PI4KB — 75 ClinVar variants

All ClinVar germline PI4KB variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 61 flagged for review →

4 Pathogenic · 6 Likely benign · 65 Uncertain significance

Full PI4KB gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 61

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.

PI4KB p.Gln121Arg Pathogenic No assertion criteria
hearing loss, autosomal dominant 87
PI4KB p.Glu682Lys Pathogenic No assertion criteria
hearing loss, autosomal dominant 87

Predictors lean, ClinVar uncertain 50

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

Predictors split 9

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

All PI4KB variants

Pathogenic 4

p.Gln121Arg No assertion criteria hearing loss, autosomal dominant 87 ⚠
p.Glu682Lys No assertion criteria hearing loss, autosomal dominant 87 ⚠
p.Met754Arg No assertion criteria hearing loss, autosomal dominant 87
p.Val449Gly No assertion criteria hearing loss, autosomal dominant 87

Likely benign 6

c.2269+17G>A Single submitter
p.Ala106= Single submitter
p.Arg291Ter Single submitter
p.Cys212= Single submitter
p.Pro518= Single submitter
p.Val37= Single submitter

Uncertain significance 65

p.Ile312Val Multiple submitters ⚠
p.Tyr175Cys Multiple submitters hearing loss, autosomal dominant 87 ⚠
c.-17G>A Single submitter
c.-6G>T Single submitter
p.Ala106Val Single submitter ⚠
p.Ala605Gly Single submitter ⚠
p.Ala67Val Single submitter ⚠
p.Ala95Ser Single submitter ⚠
p.Arg203His Single submitter
p.Arg250Lys Single submitter ⚠
p.Arg274Cys Single submitter ⚠
p.Arg422Gln Single submitter ⚠
p.Arg424Trp Single submitter ⚠
p.Arg442Gln Single submitter ⚠
p.Arg570Gln Single submitter ⚠
p.Arg570Trp Single submitter ⚠
p.Arg590Gln Single submitter ⚠
p.Arg798Trp Single submitter ⚠
p.Asn169Ser Single submitter ⚠
p.Asn288Ser Single submitter ⚠
p.Asp262Asn Single submitter ⚠
p.Cys202Tyr Single submitter ⚠
p.Glu16_Ser19del Single submitter
p.Glu16Val Single submitter ⚠
p.Glu170Lys Single submitter ⚠
p.Glu434Lys Single submitter ⚠
p.Glu473Lys Single submitter ⚠
p.Gly105Glu Single submitter ⚠
p.Gly23Glu Single submitter ⚠
p.Gly27Glu Single submitter ⚠
p.Gly2Arg Single submitter
p.Gly720Asp Single submitter ⚠
p.Gly723Asp Single submitter ⚠
p.Gly814Ser Single submitter ⚠
p.His475Arg Single submitter ⚠
p.Ile418Val Single submitter ⚠
p.Ile437Thr Single submitter ⚠
p.Leu138Val Single submitter ⚠
p.Leu257Trp Single submitter ⚠
p.Leu285Phe Single submitter ⚠
p.Leu601Val Single submitter ⚠
p.Met778Val Single submitter ⚠
p.Met780Lys Single submitter
p.Pro17Thr Single submitter ⚠
p.Pro259Leu Single submitter ⚠
p.Pro8Ser Single submitter ⚠
p.Pro93Ser Single submitter ⚠
p.Pro93Thr Single submitter ⚠
p.Ser294Arg Single submitter ⚠
p.Ser604Ala Single submitter ⚠
p.Ser629Pro Single submitter ⚠
p.Ser629Thr Single submitter ⚠
p.Ser767Asn Single submitter ⚠
p.Thr14Ala Single submitter ⚠
p.Thr18Ala Single submitter ⚠
p.Thr73Ile Single submitter ⚠
p.Thr768Ile Single submitter ⚠
p.Tyr219Phe Single submitter ⚠
p.Tyr452Cys Single submitter ⚠
p.Val37Ile Single submitter ⚠
p.Val401Met Single submitter ⚠
p.Val541Ala Single submitter ⚠
p.Val591Met Single submitter ⚠
p.Val66Met Single submitter ⚠
p.Ser256Phe No assertion criteria PI4KB-related disorder ⚠