Sugi Variant

Sugi Variant/VPS13D

VPS13D — 1790 ClinVar variants

All ClinVar germline VPS13D variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 618 flagged for review →

39 Pathogenic · 6 Pathogenic/Likely pathogenic · 35 Likely pathogenic · 36 Conflicting · 80 Benign · 38 Benign/Likely benign · 604 Likely benign · 952 Uncertain significance

Full VPS13D gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 618

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 24

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

Predictors lean, ClinVar uncertain 543

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 543

Predictors split 51

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

All VPS13D variants

Pathogenic 39

Pathogenic/Likely pathogenic 6

  • c.941+3A>G Multiple submitters autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Arg303Ter Multiple submitters
  • p.Arg316Ter Multiple submitters autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Arg3253Ter Multiple submitters Inborn genetic diseases
  • p.Gly1190Asp Multiple submitters autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Gly3607fs Multiple submitters VPS13D-related disorder

Likely pathogenic 35

  • p.Ala4139Val Multiple submitters spinocerebellar ataxia type 4 ⚠
  • p.Arg3518Ter Multiple submitters Spinocerebellar atrophy
  • c.10272+1G>A Single submitter
  • c.11191-2_11206del Single submitter
  • c.1212+1G>C Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • c.12662+1059C>G Single submitter Leigh syndrome
  • c.12794+1G>T Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • c.2103+1G>T Single submitter
  • c.447+3A>C Single submitter
  • c.669+1G>A Single submitter
  • p.Ala4248Glu Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Arg1315Ter Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Arg2995Ter Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Arg3101Trp Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Arg3363Ter Single submitter
  • p.Arg3499Ter Single submitter
  • p.Arg395Ter Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Arg624fs Single submitter Ehlers-Danlos syndrome, kyphoscoliotic type 1
  • p.Asn3521Ser Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Gln1106fs Single submitter
  • p.Gln2210Ter Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Gln3424Ter Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Gly4177Asp Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Ile1170Ser Single submitter
  • p.Lys4314fs Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Pro1697fs Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Ser4142fs Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Trp1826Ter Single submitter
  • p.Trp319Ter Single submitter VPS13D-related disorder
  • p.Tyr4137fs Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Val4081Ala Single submitter autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Arg4132Gln No assertion criteria autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
  • p.Gln1648Ter No assertion criteria VPS13D-related disorder
  • p.Ser2579fs No assertion criteria VPS13D-related disorder
  • p.Trp436Ter No assertion criteria autosomal recessive cerebellar ataxia-saccadic intrusion syndrome

Conflicting classifications of pathogenicity 36

Benign 80

Benign/Likely benign 38

Likely benign 604

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

Uncertain significance 952

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