GALNS — 1346 ClinVar variants

All ClinVar germline GALNS variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 435 flagged for review →

106 Pathogenic · 70 Pathogenic/Likely pathogenic · 125 Likely pathogenic · 147 Conflicting · 90 Benign · 10 Benign/Likely benign · 447 Likely benign · 351 Uncertain significance

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

⚑ Evidence disagreements 435

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 25

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 64

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

Predictors lean, ClinVar uncertain 186

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 186

Predictors split 160

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 160

All GALNS variants

Pathogenic 106

  • c.1139+1G>A Multiple submitters mucopolysaccharidosis type 4A
  • c.120+1G>A Multiple submitters mucopolysaccharidosis type 4A
  • c.120+1G>C Multiple submitters mucopolysaccharidosis type 4A
  • c.121-1G>A Multiple submitters mucopolysaccharidosis type 4A
  • c.1364+1G>A Multiple submitters mucopolysaccharidosis type 4A
  • c.1365-1G>C Multiple submitters mucopolysaccharidosis type 4A
  • c.320-1G>T Multiple submitters mucopolysaccharidosis type 4A
  • c.405_422+1del Multiple submitters mucopolysaccharidosis type 4A
  • c.423-11_425del Multiple submitters mucopolysaccharidosis type 4A
  • c.758+1G>A Multiple submitters mucopolysaccharidosis type 4A
  • c.898+1G>A Multiple submitters mucopolysaccharidosis type 4A
  • c.899-1G>C Multiple submitters mucopolysaccharidosis type 4A
  • p.Ala392Val Multiple submitters mucopolysaccharidosis type 4A
  • p.Arg90Trp Multiple submitters Inborn genetic diseases
  • p.Gln211Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Gln334Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Gln338Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Gln374Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Gln414Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Gln422Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Gln473Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Glu202fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Gly116Ser Multiple submitters mucopolysaccharidosis type 4A
  • p.Gly139Ser Multiple submitters mucopolysaccharidosis type 4
  • p.Gly301Cys Multiple submitters GALNS-related disorders
  • p.His398fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Met318Arg Multiple submitters Inborn genetic diseases
  • p.Met391Val Multiple submitters GALNS-related disorders ⚠
  • p.Phe167fs Multiple submitters mucopolysaccharidosis type 4
  • p.Pro381fs Multiple submitters mucopolysaccharidosis type 4
  • p.Ser162Phe Multiple submitters mucopolysaccharidosis type 4A
  • p.Thr281_Asn289del Multiple submitters mucopolysaccharidosis type 4
  • p.Trp10Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Trp159Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Trp230Ter Multiple submitters GALNS-related disorders
  • p.Val239fs Multiple submitters mucopolysaccharidosis type 4A
  • c.1139+2T>C Single submitter mucopolysaccharidosis type 4A
  • c.(120+1_121-1 Single submitter mucopolysaccharidosis type 4A
  • c.120+1G>T Single submitter mucopolysaccharidosis type 4A
  • c.121-1G>T Single submitter mucopolysaccharidosis type 4A
  • c.121-2_121-1insTGCATTTGCTGGCATA Single submitter mucopolysaccharidosis type 4A
  • c.121-2A>T Single submitter mucopolysaccharidosis type 4A
  • c.121-338_244+1del Single submitter mucopolysaccharidosis type 4A
  • c.1242+1G>A Single submitter mucopolysaccharidosis type 4A
  • c.(1364+1_1365-1 Single submitter mucopolysaccharidosis type 4A
  • c.1365-2A>G Single submitter mucopolysaccharidosis type 4A
