SLC25A13 — 920 ClinVar variants

All ClinVar germline SLC25A13 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 199 flagged for review →

84 Pathogenic · 32 Pathogenic/Likely pathogenic · 86 Likely pathogenic · 47 Conflicting · 33 Benign · 7 Benign/Likely benign · 397 Likely benign · 234 Uncertain significance

Full SLC25A13 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 199

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 16

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

Predictors lean, ClinVar uncertain 123

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 SLC25A13 variants

Pathogenic 84

Pathogenic/Likely pathogenic 32

  • c.1231-1G>A Multiple submitters citrullinemia, type II, adult-onset
  • c.1453-1G>C Multiple submitters citrullinemia, type II, adult-onset
  • c.16-2A>G Multiple submitters citrin deficiency
  • c.70-1G>A Multiple submitters citrullinemia, type II, adult-onset
  • c.848+1del Multiple submitters citrullinemia, type II, adult-onset
  • c.848+1G>T Multiple submitters citrullinemia, type II, adult-onset
  • c.848+3A>C Multiple submitters citrin deficiency
  • p.Ala541Asp Multiple submitters citrin deficiency
  • p.Arg144fs Multiple submitters citrullinemia, type II, adult-onset
  • p.Arg177fs Multiple submitters citrin deficiency
  • p.Arg191fs Multiple submitters citrullinemia, type II, adult-onset
  • p.Arg360Ter Multiple submitters citrullinemia, type II, adult-onset
  • p.Arg43Ter Multiple submitters SLC25A13-related disorder
  • p.Arg588Ter Multiple submitters citrin deficiency
  • p.Arg605Ter Multiple submitters citrullinemia
  • p.Asn30fs Multiple submitters citrin deficiency
  • p.Asp350Asn Multiple submitters citrullinemia, type II, adult-onset
  • p.Cys437Ter Multiple submitters citrullinemia, type II, adult-onset
  • p.Gln324Ter Multiple submitters citrullinemia, type II, adult-onset
  • p.Gln556fs Multiple submitters citrullinemia, type II, adult-onset
  • p.Glu106Ter Multiple submitters citrin deficiency
  • p.Glu252Lys Multiple submitters citrullinemia, type II, adult-onset ⚠
  • p.Glu77Ter Multiple submitters citrullinemia
  • p.His193fs Multiple submitters citrullinemia, type II, adult-onset
  • p.Lys23fs Multiple submitters citrullinemia
  • p.Phe92fs Multiple submitters citrin deficiency
  • p.Ser590Ter Multiple submitters neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Tyr330Ter Multiple submitters citrin deficiency
  • p.Tyr391Ter Multiple submitters citrullinemia, type II, adult-onset
  • p.Tyr559Ter Multiple submitters citrullinemia, type II, adult-onset
  • p.Val204fs Multiple submitters citrin deficiency
  • p.Val411Met Multiple submitters citrullinemia, type II, adult-onset ⚠

