Sugi Variant

Sugi Variant/LAMP2

LAMP2 — 840 ClinVar variants

All ClinVar germline LAMP2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 252 flagged for review →

95 Pathogenic · 11 Pathogenic/Likely pathogenic · 33 Likely pathogenic · 66 Conflicting · 69 Benign · 37 Benign/Likely benign · 241 Likely benign · 288 Uncertain significance

Full LAMP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 252

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 3

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

Predictors agree, ClinVar conflicts 36

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

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.

Predictors lean, ClinVar uncertain 161

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 161

Predictors split 51

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

All LAMP2 variants

Pathogenic 95

Pathogenic/Likely pathogenic 11

Likely pathogenic 33

Conflicting classifications of pathogenicity 66

Benign 69

Benign/Likely benign 37

Likely benign 241

Uncertain significance 288