XPO1 — 83 ClinVar variants

All ClinVar germline XPO1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 39 flagged for review →

16 Pathogenic · 1 Likely pathogenic · 5 Conflicting · 4 Benign · 7 Likely benign · 50 Uncertain significance

Full XPO1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 39

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.

XPO1 p.Glu513Lys Conflicting Single submitter
XPO1-associated Neurodevelopmental Disorder
XPO1 p.Pro842Arg Conflicting Single submitter
XPO1-associated Neurodevelopmental Disorder

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.

XPO1 p.Arg305Ter Conflicting Single submitter
XPO1-associated Neurodevelopmental Disorder

Predictors lean, ClinVar uncertain 30

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

Predictors split 6

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

XPO1 p.His1063Arg Uncertain significance Single submitter
XPO1 p.Ile745Met Uncertain significance Single submitter
XPO1 p.Lys331Glu Uncertain significance Single submitter
XPO1 p.Ser1031Phe Uncertain significance Single submitter
XPO1 p.Val169Glu Likely benign Single submitter
complex neurodevelopmental disorder
XPO1 p.Asn719Lys Uncertain significance No assertion criteria
neurodevelopmental disorder

All XPO1 variants

Pathogenic 16

c.1887+1G>T Single submitter XPO1-associated Neurodevelopmental Disorder
c.2022+886_2314-728del Single submitter XPO1-associated Neurodevelopmental Disorder
c.888+1G>A Single submitter XPO1-associated Neurodevelopmental Disorder
p.Arg765Ter Single submitter XPO1-associated Neurodevelopmental Disorder
p.Asn1005fs Single submitter XPO1-associated Neurodevelopmental Disorder
p.Asp716Tyr Single submitter XPO1-associated Neurodevelopmental Disorder
p.Gln185Ter Single submitter XPO1-associated Neurodevelopmental Disorder
p.Gln650Pro Single submitter XPO1-associated Neurodevelopmental Disorder
p.Glu428fs Single submitter XPO1-associated Neurodevelopmental Disorder
p.Leu525Phe Single submitter XPO1-associated Neurodevelopmental Disorder
p.Lys568Asn Single submitter XPO1-associated Neurodevelopmental Disorder
p.Met717Arg Single submitter XPO1-associated Neurodevelopmental Disorder
p.Ser913Ile Single submitter XPO1-associated Neurodevelopmental Disorder
p.Thr448Lys Single submitter XPO1-associated Neurodevelopmental Disorder
p.Tyr105Ter Single submitter XPO1-associated Neurodevelopmental Disorder
p.Tyr454Cys Single submitter XPO1-associated Neurodevelopmental Disorder

Likely pathogenic 1

p.Lys693Glu Single submitter XPO1-associated Neurodevelopmental Disorder

Conflicting classifications of pathogenicity 5

c.639+3_639+6del Single submitter XPO1-associated Neurodevelopmental Disorder
p.Arg305Ter Single submitter XPO1-associated Neurodevelopmental Disorder ⚠
p.Glu513Lys Single submitter XPO1-associated Neurodevelopmental Disorder ⚠
p.Pro842Arg Single submitter XPO1-associated Neurodevelopmental Disorder ⚠
p.Val548del Single submitter XPO1-associated Neurodevelopmental Disorder

Benign 4

c.888+9A>G Multiple submitters
p.Arg305= Multiple submitters
p.Thr846= Multiple submitters
p.Tyr721= Single submitter

Likely benign 7

p.Leu625= Multiple submitters
p.Lys757= Multiple submitters
c.2812+7A>T Single submitter
p.Ala541= Single submitter
p.Pro237= Single submitter
p.Pro57= Single submitter
p.Val169Glu Single submitter complex neurodevelopmental disorder ⚠

Uncertain significance 50

p.Val565fs Multiple submitters
c.2022+3A>T Single submitter
p.Ala795Val Single submitter ⚠
p.Asn200Ser Single submitter ⚠
p.Asn970Thr Single submitter
p.Asp1017fs Single submitter
p.Asp666Tyr Single submitter ⚠
p.Cys164Arg Single submitter ⚠
p.Gln1006His Single submitter ⚠
p.Gln42Ter Single submitter
p.Gln71Glu Single submitter ⚠
p.Gln733Ter Single submitter
p.Glu1064Asp Single submitter ⚠
p.Glu651Val Single submitter Seizure
p.Glu797fs Single submitter
p.Gly605Arg Single submitter ⚠
p.His1063Arg Single submitter ⚠
p.His223Tyr Single submitter ⚠
p.His333Arg Single submitter ⚠
p.His37Tyr Single submitter ⚠
p.His858Pro Single submitter ⚠
p.Ile137Val Single submitter ⚠
p.Ile745Met Single submitter ⚠
p.Ile786Asn Single submitter ⚠
p.Ile815Val Single submitter ⚠
p.Leu1042fs Single submitter
p.Leu306Phe Single submitter ⚠
p.Leu324fs Single submitter
p.Leu756Ile Single submitter ⚠
p.Leu996Val Single submitter ⚠
p.Lys103Ile Single submitter ⚠
p.Lys331Glu Single submitter ⚠
p.Lys479fs Single submitter
p.Lys674Thr Single submitter ⚠
p.Met508Ile Single submitter ⚠
p.Met640Thr Single submitter ⚠
p.Phe554Leu Single submitter ⚠
p.Pro220Leu Single submitter ⚠
p.Pro778Ser Single submitter
p.Pro779fs Single submitter
p.Ser1031Phe Single submitter ⚠
p.Ser162Gly Single submitter ⚠
p.Ser182Cys Single submitter ⚠
p.Ser667Asn Single submitter ⚠
p.Ser877Phe Single submitter XPO1-associated Neurodevelopmental Disorder ⚠
p.Ser913fs Single submitter
p.Thr328Ala Single submitter ⚠
p.Thr846Met Single submitter
p.Tyr381Cys Single submitter ⚠
p.Asn719Lys No assertion criteria neurodevelopmental disorder ⚠