  • c.1475_1482+1del Single submitter mucopolysaccharidosis type 4A
  • c.1482+2T>C Single submitter mucopolysaccharidosis type 4A
  • c.244+1G>T Single submitter mucopolysaccharidosis type 4A
  • c.422+2_422+8del Single submitter mucopolysaccharidosis type 4A
  • c.567-1G>T Single submitter mucopolysaccharidosis type 4A
  • c.567-2A>T Single submitter mucopolysaccharidosis type 4A
  • c.634-2A>C Single submitter
  • c.758+1G>C Single submitter mucopolysaccharidosis type 4A
  • c.(898+1_899-1 Single submitter mucopolysaccharidosis type 4A
  • c.898+2T>A Single submitter mucopolysaccharidosis type 4A
  • c.899-1G>T Single submitter mucopolysaccharidosis type 4A
  • c.899-397_1003-1862del Single submitter mucopolysaccharidosis type 4A
  • c.899-66_907delinsACTCAGTG Single submitter
  • p.Ala292fs Single submitter mucopolysaccharidosis type 4A
  • p.Ala393fs Single submitter mucopolysaccharidosis type 4A
  • p.Ala63Pro Single submitter mucopolysaccharidosis type 4A
  • p.Arg61= Single submitter mucopolysaccharidosis type 4A
  • p.Asn32fs Single submitter mucopolysaccharidosis type 4A
  • p.Asp274fs Single submitter mucopolysaccharidosis type 4A
  • p.Asp288fs Single submitter mucopolysaccharidosis type 4A
  • p.Asp39fs Single submitter mucopolysaccharidosis type 4A
  • p.Asp40His Single submitter mucopolysaccharidosis type 4A
  • p.Cys165_Asn177del Single submitter mucopolysaccharidosis type 4A
  • p.Gln122Ter Single submitter mucopolysaccharidosis type 4A
  • p.Gln148Ter Single submitter mucopolysaccharidosis type 4A
  • p.Gln250Ter Single submitter mucopolysaccharidosis type 4A
  • p.Gln29Ter Single submitter mucopolysaccharidosis type 4A
  • p.Gln474Ter Single submitter mucopolysaccharidosis type 4A
  • p.Glu112fs Single submitter mucopolysaccharidosis type 4A
  • p.Glu126Ter Single submitter mucopolysaccharidosis type 4A
  • p.Glu158Ter Single submitter mucopolysaccharidosis type 4A
  • p.Glu298Ter Single submitter mucopolysaccharidosis type 4A
  • p.Glu410Ter Single submitter
  • p.Glu450Ter Single submitter mucopolysaccharidosis type 4A
  • p.Gly445Ter Single submitter mucopolysaccharidosis type 4A
  • p.His236fs Single submitter mucopolysaccharidosis type 4A
  • p.His475fs Single submitter mucopolysaccharidosis type 4A
  • p.Ile416fs Single submitter mucopolysaccharidosis type 4A
  • p.Leu372fs Single submitter mucopolysaccharidosis type 4A
  • p.Lys506fs Single submitter mucopolysaccharidosis type 4A
  • p.Met1Leu Single submitter mucopolysaccharidosis type 4A
  • p.Met1Thr Single submitter mucopolysaccharidosis type 4A
  • p.Met318Val Single submitter mucopolysaccharidosis type 4A ⚠
  • p.Met494fs Single submitter mucopolysaccharidosis type 4A
  • p.Phe452fs Single submitter mucopolysaccharidosis type 4
  • p.Pro125fs Single submitter mucopolysaccharidosis type 4A
  • p.Pro420fs Single submitter mucopolysaccharidosis type 4A
  • p.Ser162Tyr Single submitter mucopolysaccharidosis type 4A
  • p.Thr389_Leu390insTer Single submitter mucopolysaccharidosis type 4A
  • p.Trp141Ter Single submitter mucopolysaccharidosis type 4A
  • p.Trp184Ter Single submitter mucopolysaccharidosis type 4A
  • p.Trp325Ter Single submitter mucopolysaccharidosis type 4A
  • p.Trp403Ter Single submitter mucopolysaccharidosis type 4A
  • p.Trp491Ter Single submitter mucopolysaccharidosis type 4A
  • p.Trp496Ter Single submitter mucopolysaccharidosis type 4A
  • p.Tyr170Ter Single submitter mucopolysaccharidosis type 4A
  • p.Tyr190Ter Single submitter mucopolysaccharidosis type 4A
  • p.Tyr209Ter Single submitter mucopolysaccharidosis type 4A
  • p.Tyr461Ter Single submitter mucopolysaccharidosis type 4A
  • p.Tyr98Ter Single submitter mucopolysaccharidosis type 4A

