Sugi Variant

Sugi Variant/SPECC1L

SPECC1L — 422 ClinVar variants

All ClinVar germline SPECC1L variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 227 flagged for review →

7 Pathogenic · 2 Pathogenic/Likely pathogenic · 3 Likely pathogenic · 20 Conflicting · 31 Benign · 13 Benign/Likely benign · 105 Likely benign · 241 Uncertain significance

Full SPECC1L gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 227

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 2

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

Predictors agree, ClinVar conflicts 15

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 153

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 153

Predictors split 56

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

All SPECC1L variants

Pathogenic 7

Pathogenic/Likely pathogenic 2

  • p.Arg1098Gln Multiple submitters SPECC1L-related syndrome
  • p.Thr417Pro No assertion criteria Teebi hypertelorism syndrome 1

Likely pathogenic 3

  • p.Leu431Pro Single submitter Autosomal dominant Opitz G/BBB syndrome
  • p.Thr67Met No assertion criteria Teebi hypertelorism syndrome 1 ⚠
  • p.Tyr1009Ser No assertion criteria Teebi hypertelorism syndrome

Conflicting classifications of pathogenicity 20

Benign 31

Benign/Likely benign 13

Likely benign 105

Uncertain significance 241