LAGE3 — 97 ClinVar variants

All ClinVar germline LAGE3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 57 flagged for review →

3 Pathogenic · 5 Conflicting · 8 Benign · 2 Benign/Likely benign · 19 Likely benign · 60 Uncertain significance

Full LAGE3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 57

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 5

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

LAGE3 p.Arg102Ser Conflicting Single submitter
LAGE3 p.Arg24His Conflicting Single submitter
LAGE3 p.Arg47Gly Conflicting Single submitter
LAGE3 p.Gly10Arg Conflicting Single submitter
LAGE3 p.Gly10Glu Conflicting Single submitter
Galloway-Mowat syndrome 2, X-linked

Predictors lean, ClinVar uncertain 44

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

Predictors split 8

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

LAGE3 p.Pro139Thr Uncertain significance Multiple submitters
LAGE3 p.Pro84Thr Uncertain significance Multiple submitters
LAGE3 p.Thr133Ile Uncertain significance Multiple submitters
LAGE3 p.Arg132Gln Benign Single submitter
LAGE3 p.Arg136His Uncertain significance Single submitter
LAGE3 p.Pro88Ser Uncertain significance Single submitter
Galloway-Mowat syndrome 2, X-linked
LAGE3 p.Ser128Phe Uncertain significance Single submitter
LAGE3 p.Val106Phe Pathogenic No assertion criteria
Galloway-Mowat syndrome 2, X-linked

All LAGE3 variants

Pathogenic 3

c.188+1G>A No assertion criteria Galloway-Mowat syndrome 2, X-linked
p.Phe137Ser No assertion criteria Galloway-Mowat syndrome 2, X-linked
p.Val106Phe No assertion criteria Galloway-Mowat syndrome 2, X-linked ⚠

Conflicting classifications of pathogenicity 5

p.Arg102Ser Single submitter ⚠
p.Arg24His Single submitter ⚠
p.Arg47Gly Single submitter ⚠
p.Gly10Arg Single submitter ⚠
p.Gly10Glu Single submitter Galloway-Mowat syndrome 2, X-linked ⚠

Benign 8

c.189-34G>C Multiple submitters
c.*19G>C Multiple submitters Galloway-Mowat syndrome 2, X-linked
p.Asp16Asn Multiple submitters
c.188+10C>G Single submitter
p.Ala31Thr Single submitter
p.Arg132Gln Single submitter ⚠
p.Arg59= Single submitter
p.Val131Met Single submitter

Benign/Likely benign 2

p.Ile121Thr Multiple submitters Galloway-Mowat syndrome 2, X-linked
p.Pro60Leu Multiple submitters

Likely benign 19

p.Leu116= Multiple submitters
c.188+11C>T Single submitter
p.Ala30= Single submitter
p.Ala4= Single submitter
p.Ala52= Single submitter
p.Arg54= Single submitter
p.Asp3= Single submitter
p.Gly11= Single submitter
p.Gly19Asp Single submitter
p.Gly26= Single submitter
p.Gly55= Single submitter
p.Gly9= Single submitter
p.Ile121= Single submitter
p.Ile77= Single submitter
p.Ser119= Single submitter
p.Ter144= Single submitter
p.Arg18= No assertion criteria LAGE3-related disorder
p.Gly20= No assertion criteria LAGE3-related disorder
p.His89= No assertion criteria LAGE3-related disorder

Uncertain significance 60

c.189-2A>G Multiple submitters Galloway-Mowat syndrome 2, X-linked
p.Ala37Thr Multiple submitters LAGE3-related disorder ⚠
p.Ala40fs Multiple submitters
p.Ala40Glu Multiple submitters ⚠
p.Asp125Glu Multiple submitters LAGE3-related disorder ⚠
p.Asp3His Multiple submitters ⚠
p.Gly101Asp Multiple submitters ⚠
p.Gly17Asp Multiple submitters ⚠
p.His41Pro Multiple submitters ⚠
p.Leu65Ile Multiple submitters ⚠
p.Pro139Thr Multiple submitters ⚠
p.Pro84Thr Multiple submitters ⚠
p.Thr133Ile Multiple submitters ⚠
c.188+5C>T Single submitter
c.-14G>A Single submitter
c.-5C>T Single submitter
p.Ala12Thr Single submitter ⚠
p.Ala12Val Single submitter ⚠
p.Ala32Val Single submitter LAGE3-related disorder ⚠
p.Ala50Val Single submitter ⚠
p.Ala52Thr Single submitter ⚠
p.Arg102Lys Single submitter ⚠
p.Arg136His Single submitter ⚠
p.Arg24fs Single submitter
p.Arg2Trp Single submitter ⚠
p.Arg57Ter Single submitter LAGE3-related disorder
p.Arg59Trp Single submitter ⚠
p.Arg91fs Single submitter
p.Asp3Asn Single submitter ⚠
p.Asp5Glu Single submitter ⚠
p.Asp96Val Single submitter Galloway-Mowat syndrome 2, X-linked ⚠
p.Gly11Val Single submitter ⚠
p.Gly15Arg Single submitter ⚠
p.Gly20Ala Single submitter Galloway-Mowat syndrome 2, X-linked ⚠
p.Gly44Val Single submitter ⚠
p.Gly46Asp Single submitter ⚠
p.Gly46Ser Single submitter ⚠
p.Gly9Asp Single submitter ⚠
p.Gly9Ser Single submitter ⚠
p.His21Arg Single submitter ⚠
p.His61Tyr Single submitter ⚠
p.Ile62Val Single submitter Galloway-Mowat syndrome 2, X-linked ⚠
p.Leu124Phe Single submitter ⚠
p.Lys95Arg Single submitter Galloway-Mowat syndrome 2, X-linked ⚠
p.Met1Arg Single submitter Galloway-Mowat syndrome 2, X-linked
p.Pro38Ser Single submitter ⚠
p.Pro43Thr Single submitter ⚠
p.Pro60Gln Single submitter ⚠
p.Pro70Leu Single submitter Galloway-Mowat syndrome 2, X-linked ⚠
p.Pro72Ser Single submitter ⚠
p.Pro88Ser Single submitter Galloway-Mowat syndrome 2, X-linked ⚠
p.Ser128Phe Single submitter ⚠
p.Ser22fs Single submitter
p.Ser66Arg Single submitter ⚠
p.Thr133Ser Single submitter ⚠
p.Thr29Ala Single submitter ⚠
p.Val106Ala Single submitter ⚠
p.Val130Glu Single submitter Galloway-Mowat syndrome 2, X-linked ⚠
p.Val130Gly Single submitter Galloway-Mowat syndrome 2, X-linked ⚠
p.Val92Met Single submitter ⚠