SLC5A1 — 538 ClinVar variants

All ClinVar germline SLC5A1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 173 flagged for review →

19 Pathogenic · 3 Pathogenic/Likely pathogenic · 25 Likely pathogenic · 28 Conflicting · 33 Benign · 7 Benign/Likely benign · 197 Likely benign · 226 Uncertain significance

Full SLC5A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 173

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 9

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

Predictors lean, ClinVar uncertain 130

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

Predictors split 34

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

All SLC5A1 variants

Pathogenic 19

Pathogenic/Likely pathogenic 3

Likely pathogenic 25

  • p.Arg336His Multiple submitters glucose-galactose malabsorption
  • p.Ser159Pro Multiple submitters glucose-galactose malabsorption
  • p.Trp67Ter Multiple submitters SLC5A1-related disorder
  • c.1021+1G>A Single submitter glucose-galactose malabsorption
  • c.136-1G>A Single submitter glucose-galactose malabsorption
  • c.1772-1G>A Single submitter glucose-galactose malabsorption
  • c.205_207+2delinsAA Single submitter glucose-galactose malabsorption
  • c.207+2T>C Single submitter glucose-galactose malabsorption
  • c.372+1_372+2insCTTATAT Single submitter glucose-galactose malabsorption
  • c.665-2A>G Single submitter glucose-galactose malabsorption
  • c.885+1G>A Single submitter glucose-galactose malabsorption
  • p.Ala76fs Single submitter glucose-galactose malabsorption
  • p.Arg300His Single submitter glucose-galactose malabsorption
  • p.Arg499Cys Single submitter glucose-galactose malabsorption
  • p.Arg499His Single submitter glucose-galactose malabsorption
  • p.Cys355Ser Single submitter glucose-galactose malabsorption
  • p.Glu253Ter Single submitter glucose-galactose malabsorption
  • p.Gly318Arg Single submitter SLC5A1-related disorder
  • p.Leu185Ser Single submitter glucose-galactose malabsorption
  • p.Leu316Pro Single submitter glucose-galactose malabsorption
  • p.Met1Thr Single submitter glucose-galactose malabsorption
  • p.Met233fs Single submitter SLC5A1-related disorder
  • p.Trp477Ter Single submitter glucose-galactose malabsorption
  • p.Tyr256fs Single submitter Renal glycosuria
  • p.Tyr526Ter Single submitter SLC5A1-related disorder

Conflicting classifications of pathogenicity 28

  • c.1280+8C>G Single submitter glucose-galactose malabsorption
  • c.207+2dup Single submitter SLC5A1-related disorder
  • c.208-13T>A Single submitter glucose-galactose malabsorption
  • p.Ala12Val Single submitter glucose-galactose malabsorption ⚠
  • p.Ala468= Single submitter glucose-galactose malabsorption
  • p.Ala575= Single submitter glucose-galactose malabsorption
  • p.Arg336Cys Single submitter glucose-galactose malabsorption ⚠
  • p.Arg558His Single submitter SLC5A1-related disorder ⚠
  • p.Arg603= Single submitter glucose-galactose malabsorption
  • p.Asn376= Single submitter glucose-galactose malabsorption
  • p.Asp572= Single submitter glucose-galactose malabsorption
  • p.Glu589Ter Single submitter SLC5A1-related disorder
  • p.Gly616Ser Single submitter glucose-galactose malabsorption ⚠
  • p.Ile343Thr Single submitter SLC5A1-related disorder ⚠
  • p.Ile397= Single submitter glucose-galactose malabsorption
  • p.Ile438= Single submitter glucose-galactose malabsorption
  • p.Ile467Thr Single submitter glucose-galactose malabsorption ⚠
  • p.Ile588Thr Single submitter glucose-galactose malabsorption ⚠
  • p.Leu183= Single submitter glucose-galactose malabsorption
  • p.Leu288Val Single submitter Inborn genetic diseases ⚠
  • p.Thr203= Single submitter glucose-galactose malabsorption
  • p.Thr208= Single submitter glucose-galactose malabsorption
  • p.Thr271= Single submitter glucose-galactose malabsorption
  • p.Thr508= Single submitter glucose-galactose malabsorption
  • p.Thr519Met Single submitter Inborn genetic diseases ⚠
  • p.Trp477Cys Single submitter glucose-galactose malabsorption ⚠
  • p.Val209Leu Single submitter glucose-galactose malabsorption ⚠
  • p.Val33Ile Single submitter glucose-galactose malabsorption ⚠

