Sugi Variant

Sugi Variant/SPEN

SPEN — 1036 ClinVar variants

All ClinVar germline SPEN variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 501 flagged for review →

65 Pathogenic · 5 Pathogenic/Likely pathogenic · 41 Likely pathogenic · 19 Conflicting · 35 Benign · 8 Benign/Likely benign · 246 Likely benign · 617 Uncertain significance

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

⚑ Evidence disagreements 501

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.

Predictors agree, ClinVar conflicts 11

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

Predicted LoF vs a conflicting call 4

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 391

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 391

Predictors split 94

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

All SPEN variants

Pathogenic 65

Pathogenic/Likely pathogenic 5

Likely pathogenic 41

Conflicting classifications of pathogenicity 19

Benign 35

Benign/Likely benign 8

Likely benign 246

Uncertain significance 617

Showing the top 300 by review status; the full set is in the sitemap.