Likely pathogenic 86

  • c.1178-1G>C Multiple submitters citrin deficiency
  • c.1178-1G>T Multiple submitters citrullinemia, type II, adult-onset
  • c.1452+1G>A Multiple submitters citrin deficiency
  • c.1591+1G>A Multiple submitters neonatal intrahepatic cholestasis due to citrin deficiency
  • c.1750+1G>C Multiple submitters citrullinemia
  • c.934-2A>T Multiple submitters citrullinemia
  • p.Gln311Ter Multiple submitters neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Gln357Ter Multiple submitters citrullinemia
  • p.Glu404Ter Multiple submitters citrullinemia type II
  • p.Gly436Glu Multiple submitters citrullinemia type II
  • p.Gly531Asp Multiple submitters citrullinemia
  • p.Phe254fs Multiple submitters citrullinemia
  • p.Thr539fs Multiple submitters citrullinemia, type II, adult-onset
  • p.Thr546Met Multiple submitters citrullinemia type II
  • p.Trp606Ter Multiple submitters citrullinemia
  • p.Tyr24Ter Multiple submitters citrullinemia
  • c.1176_1177+1delinsT Single submitter citrullinemia, type II, adult-onset
  • c.1311+2dup Single submitter citrullinemia, type II, adult-onset
  • c.1592-2A>T Single submitter citrullinemia
  • c.16-2A>T Single submitter citrullinemia
  • c.1750+1G>A Single submitter citrullinemia
  • c.1750+1G>T Single submitter citrullinemia, type II, adult-onset
  • c.1750+2T>C Single submitter citrin deficiency
  • c.1841+1G>T Single submitter citrullinemia, type II, adult-onset
  • c.1841+3_1841+4del Single submitter citrin deficiency
  • c.212+1G>A Single submitter citrullinemia
  • c.213-1G>C Single submitter citrullinemia, type II, adult-onset
  • c.213-2A>C Single submitter citrin deficiency
  • c.213-2A>G Single submitter citrin deficiency
  • c.328+1G>C Single submitter citrullinemia
  • c.328+1G>T Single submitter citrin deficiency
  • c.329-1G>A Single submitter citrin deficiency
  • c.329-2A>G Single submitter citrin deficiency
  • c.468+1G>C Single submitter citrullinemia, type II, adult-onset
  • c.468+4958_502del Single submitter citrullinemia, type II, adult-onset
  • c.468+5G>A Single submitter
  • c.469-2A>G Single submitter citrin deficiency
  • c.616-2del Single submitter citrin deficiency
  • c.70-1G>T Single submitter citrin deficiency
  • c.70-2A>T Single submitter citrullinemia, type II, adult-onset
  • c.755-1G>C Single submitter citrin deficiency
  • p.Arg234fs Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Arg392_Gly393delinsCys Single submitter citrullinemia, type II, adult-onset
  • p.Arg475fs Single submitter citrullinemia
  • p.Arg492Trp Single submitter citrin deficiency
  • p.Arg553fs Single submitter citrullinemia
  • p.Asn224fs Single submitter citrullinemia, type II, adult-onset
  • p.Asp111fs Single submitter citrullinemia, type II, adult-onset
  • p.Asp89fs Single submitter citrullinemia, type II, adult-onset
  • p.Gln118fs Single submitter citrullinemia, type II, adult-onset
  • p.Gln169Ter Single submitter citrullinemia, type II, adult-onset
  • p.Gln274fs Single submitter citrullinemia
  • p.Gln309Ter Single submitter citrullinemia, type II, adult-onset
  • p.Gln517Ter Single submitter citrullinemia, type II, adult-onset
  • p.Glu297fs Single submitter citrullinemia, type II, adult-onset
  • p.Glu368Ter Single submitter citrullinemia
  • p.Glu404fs Single submitter
  • p.Glu431Ter Single submitter citrullinemia
  • p.Glu77fs Single submitter citrullinemia, type II, adult-onset
  • p.Gly386Val Single submitter citrullinemia
  • p.Gly439Arg Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Gly439Glu Single submitter citrin deficiency
  • p.Gly460Ter Single submitter citrullinemia
  • p.Gly594Asp Single submitter citrin deficiency
  • p.Ile349Thr Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Ile563fs Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Ile609fs Single submitter citrullinemia, type II, adult-onset
  • p.Leu278_Tyr279insTer Single submitter citrullinemia, type II, adult-onset
  • p.Lys143Ter Single submitter citrullinemia
  • p.Met370fs Single submitter citrullinemia, type II, adult-onset
  • p.Pro197fs Single submitter citrullinemia, type II, adult-onset
  • p.Pro88fs Single submitter citrullinemia
  • p.Ser374fs Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Ser74fs Single submitter citrullinemia, type II, adult-onset
  • p.Ser83fs Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Thr546fs Single submitter citrullinemia, type II, adult-onset
  • p.Thr599fs Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Tyr347fs Single submitter citrullinemia, type II, adult-onset
  • p.Tyr371Ter Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Tyr500fs Single submitter citrullinemia, type II, adult-onset
  • p.Val255fs Single submitter neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Val562fs Single submitter citrullinemia
  • p.Val6fs Single submitter citrullinemia
  • p.Ala670fs No assertion criteria neonatal intrahepatic cholestasis due to citrin deficiency
  • p.Leu597fs No assertion criteria SLC25A13-related disorder
  • p.Val381fs No assertion criteria SLC25A13-related disorder

Conflicting classifications of pathogenicity 47

Benign 33

Benign/Likely benign 7

Likely benign 397

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

Uncertain significance 234