Benign 33

  • c.1130-9C>T Multiple submitters glucose-galactose malabsorption
  • c.1666-5T>C Multiple submitters glucose-galactose malabsorption
  • c.313-79G>A Multiple submitters
  • c.373-9C>T Multiple submitters glucose-galactose malabsorption
  • c.*1432G>T Multiple submitters glucose-galactose malabsorption
  • c.*1804T>C Multiple submitters glucose-galactose malabsorption
  • c.*2245C>T Multiple submitters glucose-galactose malabsorption
  • c.*2257A>G Multiple submitters glucose-galactose malabsorption
  • c.*706C>T Multiple submitters glucose-galactose malabsorption
  • c.*795G>T Multiple submitters glucose-galactose malabsorption
  • c.*902T>G Multiple submitters glucose-galactose malabsorption
  • p.Ala411Thr Multiple submitters glucose-galactose malabsorption
  • p.Ala425= Multiple submitters glucose-galactose malabsorption
  • p.Asn51Ser Multiple submitters glucose-galactose malabsorption
  • p.Asn646= Multiple submitters glucose-galactose malabsorption
  • p.Asp2= Multiple submitters glucose-galactose malabsorption
  • p.His615Gln Multiple submitters glucose-galactose malabsorption
  • p.Leu612= Multiple submitters glucose-galactose malabsorption
  • p.Thr633= Multiple submitters glucose-galactose malabsorption
  • p.Val17Ala Multiple submitters glucose-galactose malabsorption
  • c.1771+3G>A Single submitter glucose-galactose malabsorption
  • c.312+317_312+318insAT Single submitter
  • c.312+329_312+330del Single submitter
  • c.584-88dup Single submitter
  • c.885+20G>A Single submitter glucose-galactose malabsorption
  • c.-170C>T Single submitter glucose-galactose malabsorption
  • c.*1508C>A Single submitter glucose-galactose malabsorption
  • c.*1940G>A Single submitter glucose-galactose malabsorption
  • c.*2244C>T Single submitter glucose-galactose malabsorption
  • c.*2275C>T Single submitter glucose-galactose malabsorption
  • c.*400C>T Single submitter glucose-galactose malabsorption
  • c.*771C>T Single submitter glucose-galactose malabsorption
  • p.Phe453= Single submitter glucose-galactose malabsorption

Benign/Likely benign 7

  • c.1129+7T>G Multiple submitters glucose-galactose malabsorption
  • c.1130-10_1130-8del Multiple submitters glucose-galactose malabsorption
  • c.1772-6G>A Multiple submitters glucose-galactose malabsorption
  • c.373-13G>A Multiple submitters glucose-galactose malabsorption
  • p.Asn248= Multiple submitters glucose-galactose malabsorption
  • p.Ile364= Multiple submitters glucose-galactose malabsorption
  • p.Ser400= Multiple submitters glucose-galactose malabsorption

