VPS37A — 249 ClinVar variants

All ClinVar germline VPS37A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 117 flagged for review →

1 Pathogenic · 4 Conflicting · 27 Benign · 6 Benign/Likely benign · 81 Likely benign · 130 Uncertain significance

Full VPS37A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 117

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.

Predictors lean, ClinVar uncertain 99

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

All VPS37A variants

Pathogenic 1

  • p.Lys382Asn No assertion criteria hereditary spastic paraplegia 53

Conflicting classifications of pathogenicity 4

  • c.642+10G>A Single submitter hereditary spastic paraplegia 53
  • p.Ala386Val Single submitter hereditary spastic paraplegia 53 ⚠
  • p.Ile33= Single submitter hereditary spastic paraplegia 53
  • p.Leu234Ile Single submitter hereditary spastic paraplegia 53 ⚠

Benign 27

Benign/Likely benign 6

  • c.315+14A>C Multiple submitters hereditary spastic paraplegia 53
  • c.-19G>A Multiple submitters
  • p.Gln392= Multiple submitters hereditary spastic paraplegia 53
  • p.Glu278= Multiple submitters hereditary spastic paraplegia 53
  • p.Ile213Val Multiple submitters hereditary spastic paraplegia
  • p.Thr8= Multiple submitters hereditary spastic paraplegia

Likely benign 81

  • c.1113+151T>C Multiple submitters
  • c.1114-186T>C Multiple submitters
  • c.416+17T>C Multiple submitters hereditary spastic paraplegia 53
  • c.642+141A>G Multiple submitters
  • c.643-50C>T Multiple submitters
  • c.714-276G>C Multiple submitters
  • p.Gln306= Multiple submitters hereditary spastic paraplegia 53
  • c.1113+13C>T Single submitter hereditary spastic paraplegia 53
  • c.1113+191C>G Single submitter
  • c.1114-18C>T Single submitter hereditary spastic paraplegia 53
  • c.1114-5T>C Single submitter hereditary spastic paraplegia 53
  • c.125+11_125+15del Single submitter hereditary spastic paraplegia 53
  • c.125+11G>T Single submitter
  • c.125+15C>T Single submitter hereditary spastic paraplegia 53
  • c.125+16C>T Single submitter hereditary spastic paraplegia 53
  • c.125+41T>G Single submitter
  • c.125+45A>G Single submitter
  • c.125+49C>G Single submitter
  • c.126-14A>C Single submitter hereditary spastic paraplegia 53
  • c.126-16A>C Single submitter hereditary spastic paraplegia 53
  • c.200+15A>G Single submitter hereditary spastic paraplegia 53
  • c.201-10C>T Single submitter hereditary spastic paraplegia 53
  • c.201-57A>G Single submitter
  • c.201-6T>C Single submitter
  • c.315+11G>A Single submitter hereditary spastic paraplegia 53
  • c.316-19C>T Single submitter hereditary spastic paraplegia 53
  • c.416+11T>G Single submitter hereditary spastic paraplegia 53
  • c.416+19A>G Single submitter
  • c.417-20T>C Single submitter hereditary spastic paraplegia 53
  • c.417-8C>T Single submitter hereditary spastic paraplegia 53
  • c.417-9T>C Single submitter hereditary spastic paraplegia 53
  • c.642+11T>C Single submitter hereditary spastic paraplegia 53
  • c.642+19C>G Single submitter hereditary spastic paraplegia 53
  • c.642+9C>T Single submitter hereditary spastic paraplegia 53
  • c.643-11C>T Single submitter hereditary spastic paraplegia 53
  • c.643-19A>C Single submitter hereditary spastic paraplegia 53
  • c.713+11A>G Single submitter hereditary spastic paraplegia 53
  • c.714-216_714-215del Single submitter
  • c.714-61T>C Single submitter
  • c.841+12C>T Single submitter hereditary spastic paraplegia 53
  • c.841+16C>T Single submitter hereditary spastic paraplegia 53
  • c.841+19G>T Single submitter hereditary spastic paraplegia 53
  • c.901-18T>C Single submitter hereditary spastic paraplegia 53
  • c.901-9C>G Single submitter hereditary spastic paraplegia 53
  • c.969+13A>G Single submitter hereditary spastic paraplegia 53
  • c.969+187A>G Single submitter
  • c.969+236C>T Single submitter
  • c.969+7C>G Single submitter
  • c.-13G>A Single submitter
  • c.-31C>T Single submitter
  • p.Ala192= Single submitter hereditary spastic paraplegia 53
  • p.Ala386= Single submitter hereditary spastic paraplegia 53
  • p.Arg294= Single submitter hereditary spastic paraplegia 53
  • p.Arg53= Single submitter hereditary spastic paraplegia 53
  • p.Arg87= Single submitter hereditary spastic paraplegia 53
  • p.Asp210= Single submitter hereditary spastic paraplegia 53
  • p.Cys325= Single submitter hereditary spastic paraplegia 53
  • p.Glu233= Single submitter hereditary spastic paraplegia 53
  • p.Glu312= Single submitter hereditary spastic paraplegia 53
  • p.Gly146= Single submitter hereditary spastic paraplegia 53
  • p.His40= Single submitter
  • p.Ile58Val Single submitter
  • p.Leu140= Single submitter hereditary spastic paraplegia 53
  • p.Leu202= Single submitter hereditary spastic paraplegia 53
  • p.Leu234= Single submitter hereditary spastic paraplegia 53
  • p.Leu25= Single submitter hereditary spastic paraplegia 53
  • p.Leu259= Single submitter hereditary spastic paraplegia 53
  • p.Leu284= Single submitter hereditary spastic paraplegia 53
  • p.Leu304= Single submitter hereditary spastic paraplegia 53
  • p.Leu54= Single submitter hereditary spastic paraplegia 53
  • p.Phe220= Single submitter hereditary spastic paraplegia 53
  • p.Pro101= Single submitter hereditary spastic paraplegia 53
  • p.Pro149Leu Single submitter hereditary spastic paraplegia 53
  • p.Ser200= Single submitter hereditary spastic paraplegia 53
  • p.Ser24= Single submitter hereditary spastic paraplegia 53
  • p.Ter398Gln Single submitter hereditary spastic paraplegia 53
  • p.Thr171= Single submitter
  • p.Thr267= Single submitter hereditary spastic paraplegia 53
  • p.Thr305= Single submitter hereditary spastic paraplegia 53
  • p.Thr99= Single submitter hereditary spastic paraplegia 53
  • p.Ile58= No assertion criteria VPS37A-related disorder

Uncertain significance 130