Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.90-13C>T Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.90-16C>T Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.90-18C>G Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.90-18CT[4] Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.90-4A>G Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.90-9G>C Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.*9T>G Single submitter
  • p.Ala10= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ala113= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ala144= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ala160= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ala53= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ala9= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Arg4= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Asp13= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Gly88= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.His26= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ile41= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Leu33= Single submitter
  • p.Leu40= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Leu62= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Leu83= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Leu90= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Lys180= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Lys39= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Phe110= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Pro77= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Pro93= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ser146= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ser56= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ter184= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Thr12= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Thr175= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Tyr165= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Tyr35= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Tyr76= Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Pro84= No assertion criteria JAGN1-related disorder

Uncertain significance 85

  • p.Ala24Val Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Arg131His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg22Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Arg4Pro Multiple submitters Inborn genetic diseases ⚠
  • p.Arg94Gly Multiple submitters Inborn genetic diseases ⚠
  • p.Asp16Tyr Multiple submitters Inborn genetic diseases ⚠
  • p.Ile105Val Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Ile112Val Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Leu87fs Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Lys181Gln Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Met25Thr Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Phe174Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Pro71Ser Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Pro71Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Ser166Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Thr12Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Tyr130Cys Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Val43Ile Multiple submitters autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • c.89+1G>A Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • c.89+5G>A Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ala24fs Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Ala69Thr Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Ala9fs Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Arg131Cys Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Arg137Cys Single submitter Inborn genetic diseases
  • p.Arg4Leu Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Asp13Asn Single submitter ⚠
  • p.Asp16Gly Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Gln127Ter Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Gly141Arg Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Gly14Asp Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Gly58Arg Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Gly6Asp Single submitter Inborn genetic diseases ⚠
  • p.Gly88Asp Single submitter Inborn genetic diseases ⚠
  • p.His132Tyr Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.His159Tyr Single submitter Inborn genetic diseases ⚠
  • p.His26Leu Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.His59Leu Single submitter Inborn genetic diseases ⚠
  • p.His65Tyr Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Ile116Val Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Ile147Leu Single submitter Inborn genetic diseases ⚠
  • p.Ile37Met Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Leu163Ser Single submitter frontotemporal dementia and/or amyotrophic lateral sclerosis 7 ⚠
  • p.Leu163Val Single submitter ⚠
  • p.Leu169Phe Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Leu49Val Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Leu60Pro Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Leu62Phe Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Leu87Ser Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Leu90Phe Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Lys167Glu Single submitter Inborn genetic diseases ⚠
  • p.Lys168Arg Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Lys181Arg Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Lys181del Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Lys34Asn Single submitter Inborn genetic diseases ⚠
  • p.Met104Val Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Met107Val Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Met148Thr Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Met25Arg Single submitter Inborn genetic diseases ⚠
  • p.Met55Leu Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Phe138Ser Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Phe140Cys Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Phe140fs Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
  • p.Phe140Ser Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Phe17Leu Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Pro77Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro84Ala Single submitter Inborn genetic diseases
  • p.Pro84Arg Single submitter Inborn genetic diseases ⚠
  • p.Pro93Leu Single submitter ⚠
  • p.Ser106Asn Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Ser15Gly Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Ser30Asn Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Ser56Asn Single submitter Inborn genetic diseases ⚠
  • p.Ser85Phe Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Ser91Cys Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Thr12Ser Single submitter Inborn genetic diseases ⚠
  • p.Thr175Ser Single submitter ⚠
  • p.Thr32Ile Single submitter Inborn genetic diseases ⚠
  • p.Trp173Arg Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Trp173Cys Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Trp48Arg Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Tyr42His Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Tyr72Cys Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Tyr99Asn Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠
  • p.Val145Ile Single submitter autosomal recessive severe congenital neutropenia due to JAGN1 deficiency ⚠