Likely benign 197

  • c.1280+17C>T Multiple submitters glucose-galactose malabsorption
  • c.1666-10T>C Multiple submitters glucose-galactose malabsorption
  • c.208-8G>A Multiple submitters glucose-galactose malabsorption
  • c.373-7del Multiple submitters glucose-galactose malabsorption
  • c.584-6G>A Multiple submitters glucose-galactose malabsorption
  • c.886-10T>C Multiple submitters glucose-galactose malabsorption
  • p.Ala198= Multiple submitters glucose-galactose malabsorption
  • p.Ala27= Multiple submitters glucose-galactose malabsorption
  • p.Leu527= Multiple submitters glucose-galactose malabsorption
  • p.Pro552= Multiple submitters glucose-galactose malabsorption
  • p.Pro584= Multiple submitters glucose-galactose malabsorption
  • p.Thr10= Multiple submitters glucose-galactose malabsorption
  • p.Thr11= Multiple submitters glucose-galactose malabsorption
  • c.1021+15T>G Single submitter glucose-galactose malabsorption
  • c.1021+19C>T Single submitter glucose-galactose malabsorption
  • c.1021+9T>C Single submitter glucose-galactose malabsorption
  • c.1022-6T>G Single submitter glucose-galactose malabsorption
  • c.1022-7T>C Single submitter glucose-galactose malabsorption
  • c.1129+23_1129+26del Single submitter glucose-galactose malabsorption
  • c.1130-7C>A Single submitter glucose-galactose malabsorption
  • c.1130-7C>T Single submitter glucose-galactose malabsorption
  • c.1280+13T>C Single submitter glucose-galactose malabsorption
  • c.1280+7G>T Single submitter glucose-galactose malabsorption
  • c.1281-13G>T Single submitter glucose-galactose malabsorption
  • c.1281-8_1281-4dup Single submitter glucose-galactose malabsorption
  • c.135+10G>A Single submitter glucose-galactose malabsorption
  • c.135+12G>T Single submitter glucose-galactose malabsorption
  • c.135+14T>G Single submitter glucose-galactose malabsorption
  • c.135+16T>G Single submitter glucose-galactose malabsorption
  • c.135+9C>T Single submitter glucose-galactose malabsorption
  • c.136-17dup Single submitter glucose-galactose malabsorption
  • c.1449+13T>C Single submitter
  • c.1449+14G>A Single submitter glucose-galactose malabsorption
  • c.1450-18C>T Single submitter glucose-galactose malabsorption
  • c.1450-20C>T Single submitter glucose-galactose malabsorption
  • c.1450-5del Single submitter glucose-galactose malabsorption
  • c.1665+19G>C Single submitter glucose-galactose malabsorption
  • c.1665+7A>G Single submitter glucose-galactose malabsorption
  • c.1666-13G>A Single submitter glucose-galactose malabsorption
  • c.1666-20C>G Single submitter glucose-galactose malabsorption
  • c.1771+14C>G Single submitter glucose-galactose malabsorption
  • c.1771+20A>G Single submitter glucose-galactose malabsorption
  • c.1771+9T>C Single submitter glucose-galactose malabsorption
  • c.1772-10C>T Single submitter
  • c.1772-14A>G Single submitter glucose-galactose malabsorption
  • c.1772-18T>A Single submitter glucose-galactose malabsorption
  • c.1772-6G>T Single submitter glucose-galactose malabsorption
  • c.207+19G>A Single submitter glucose-galactose malabsorption
  • c.207+19G>C Single submitter glucose-galactose malabsorption
  • c.208-13T>C Single submitter glucose-galactose malabsorption
  • c.208-13T>G Single submitter glucose-galactose malabsorption
  • c.208-16T>C Single submitter glucose-galactose malabsorption
  • c.208-20A>C Single submitter glucose-galactose malabsorption
  • c.208-9C>T Single submitter glucose-galactose malabsorption
  • c.312+17C>A Single submitter glucose-galactose malabsorption
  • c.312+18C>A Single submitter glucose-galactose malabsorption
  • c.312+19A>G Single submitter glucose-galactose malabsorption
  • c.313-7A>G Single submitter glucose-galactose malabsorption
  • c.372+15T>G Single submitter glucose-galactose malabsorption
  • c.372+7_372+8del Single submitter glucose-galactose malabsorption
  • c.372+8T>G Single submitter glucose-galactose malabsorption
  • c.373-12C>T Single submitter glucose-galactose malabsorption
  • c.373-6A>G Single submitter glucose-galactose malabsorption
  • c.373-8C>T Single submitter glucose-galactose malabsorption
