Sugi Variant

Sugi Variant/SEMA3A

SEMA3A — 365 ClinVar variants

All ClinVar germline SEMA3A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 166 flagged for review →

1 Pathogenic · 4 Likely pathogenic · 5 Conflicting · 53 Benign · 6 Benign/Likely benign · 107 Likely benign · 189 Uncertain significance

Full SEMA3A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 166

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 2

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 127

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

Predictors split 36

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

All SEMA3A variants

Pathogenic 1

  • c.1860+1G>A Single submitter Hereditary Spastic Paraplegia (HSP)

Likely pathogenic 4

  • c.333+2T>C Single submitter hypogonadotropic hypogonadism 16 with or without anosmia
  • p.Gln511Ter Single submitter
  • p.Arg203fs No assertion criteria SEMA3A-related disorder
  • p.Arg531Ter No assertion criteria SEMA3A-related disorder

Conflicting classifications of pathogenicity 5

  • p.Arg484Trp Single submitter Male infertility with azoospermia or oligozoospermia due to single gene mutation ⚠
  • p.Arg555Ter Single submitter ⚠
  • p.Asn153Ser Single submitter hypogonadotropic hypogonadism 16 with or without anosmia ⚠
  • p.Ile400Val Single submitter hypogonadotropic hypogonadism 16 with or without anosmia ⚠
  • p.Val461Ala Single submitter

Benign 53

Benign/Likely benign 6

Likely benign 107

Uncertain significance 189