Sugi Variant

Sugi Variant/B3GAT3

B3GAT3 — 297 ClinVar variants

All ClinVar germline B3GAT3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 134 flagged for review →

15 Pathogenic · 9 Pathogenic/Likely pathogenic · 8 Likely pathogenic · 7 Conflicting · 9 Benign · 2 Benign/Likely benign · 112 Likely benign · 135 Uncertain significance

Full B3GAT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 134

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 2

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

Predictors agree, ClinVar conflicts 3

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

Predictors lean, ClinVar uncertain 56

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

Predictors split 73

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

All B3GAT3 variants

Pathogenic 15

  • p.Arg211fs Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Arg297Trp Single submitter Larsen-like syndrome, B3GAT3 type ⚠
  • p.Gln46fs Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Glu202Ter Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Gly223Ser Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ile51fs Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ile77fs Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu100fs Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu224Gln Single submitter
  • p.Leu93Val Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ser52delinsCysSerTyrGlyArgArgIleTer Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Thr83fs Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Tyr12Ter Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Pro140Leu No assertion criteria MULTIPLE JOINT DISLOCATIONS, SHORT STATURE, AND CRANIOFACIAL DYSMORPHISM WITHOUT CONGENITAL HEART DEFECTS ⚠
  • p.Pro82Leu No assertion criteria Larsen-like syndrome, B3GAT3 type

Pathogenic/Likely pathogenic 9

  • p.Arg169Trp Multiple submitters Larsen-like syndrome, B3GAT3 type ⚠
  • p.Arg225Ter Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Arg277Gln Multiple submitters Larsen-like syndrome, B3GAT3 type ⚠
  • p.Arg59Ter Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Arg95Ter Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Gln29Ter Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Glu112Ter Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Gly173fs Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Met1Leu Multiple submitters Larsen-like syndrome, B3GAT3 type

Likely pathogenic 8

  • c.257+1G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-1G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+1G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Met1Arg Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Met1Val Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ser329Ter Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Trp243Ter Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val111Met Single submitter

Conflicting classifications of pathogenicity 7

  • c.910-3C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Arg161Trp Single submitter Larsen-like syndrome, B3GAT3 type ⚠
  • p.Arg327Trp Single submitter Larsen-like syndrome, B3GAT3 type ⚠
  • p.Met1Thr Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val15Leu Single submitter Larsen-like syndrome, B3GAT3 type ⚠
  • p.Val236Glu Single submitter Larsen-like syndrome, B3GAT3 type ⚠
  • p.Val237Met Single submitter Inborn genetic diseases ⚠

Benign 9

Benign/Likely benign 2

Likely benign 112

  • c.258-9C>T Multiple submitters Larsen-like syndrome, B3GAT3 type
  • c.619-12G>A Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Ala257= Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Arg247= Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Arg310= Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Asp194= Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Pro71= Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Thr302= Multiple submitters Larsen-like syndrome, B3GAT3 type
  • p.Val258Met Multiple submitters Larsen-like syndrome, B3GAT3 type ⚠
  • c.257+11T>G Single submitter Larsen-like syndrome, B3GAT3 type
  • c.257+17A>G Single submitter Larsen-like syndrome, B3GAT3 type
  • c.257+20C>G Single submitter Larsen-like syndrome, B3GAT3 type
  • c.258-16C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.258-20G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.618+11G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.618+16G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.618+8C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-10C>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-10C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-11A>G Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-13C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-17C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-19C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-20T>C Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-5G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-6C>G Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-6C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-6dup Single submitter Larsen-like syndrome, B3GAT3 type
  • c.619-9C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+10G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+10G>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+11del Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+13G>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+15G>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+18G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+4_82+8dup Single submitter Larsen-like syndrome, B3GAT3 type
  • c.82+6CGGGG[2] Single submitter Larsen-like syndrome, B3GAT3 type
  • c.83-11C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.83-13T>C Single submitter Larsen-like syndrome, B3GAT3 type
  • c.83-20T>C Single submitter Larsen-like syndrome, B3GAT3 type
  • c.909+20C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.909+270_909+271del Single submitter
  • c.909+279del Single submitter
  • c.910-10C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.910-13C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.910-16A>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.910-6G>A Single submitter Larsen-like syndrome, B3GAT3 type
  • c.910-9C>T Single submitter Larsen-like syndrome, B3GAT3 type
  • c.*10del Single submitter
  • c.*5G>A Single submitter
  • p.Ala127= Single submitter
  • p.Ala164= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ala18= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ala23= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ala41= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ala56= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Arg327= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Arg59= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Arg60= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Arg95= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Asn162= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Asn197= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Asp233= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Asp32= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Gln160= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Gln270= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Glu115= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Glu227= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Glu334= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Gly148= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Gly170= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Gly19= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Gly222= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Gly228= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.His154= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu100= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu102= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu124= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu130= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu138= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu20= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu21= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu44= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu54= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu87= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Leu93= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Phe192= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Phe226= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Pro119= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Pro155= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Pro183Arg Single submitter Inborn genetic diseases
  • p.Pro245= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Pro62= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ser101= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ser16= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ser246= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ser273= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ser282= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Ser52= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Thr139= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Thr274= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Thr76= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Thr81= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Tyr199= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val121= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val153= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val158= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val189= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val190= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val79= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val8= Single submitter Larsen-like syndrome, B3GAT3 type
  • p.Val80= Single submitter Larsen-like syndrome, B3GAT3 type

Uncertain significance 135