  • c.477+15C>T Single submitter glucose-galactose malabsorption
  • c.477+9A>G Single submitter glucose-galactose malabsorption
  • c.478-12C>T Single submitter glucose-galactose malabsorption
  • c.478-13C>T Single submitter glucose-galactose malabsorption
  • c.478-15C>G Single submitter glucose-galactose malabsorption
  • c.478-15C>T Single submitter glucose-galactose malabsorption
  • c.478-16T>C Single submitter glucose-galactose malabsorption
  • c.478-19G>A Single submitter glucose-galactose malabsorption
  • c.478-20C>T Single submitter glucose-galactose malabsorption
  • c.478-7dup Single submitter glucose-galactose malabsorption
  • c.583+20C>A Single submitter glucose-galactose malabsorption
  • c.584-19T>C Single submitter glucose-galactose malabsorption
  • c.584-4T>A Single submitter glucose-galactose malabsorption
  • c.584-5C>T Single submitter glucose-galactose malabsorption
  • c.664+14G>A Single submitter glucose-galactose malabsorption
  • c.665-12G>A Single submitter glucose-galactose malabsorption
  • c.665-13C>T Single submitter glucose-galactose malabsorption
  • c.885+15T>C Single submitter glucose-galactose malabsorption
  • c.885+16G>A Single submitter glucose-galactose malabsorption
  • c.885+19C>G Single submitter glucose-galactose malabsorption
  • c.885+19C>T Single submitter glucose-galactose malabsorption
  • c.886-15G>A Single submitter glucose-galactose malabsorption
  • c.886-5G>C Single submitter glucose-galactose malabsorption
  • c.-11dup Single submitter
  • c.-15C>T Single submitter
  • c.-36G>A Single submitter glucose-galactose malabsorption
  • c.*1203A>G Single submitter glucose-galactose malabsorption
  • c.*1237A>G Single submitter glucose-galactose malabsorption
  • c.*1455C>A Single submitter glucose-galactose malabsorption
  • c.*1476A>G Single submitter glucose-galactose malabsorption
  • p.Ala12= Single submitter glucose-galactose malabsorption
  • p.Ala123= Single submitter glucose-galactose malabsorption
  • p.Ala199= Single submitter glucose-galactose malabsorption
  • p.Ala239= Single submitter glucose-galactose malabsorption
  • p.Ala260= Single submitter glucose-galactose malabsorption
  • p.Ala401= Single submitter glucose-galactose malabsorption
  • p.Ala41= Single submitter glucose-galactose malabsorption
  • p.Ala411= Single submitter glucose-galactose malabsorption
  • p.Ala535= Single submitter glucose-galactose malabsorption
  • p.Ala535Val Single submitter Inborn genetic diseases
  • p.Ala72= Single submitter glucose-galactose malabsorption
  • p.Ala88= Single submitter glucose-galactose malabsorption
  • p.Arg140= Single submitter glucose-galactose malabsorption
  • p.Arg336= Single submitter glucose-galactose malabsorption
  • p.Arg427= Single submitter Inborn genetic diseases
  • p.Arg558= Single submitter glucose-galactose malabsorption
  • p.Arg564= Single submitter glucose-galactose malabsorption
  • p.Asn25= Single submitter glucose-galactose malabsorption
  • p.Asn363= Single submitter glucose-galactose malabsorption
  • p.Asn51= Single submitter glucose-galactose malabsorption
  • p.Asn579Asp Single submitter Inborn genetic diseases
  • p.Asn78= Single submitter glucose-galactose malabsorption
  • p.Asp230= Single submitter glucose-galactose malabsorption
  • p.Asp246= Single submitter glucose-galactose malabsorption
  • p.Asp261= Single submitter
  • p.Cys301= Single submitter glucose-galactose malabsorption
  • p.Cys314= Single submitter glucose-galactose malabsorption
  • p.Cys317= Single submitter glucose-galactose malabsorption
  • p.Cys345= Single submitter glucose-galactose malabsorption
  • p.Cys355= Single submitter glucose-galactose malabsorption
  • p.Glu18= Single submitter glucose-galactose malabsorption
  • p.Glu624= Single submitter glucose-galactose malabsorption
  • p.Gly227= Single submitter glucose-galactose malabsorption
  • p.Gly57= Single submitter glucose-galactose malabsorption
  • p.Gly611= Single submitter glucose-galactose malabsorption
  • p.Gly80= Single submitter glucose-galactose malabsorption