Pathogenic/Likely pathogenic 70

  • c.121-2A>G Multiple submitters mucopolysaccharidosis type 4A
  • c.1242+1G>C Multiple submitters mucopolysaccharidosis type 4A
  • c.319+2T>C Multiple submitters mucopolysaccharidosis type 4A
  • c.320-1G>C Multiple submitters mucopolysaccharidosis type 4A
  • c.423-1G>A Multiple submitters mucopolysaccharidosis type 4A
  • c.423-862C>T Multiple submitters mucopolysaccharidosis type 4A
  • c.898+1G>C Multiple submitters mucopolysaccharidosis type 4A
  • c.899-2A>C Multiple submitters mucopolysaccharidosis type 4A
  • c.899-2A>G Multiple submitters mucopolysaccharidosis type 4
  • p.Ala107Thr Multiple submitters mucopolysaccharidosis type 4 ⚠
  • p.Ala27fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Ala291Thr Multiple submitters mucopolysaccharidosis type 4
  • p.Ala492Thr Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Arg251Gln Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Arg251Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Arg259Gln Multiple submitters GALNS-related disorders ⚠
  • p.Arg386Cys Multiple submitters GALNS-related disorders ⚠
  • p.Arg61Trp Multiple submitters mucopolysaccharidosis type 4 ⚠
  • p.Arg94Cys Multiple submitters mucopolysaccharidosis type 4A
  • p.Arg94Gly Multiple submitters mucopolysaccharidosis type 4
  • p.Arg94His Multiple submitters GALNS-related disorders ⚠
  • p.Arg94Leu Multiple submitters mucopolysaccharidosis type 4
  • p.Asn164fs Multiple submitters mucopolysaccharidosis type 4
  • p.Asn164Thr Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Asn204Ser Multiple submitters skeletal dysplasia ⚠
  • p.Asn204Thr Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Asp233Asn Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Asp388Asn Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Asp39Gly Multiple submitters mucopolysaccharidosis type 4A
  • p.Asp447Asn Multiple submitters mucopolysaccharidosis type 4
  • p.Asp60Asn Multiple submitters GALNS-related disorders ⚠
  • p.Cys79Arg Multiple submitters mucopolysaccharidosis type 4A
  • p.Cys79fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Gln111Ter Multiple submitters mucopolysaccharidosis type 4
  • p.Gln273Ter Multiple submitters GALNS-related disorder
  • p.Glu433fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Gly116Val Multiple submitters mucopolysaccharidosis type 4A
  • p.Gly155Arg Multiple submitters GALNS-related disorders
  • p.Gly168Arg Multiple submitters mucopolysaccharidosis type 4
  • p.Gly201Glu Multiple submitters mucopolysaccharidosis type 4 ⚠
  • p.Gly290Ser Multiple submitters mucopolysaccharidosis type 4A
  • p.Gly340Asp Multiple submitters mucopolysaccharidosis type 4
  • p.His145Tyr Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Ile113Phe Multiple submitters mucopolysaccharidosis type 4
  • p.Leu350Pro Multiple submitters mucopolysaccharidosis type 4A
  • p.Leu36Arg Multiple submitters mucopolysaccharidosis type 4A
  • p.Leu440fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Lys218fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Lys399fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Met1_Val5del Multiple submitters mucopolysaccharidosis type 4A
  • p.Met41Leu Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Phe156Leu Multiple submitters mucopolysaccharidosis type 4
  • p.Phe216Ser Multiple submitters mucopolysaccharidosis type 4A
  • p.Phe226fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Phe285del Multiple submitters mucopolysaccharidosis type 4
  • p.Pro125Leu Multiple submitters GALNS-related disorders
  • p.Pro151_Leu152insTer Multiple submitters mucopolysaccharidosis type 4A
  • p.Pro151Leu Multiple submitters mucopolysaccharidosis type 4A
  • p.Pro151Thr Multiple submitters mucopolysaccharidosis type 4
  • p.Pro357fs Multiple submitters mucopolysaccharidosis type 4A
  • p.Pro77Arg Multiple submitters mucopolysaccharidosis type 4A
  • p.Ser287Leu Multiple submitters GALNS-related disorders
  • p.Ser295Phe Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Ser80Leu Multiple submitters GALNS-related disorder
  • p.Ter523Glu Multiple submitters mucopolysaccharidosis type 4A
  • p.Thr235Lys Multiple submitters mucopolysaccharidosis type 4A
  • p.Thr313Met Multiple submitters mucopolysaccharidosis type 4A ⚠
  • p.Tyr240Cys Multiple submitters mucopolysaccharidosis type 4A
  • p.Tyr385Ter Multiple submitters mucopolysaccharidosis type 4A
  • p.Val48Gly Multiple submitters mucopolysaccharidosis type 4 ⚠

Likely pathogenic 125

Conflicting classifications of pathogenicity 147

Benign 90

Benign/Likely benign 10

  • c.1003-42C>T Multiple submitters mucopolysaccharidosis type 4A
  • c.-68C>T Multiple submitters mucopolysaccharidosis type 4A
  • c.-92T>C Multiple submitters mucopolysaccharidosis type 4A
  • c.*224C>G Multiple submitters mucopolysaccharidosis type 4A
  • c.*296A>G Multiple submitters mucopolysaccharidosis type 4A
  • c.*524G>C Multiple submitters mucopolysaccharidosis type 4A
  • p.Ala241= Multiple submitters mucopolysaccharidosis type 4A
  • p.His142= Multiple submitters mucopolysaccharidosis type 4A
  • p.Pro481= Multiple submitters mucopolysaccharidosis type 4A
  • p.Val480Phe Multiple submitters mucopolysaccharidosis type 4A ⚠

Likely benign 447

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

Uncertain significance 351

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