VPS13A — 3781 ClinVar variants

All ClinVar germline VPS13A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 625 flagged for review →

225 Pathogenic · 57 Pathogenic/Likely pathogenic · 205 Likely pathogenic · 93 Conflicting · 209 Benign · 69 Benign/Likely benign · 2005 Likely benign · 918 Uncertain significance

Full VPS13A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 625

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 43

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

Predictors lean, ClinVar uncertain 540

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 540

Predictors split 41

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

All VPS13A variants

Pathogenic 225

Pathogenic/Likely pathogenic 57

  • c.1596-1G>C Multiple submitters VPS13A-related neurodegenerative disease
  • c.187+1dup Multiple submitters VPS13A-related neurodegenerative disease
  • c.4956+1G>A Multiple submitters VPS13A-related disorder
  • c.555+1G>A Multiple submitters VPS13A-related neurodegenerative disease
  • c.7156-2A>T Multiple submitters VPS13A-related neurodegenerative disease
  • c.7157_7172del Multiple submitters VPS13A-related neurodegenerative disease
  • c.7419+1G>A Multiple submitters VPS13A-related neurodegenerative disease
  • c.755-1G>A Multiple submitters VPS13A-related neurodegenerative disease
  • c.755-2A>G Multiple submitters VPS13A-related neurodegenerative disease
  • c.9276-2A>T Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ala332fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ala969fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Arg1297Ter Multiple submitters Inborn genetic diseases
  • p.Arg2032Ter Multiple submitters VPS13A-related disorder
  • p.Arg2234Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Arg2579fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Arg2623Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Asn73fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Asp1483fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Cys1979fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Gln1053Ter Multiple submitters VPS13A-related disorder
  • p.Gln1188Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Gln1634Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Gln2293Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Gln2358Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Gln2496Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Gln985Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu2886Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu3032Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu3131fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu3144fs Multiple submitters VPS13A-related disorder
  • p.Gly2281Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Gly3023fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ile1152fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Leu1289fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Leu2161fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Leu2405Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Leu782fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Lys1113fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Lys752fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Phe1565fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser1324fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser1416fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser2136fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser2792Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser375fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser539Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser734fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Thr2306fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Thr3098fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Trp1782Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Trp430Ter Multiple submitters VPS13A-related neurodegenerative disease
  • p.Trp435fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Tyr2447fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Tyr3073Ter Multiple submitters
  • p.Val834fs Multiple submitters VPS13A-related neurodegenerative disease
  • p.Val905_Val906insTer Multiple submitters VPS13A-related neurodegenerative disease

Likely pathogenic 205

Conflicting classifications of pathogenicity 93

Benign 209

Benign/Likely benign 69

  • c.101-3dup Multiple submitters
  • c.101-7T>C Multiple submitters VPS13A-related neurodegenerative disease
  • c.1358-29A>G Multiple submitters
  • c.1452+13C>A Multiple submitters
  • c.1453-15C>T Multiple submitters VPS13A-related neurodegenerative disease
  • c.1596-8del Multiple submitters
  • c.2037+8C>A Multiple submitters VPS13A-related neurodegenerative disease
  • c.2289-16del Multiple submitters
  • c.2667+12G>A Multiple submitters VPS13A-related neurodegenerative disease
  • c.2964+18A>G Multiple submitters
  • c.3119-5del Multiple submitters
  • c.3119-5dup Multiple submitters
  • c.3813-15T>C Multiple submitters VPS13A-related neurodegenerative disease
  • c.385+6_385+15del Multiple submitters VPS13A-related neurodegenerative disease
  • c.3961-6dup Multiple submitters VPS13A-related neurodegenerative disease
  • c.3961-7_3961-6dup Multiple submitters
  • c.4630+17A>G Multiple submitters VPS13A-related neurodegenerative disease
  • c.4631-17A>G Multiple submitters
  • c.556-10dup Multiple submitters
  • c.5831-8T>C Multiple submitters VPS13A-related neurodegenerative disease
  • c.6096-16A>T Multiple submitters
  • c.6096-7C>T Multiple submitters VPS13A-related neurodegenerative disease
  • c.615+20G>C Multiple submitters VPS13A-related neurodegenerative disease
  • c.6379-17T>G Multiple submitters
  • c.6379-7A>T Multiple submitters VPS13A-related neurodegenerative disease
  • c.6880-19G>C Multiple submitters VPS13A-related neurodegenerative disease
  • c.7155+14del Multiple submitters
  • c.7155+14dup Multiple submitters VPS13A-related neurodegenerative disease
  • c.7155+21dup Multiple submitters
  • c.7954-11del Multiple submitters
  • c.8472-12C>T Multiple submitters VPS13A-related neurodegenerative disease
  • c.8472-18T>C Multiple submitters
  • c.883-16A>C Multiple submitters VPS13A-related neurodegenerative disease
  • c.8907+10T>G Multiple submitters VPS13A-related neurodegenerative disease
  • c.8954-16T>G Multiple submitters
  • c.8954-9dup Multiple submitters
  • c.9078-7C>T Multiple submitters VPS13A-related neurodegenerative disease
  • c.9189+2545TGA[6] Multiple submitters VPS13A-related neurodegenerative disease
  • c.9189+2818G>T Multiple submitters
  • c.9190-20C>T Multiple submitters
  • c.9400-15A>C Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ala1347= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ala1813= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ala586= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Arg1993= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Asp2230= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu1028Gly Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu1548Lys Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu2137Gly Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu2385= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Glu916= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Gly1119Glu Multiple submitters VPS13A-related neurodegenerative disease
  • p.His196= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ile2486Val Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ile2892= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Leu1761= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Leu1934= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Lys2743Thr Multiple submitters VPS13A-related neurodegenerative disease
  • p.Pro797= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser1728= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser1916Asn Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser2784Ala Multiple submitters VPS13A-related neurodegenerative disease
  • p.Ser708= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Thr1026= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Thr1861= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Thr404= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Tyr2857= Multiple submitters VPS13A-related neurodegenerative disease
  • p.Val1973Ile Multiple submitters VPS13A-related neurodegenerative disease
  • p.Val898Ala Multiple submitters VPS13A-related neurodegenerative disease

Likely benign 2005

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

Uncertain significance 918

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