  • p.Gly82= Single submitter glucose-galactose malabsorption
  • p.His20= Single submitter
  • p.His224= Single submitter glucose-galactose malabsorption
  • p.His309= Single submitter glucose-galactose malabsorption
  • p.His615= Single submitter glucose-galactose malabsorption
  • p.Ile119= Single submitter glucose-galactose malabsorption
  • p.Ile158= Single submitter glucose-galactose malabsorption
  • p.Ile285= Single submitter glucose-galactose malabsorption
  • p.Ile327= Single submitter glucose-galactose malabsorption
  • p.Ile334= Single submitter glucose-galactose malabsorption
  • p.Ile34= Single submitter glucose-galactose malabsorption
  • p.Ile541= Single submitter glucose-galactose malabsorption
  • p.Ile544= Single submitter glucose-galactose malabsorption
  • p.Ile580= Single submitter glucose-galactose malabsorption
  • p.Leu112= Single submitter glucose-galactose malabsorption
  • p.Leu151= Single submitter glucose-galactose malabsorption
  • p.Leu171= Single submitter glucose-galactose malabsorption
  • p.Leu173= Single submitter glucose-galactose malabsorption
  • p.Leu177= Single submitter glucose-galactose malabsorption
  • p.Leu179= Single submitter glucose-galactose malabsorption
  • p.Leu206= Single submitter glucose-galactose malabsorption
  • p.Leu218= Single submitter glucose-galactose malabsorption
  • p.Leu288= Single submitter glucose-galactose malabsorption
  • p.Leu316= Single submitter glucose-galactose malabsorption
  • p.Leu383= Single submitter glucose-galactose malabsorption
  • p.Leu394= Single submitter glucose-galactose malabsorption
  • p.Leu491= Single submitter glucose-galactose malabsorption
  • p.Leu546= Single submitter glucose-galactose malabsorption
  • p.Leu563= Single submitter glucose-galactose malabsorption
  • p.Leu640= Single submitter glucose-galactose malabsorption
  • p.Leu652= Single submitter glucose-galactose malabsorption
  • p.Lys305= Single submitter glucose-galactose malabsorption
  • p.Lys321= Single submitter glucose-galactose malabsorption
  • p.Lys412= Single submitter glucose-galactose malabsorption
  • p.Lys415= Single submitter glucose-galactose malabsorption
  • p.Lys478= Single submitter glucose-galactose malabsorption
  • p.Pro331= Single submitter glucose-galactose malabsorption
  • p.Pro514= Single submitter glucose-galactose malabsorption
  • p.Ser149= Single submitter glucose-galactose malabsorption
  • p.Ser164= Single submitter glucose-galactose malabsorption
  • p.Ser245= Single submitter glucose-galactose malabsorption
  • p.Ser392= Single submitter glucose-galactose malabsorption
  • p.Ser393= Single submitter glucose-galactose malabsorption
  • p.Ser77= Single submitter glucose-galactose malabsorption
  • p.Thr395= Single submitter glucose-galactose malabsorption
  • p.Thr502= Single submitter glucose-galactose malabsorption
  • p.Thr519= Single submitter glucose-galactose malabsorption
  • p.Thr54= Single submitter glucose-galactose malabsorption
  • p.Thr540Ile Single submitter Inborn genetic diseases
  • p.Thr654= Single submitter glucose-galactose malabsorption
  • p.Tyr191= Single submitter glucose-galactose malabsorption
  • p.Tyr236= Single submitter glucose-galactose malabsorption
  • p.Tyr410= Single submitter glucose-galactose malabsorption
  • p.Tyr506= Single submitter glucose-galactose malabsorption
  • p.Val110= Single submitter glucose-galactose malabsorption
  • p.Val126= Single submitter glucose-galactose malabsorption
  • p.Val143= Single submitter glucose-galactose malabsorption
  • p.Val200= Single submitter glucose-galactose malabsorption
  • p.Val329= Single submitter glucose-galactose malabsorption
  • p.Val346= Single submitter glucose-galactose malabsorption
  • p.Val38= Single submitter glucose-galactose malabsorption
  • p.Val413= Single submitter glucose-galactose malabsorption
  • p.Val42= Single submitter glucose-galactose malabsorption
  • p.Val554= Single submitter glucose-galactose malabsorption
  • p.Val647= Single submitter glucose-galactose malabsorption
  • p.Val647Ile Single submitter Inborn genetic diseases
  • p.Val657= Single submitter

Uncertain significance 226