SLC26A3 — 858 ClinVar variants

All ClinVar germline SLC26A3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 222 flagged for review →

59 Pathogenic · 13 Pathogenic/Likely pathogenic · 56 Likely pathogenic · 18 Conflicting · 43 Benign · 16 Benign/Likely benign · 405 Likely benign · 248 Uncertain significance

Full SLC26A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 222

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 9

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

Predictors lean, ClinVar uncertain 153

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 153

Predictors split 59

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

All SLC26A3 variants

Pathogenic 59

Pathogenic/Likely pathogenic 13

  • c.1312-1G>T Multiple submitters congenital secretory chloride diarrhea 1
  • c.1515-2del Multiple submitters SLC26A3-related disorder
  • c.571-2A>G Multiple submitters congenital secretory chloride diarrhea 1
  • p.Ala347Thr Multiple submitters SLC26A3-related disorder ⚠
  • p.Asp308_Phe309insTer Multiple submitters congenital secretory chloride diarrhea 1
  • p.Asp558fs Multiple submitters congenital secretory chloride diarrhea 1
  • p.Gln584Ter Multiple submitters
  • p.Gly120Ser Multiple submitters SLC26A3-related disorder
  • p.Ile544Asn Multiple submitters congenital secretory chloride diarrhea 1
  • p.Ile675dup Multiple submitters SLC26A3-related disorder
  • p.Met1fs Multiple submitters congenital secretory chloride diarrhea 1
  • p.Pro131Leu Multiple submitters congenital secretory chloride diarrhea 1
  • p.Lys49fs No assertion criteria congenital secretory chloride diarrhea 1

Likely pathogenic 56

  • p.Gly393Trp Multiple submitters congenital secretory chloride diarrhea 1 ⚠
  • c.1120-1G>A Single submitter
  • c.1120-2A>G Single submitter congenital secretory chloride diarrhea 1
  • c.1234-1G>A Single submitter
  • c.1407+6T>C Single submitter SLC26A3-related disorder
  • c.1514+1G>T Single submitter congenital secretory chloride diarrhea 1
  • c.2007+2T>G Single submitter
  • c.2205+1G>T Single submitter congenital secretory chloride diarrhea 1
  • c.2206-2A>G Single submitter
  • c.271+2T>C Single submitter
  • c.382+1G>A Single submitter
  • c.383-1G>A Single submitter
  • c.570+1G>T Single submitter
  • c.736-2del Single submitter
  • c.889-2A>G Single submitter
  • c.971+3_971+4del Single submitter congenital secretory chloride diarrhea 1
  • c.972-1G>A Single submitter
  • p.Ala192fs Single submitter congenital secretory chloride diarrhea 1
  • p.Ala512fs Single submitter congenital secretory chloride diarrhea 1
  • p.Asp701Ter Single submitter congenital secretory chloride diarrhea 1
  • p.Gln436Arg Single submitter congenital secretory chloride diarrhea 1
  • p.Glu293Lys Single submitter congenital secretory chloride diarrhea 1
  • p.Glu374Ter Single submitter congenital secretory chloride diarrhea 1
  • p.Gly128Ser Single submitter congenital secretory chloride diarrhea 1 ⚠
  • p.Leu470Ter Single submitter congenital secretory chloride diarrhea 1
  • p.Met136Val Single submitter congenital secretory chloride diarrhea 1
  • p.Phe551fs Single submitter congenital secretory chloride diarrhea 1
  • p.Ser224fs Single submitter congenital secretory chloride diarrhea 1
  • p.Ser438Pro Single submitter congenital secretory chloride diarrhea 1
  • p.Trp472Ter Single submitter SLC26A3-related disorder
  • p.Tyr16Ter Single submitter congenital secretory chloride diarrhea 1
  • p.Val176fs Single submitter congenital secretory chloride diarrhea 1
  • p.Val421fs Single submitter congenital secretory chloride diarrhea 1
  • c.1312-1G>A No assertion criteria congenital secretory chloride diarrhea 1
  • c.1408-1G>A No assertion criteria congenital secretory chloride diarrhea 1
  • c.2205+3A>G No assertion criteria congenital secretory chloride diarrhea 1
  • p.Arg175Ser No assertion criteria congenital secretory chloride diarrhea 1
  • p.Asp468Val No assertion criteria congenital secretory chloride diarrhea 1
  • p.Cys343Tyr No assertion criteria congenital secretory chloride diarrhea 1
  • p.Gln454fs No assertion criteria congenital secretory chloride diarrhea 1
  • p.Gln454Ter No assertion criteria congenital secretory chloride diarrhea 1
  • p.Gly702delinsThrGlyPheGluValLysIleGlnAsnPhe No assertion criteria congenital secretory chloride diarrhea 1
  • p.His220Pro No assertion criteria congenital secretory chloride diarrhea 1
  • p.Leu448fs No assertion criteria congenital secretory chloride diarrhea 1
  • p.Leu496Arg No assertion criteria congenital secretory chloride diarrhea 1
  • p.Leu711Ter No assertion criteria congenital secretory chloride diarrhea 1
  • p.Lys521Asn No assertion criteria congenital secretory chloride diarrhea 1 ⚠
  • p.Met136Ile No assertion criteria congenital secretory chloride diarrhea 1
  • p.Phe111fs No assertion criteria congenital secretory chloride diarrhea 1
  • p.Phe344_Val349delinsAspAla No assertion criteria congenital secretory chloride diarrhea 1
  • p.Pro131fs No assertion criteria congenital secretory chloride diarrhea 1
  • p.Pro506fs No assertion criteria congenital secretory chloride diarrhea 1
  • p.Ser206Pro No assertion criteria congenital secretory chloride diarrhea 1
  • p.Ser509fs No assertion criteria congenital secretory chloride diarrhea 1
  • p.Ser542fs No assertion criteria congenital secretory chloride diarrhea 1
  • p.Ser663_Val664insTer No assertion criteria congenital secretory chloride diarrhea 1

Conflicting classifications of pathogenicity 18

Benign 43

Benign/Likely benign 16

  • c.271+14del Multiple submitters
  • c.889-6T>C Multiple submitters congenital secretory chloride diarrhea 1
  • c.972-14A>C Multiple submitters congenital secretory chloride diarrhea 1
  • p.Arg197Gln Multiple submitters congenital secretory chloride diarrhea 1
  • p.Arg68Gln Multiple submitters congenital secretory chloride diarrhea 1
  • p.Asn753Ser Multiple submitters congenital secretory chloride diarrhea 1
  • p.Asp332= Multiple submitters congenital secretory chloride diarrhea 1
  • p.Ile601Thr Multiple submitters congenital secretory chloride diarrhea 1
  • p.Ile81Val Multiple submitters congenital secretory chloride diarrhea 1
  • p.Leu616= Multiple submitters
  • p.Leu651= Multiple submitters congenital secretory chloride diarrhea 1
  • p.Phe119= Multiple submitters congenital secretory chloride diarrhea 1
  • p.Ser126= Multiple submitters congenital secretory chloride diarrhea 1
  • p.Ser438= Multiple submitters congenital secretory chloride diarrhea 1
  • p.Thr395= Multiple submitters
  • p.Thr510Met Multiple submitters congenital secretory chloride diarrhea 1

Likely benign 405

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

Uncertain significance 248