CA5A — 225 ClinVar variants

All ClinVar germline CA5A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 111 flagged for review →

5 Pathogenic · 1 Pathogenic/Likely pathogenic · 3 Likely pathogenic · 11 Conflicting · 10 Benign · 2 Benign/Likely benign · 83 Likely benign · 110 Uncertain significance

Full CA5A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 111

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 5

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

Predictors lean, ClinVar uncertain 47

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

Predictors split 59

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

All CA5A variants

Pathogenic 5

  • p.Arg32Ter Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ser141fs Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Trp159Arg Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Trp228Ter Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.619-3421_774+502del No assertion criteria hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency

Pathogenic/Likely pathogenic 1

  • p.Glu241Lys Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency

Likely pathogenic 3

  • c.459+1G>C Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.618+1G>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Gln194Ter Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency

Conflicting classifications of pathogenicity 11

  • c.767_774+13del Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ala149Val Single submitter Inborn genetic diseases ⚠
  • p.Arg263His Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Asn166Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly181= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ile95Val Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Leu186Phe Single submitter Inborn genetic diseases ⚠
  • p.Lys185= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ser233Pro Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Val172Leu Single submitter Inborn genetic diseases ⚠
  • p.Val58Met Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠

Benign 10

  • c.143-9T>A Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ala269= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Asn45Lys Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Asn46Lys Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Phe215= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro151= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.340+2435T>C Single submitter
  • c.460-14C>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.555+12C>G Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.618+1769A>G Single submitter

Benign/Likely benign 2

  • c.340+20C>G Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ala294= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency

Likely benign 83

  • p.Arg72= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Asp73= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Glu250Gly Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Leu186= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro251= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro82Thr Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ser86= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Thr219Ala Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Tyr150= Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.142+14C>G Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.143-11T>C Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.143-15TC[5] Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.143-16G>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.143-20C>G Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.143-4G>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.340+16G>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.340+17G>C Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.340+7G>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.459+10C>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.459+11G>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.459+7A>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.555+16G>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.555+19G>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.556-13G>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.618+10A>G Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.618+16G>C Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.619-11C>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.619-7C>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.774+13C>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.774+14G>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.774+7C>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.775-10T>A Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.775-20C>T Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ala149= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ala170= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ala208= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ala210= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ala231Val Single submitter Inborn genetic diseases
  • p.Ala89= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Arg282= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Asn137= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Asn289= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Asp146= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Glu138= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Glu273= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Gly60Arg Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Gly61= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.His143= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.His148= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ile115= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ile199Val Single submitter Inborn genetic diseases
  • p.Leu196= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Leu221= Single submitter
  • p.Leu259= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Leu265= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Leu284= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Leu51= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Leu83= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Leu93= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro201= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro237= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro238= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro283= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro55= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ser10= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ser233= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ser242= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ser27= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ser27Trp Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ser295= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Thr219= Single submitter
  • p.Thr229= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Thr240= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Thr244= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Thr53= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Thr6= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Thr9= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Tyr100= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Tyr230= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Val171= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Val85= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • c.618+7T>G No assertion criteria CA5A-related disorder
  • c.*10G>A No assertion criteria CA5A-related disorder

Uncertain significance 110

  • p.Ala149Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Ala208Val Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ala261Val Multiple submitters Inborn genetic diseases ⚠
  • p.Arg26His Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Asp216Ala Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Gln79Glu Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.His143Asp Multiple submitters Inborn genetic diseases ⚠
  • p.His158Pro Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.His205Gln Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Leu259Val Multiple submitters Inborn genetic diseases ⚠
  • p.Phe14Ser Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Phe215Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Pro222Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Pro30Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Pro50Gln Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Thr192Met Multiple submitters Inborn genetic diseases ⚠
  • p.Thr223Asn Multiple submitters Inborn genetic diseases ⚠
  • p.Trp96Ser Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Val145Met Multiple submitters Inborn genetic diseases ⚠
  • p.Val182Met Multiple submitters hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • c.340+277G>A Single submitter
  • c.340+8191G>A Single submitter
  • c.341-7517G>T Single submitter
  • c.774+4A>G Single submitter Inborn genetic diseases
  • p.Ala135Val Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ala170Ser Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ala208Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala210Val Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ala231Gly Single submitter ⚠
  • p.Ala231Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala255Thr Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ala294Val Single submitter Inborn genetic diseases ⚠
  • p.Arg209Gln Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Arg209Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg213Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg213His Single submitter Inborn genetic diseases ⚠
  • p.Arg213Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg263Cys Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Arg282Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg290Gln Single submitter ⚠
  • p.Arg290Trp Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Arg37Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg37His Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Arg63Trp Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Asn175Asp Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Asn280His Single submitter Inborn genetic diseases ⚠
  • p.Asp108Asn Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Asp198Asn Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Asp216Asn Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Asp226Asn Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Cys92Tyr Single submitter Inborn genetic diseases ⚠
  • p.Gln248His Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Gln258His Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Gln70Arg Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Glu138Lys Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Gly140Ala Single submitter Inborn genetic diseases ⚠
  • p.Gly271Ala Single submitter Inborn genetic diseases ⚠
  • p.Gly61Cys Single submitter Inborn genetic diseases ⚠
  • p.Gly61Ser Single submitter Inborn genetic diseases ⚠
  • p.His158Tyr Single submitter ⚠
  • p.His189Tyr Single submitter Inborn genetic diseases ⚠
  • p.His205Asp Single submitter Inborn genetic diseases ⚠
  • p.His300Arg Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Ile199Phe Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ile203Val Single submitter Inborn genetic diseases ⚠
  • p.Leu126Val Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Leu15= Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Leu15Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu186Val Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Leu259Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu270Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu2Phe Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Lys206Glu Single submitter Inborn genetic diseases ⚠
  • p.Met19Ile Single submitter Inborn genetic diseases ⚠
  • p.Met212Ile Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Met28Lys Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Phe106Ser Single submitter Inborn genetic diseases ⚠
  • p.Phe129Leu Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Phe131Leu Single submitter Inborn genetic diseases ⚠
  • p.Phe267Leu Single submitter ⚠
  • p.Pro201Thr Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Pro214Ala Single submitter Inborn genetic diseases ⚠
  • p.Pro217Thr Single submitter Inborn genetic diseases ⚠
  • p.Pro222Ala Single submitter Inborn genetic diseases ⚠
  • p.Pro22Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro22Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro237Arg Single submitter Inborn genetic diseases ⚠
  • p.Pro237Leu Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Pro283Glu Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Pro55Leu Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Pro66Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro78Ala Single submitter Inborn genetic diseases ⚠
  • p.Ser13Phe Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ser242Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser44Gly Single submitter Inborn genetic diseases ⚠
  • p.Ser91Pro Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Ter306Trp Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Thr229Ile Single submitter ⚠
  • p.Thr43Ser Single submitter Inborn genetic diseases ⚠
  • p.Thr53Met Single submitter Inborn genetic diseases ⚠
  • p.Thr62Ile Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Trp245Ter Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
  • p.Trp41Cys Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Trp52Arg Single submitter Inborn genetic diseases ⚠
  • p.Tyr100Asn Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Val145Ala Single submitter ⚠
  • p.Val171Ala Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Val172Met Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠
  • p.Val85Ile Single submitter Inborn genetic diseases ⚠
  • p.Val85Phe Single submitter hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency ⚠