ESX1 — 74 ClinVar variants

All ClinVar germline ESX1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 62 flagged for review →

1 Likely pathogenic · 3 Conflicting · 2 Benign · 15 Likely benign · 53 Uncertain significance

Full ESX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 62

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 vs ClinVar 1

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

ESX1 p.Pro365Arg Likely pathogenic Single submitter
Male infertility with azoospermia or oligozoospermia due to single gene mutation

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 16

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

Predictors split 43

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

All ESX1 variants

Likely pathogenic 1

p.Pro365Arg Single submitter Male infertility with azoospermia or oligozoospermia due to single gene mutation ⚠

Conflicting classifications of pathogenicity 3

p.Arg290Pro Single submitter ⚠
p.Glu44Asp Single submitter ⚠
p.Val19Phe Single submitter ⚠

Benign 2

p.Pro320Arg Multiple submitters
p.342GPPMAPLPP[3] Single submitter

Likely benign 15

p.Trp297Gly Multiple submitters
p.342GPPMAPLPP[2] Single submitter
p.Ala301Val Single submitter ⚠
p.Ala355Val Single submitter ⚠
p.Gly288= Single submitter
p.Gly333Arg Single submitter ⚠
p.Gly76= Single submitter
p.Gly78= Single submitter
p.Leu357Val Single submitter ⚠
p.Pro289= Single submitter
p.Pro289Ser Single submitter ⚠
p.Pro343= Single submitter
p.Pro347_Pro356del Single submitter
p.Pro347delinsArgAla Single submitter
p.Thr55Ala Single submitter

Uncertain significance 53

p.Ala292Val Single submitter ⚠
p.Ala301Thr Single submitter ⚠
p.Ala319Val Single submitter ⚠
p.Ala337Glu Single submitter ⚠
p.Ala402Val Single submitter ⚠
p.Ala57Val Single submitter ⚠
p.Arg329His Single submitter ⚠
p.Asn177Lys Single submitter ⚠
p.Asp159His Single submitter ⚠
p.Asp165Glu Single submitter ⚠
p.Asp181Gly Single submitter ⚠
p.Asp70Glu Single submitter ⚠
p.Asp70Gly Single submitter ⚠
p.Gln134His Single submitter ⚠
p.Gln148His Single submitter ⚠
p.Gln198Arg Single submitter ⚠
p.Gln85Glu Single submitter ⚠
p.Glu109Asp Single submitter ⚠
p.Glu45Lys Single submitter ⚠
p.Glu58Lys Single submitter ⚠
p.Glu99Lys Single submitter ⚠
p.Gly13Asp Single submitter ⚠
p.Gly279Ser Single submitter ⚠
p.Gly315Glu Single submitter ⚠
p.Gly315Trp Single submitter ⚠
p.Gly6Arg Single submitter ⚠
p.His80Asp Single submitter ⚠
p.Leu201Ile Single submitter ⚠
p.Leu229Pro Single submitter ⚠
p.Leu357Pro Single submitter ⚠
p.Met282Thr Single submitter ⚠
p.Met300Lys Single submitter ⚠
p.Met345Thr Single submitter ⚠
p.Pro123Gln Single submitter ⚠
p.Pro135Leu Single submitter ⚠
p.Pro214Leu Single submitter ⚠
p.Pro277Leu Single submitter ⚠
p.Pro307Leu Single submitter ⚠
p.Pro308Ser Single submitter ⚠
p.Pro325Leu Single submitter ⚠
p.Pro326Ser Single submitter ⚠
p.Pro334Gln Single submitter ⚠
p.Pro350Leu Single submitter ⚠
p.Pro352Gln Single submitter ⚠
p.Pro395Ala Single submitter ⚠
p.Pro68Thr Single submitter ⚠
p.Pro82Arg Single submitter ⚠
p.Ser10Asn Single submitter ⚠
p.Ser3Phe Single submitter ⚠
p.Thr179Ser Single submitter ⚠
p.Thr34Ile Single submitter ⚠
p.Thr92Asn Single submitter ⚠
p.Val330Leu Single submitter ⚠