PDXK — 85 ClinVar variants
All ClinVar germline PDXK variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 30 flagged for review →
3 Pathogenic · 1 Likely pathogenic · 25 Benign · 26 Likely benign · 30 Uncertain significance
Full PDXK gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 30
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 3
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
-
PDXK p.Ala228Thr
Pathogenic
Multiple submitters
PDXK-related disorder
-
PDXK p.Asn75Lys
Likely pathogenic
Single submitter
neuropathy, hereditary motor and sensory, type VIc, with optic atrophy
-
PDXK p.Arg220Gln
Pathogenic
No assertion criteria
neuropathy, hereditary motor and sensory, type VIc, with optic atrophy
Predictors lean, ClinVar uncertain 22
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PDXK p.Ala211Thr Uncertain significance Multiple submitters
- PDXK p.Ala37Val Uncertain significance Multiple submitters
- PDXK p.Met126Thr Uncertain significance Multiple submitters
- PDXK p.Ala276Val Uncertain significance Single submitter
- PDXK p.Ala50Thr Uncertain significance Single submitter
-
PDXK p.Arg170Gln
Uncertain significance
Single submitter
neuropathy, hereditary motor and sensory, type VIc, with optic atrophy
- PDXK p.Arg86Lys Uncertain significance Single submitter
- PDXK p.Asn197Lys Uncertain significance Single submitter
- PDXK p.Asn250Ser Uncertain significance Single submitter
- PDXK p.Asp181Glu Uncertain significance Single submitter
- PDXK p.Gln63Leu Uncertain significance Single submitter
- PDXK p.Glu304Ala Uncertain significance Single submitter
- PDXK p.Ile97Val Uncertain significance Single submitter
- PDXK p.Leu263Val Uncertain significance Single submitter
- PDXK p.Met293Leu Uncertain significance Single submitter
- PDXK p.Pro129Leu Uncertain significance Single submitter
- PDXK p.Ser213Cys Uncertain significance Single submitter
- PDXK p.Thr47Ile Uncertain significance Single submitter
- PDXK p.Tyr136Cys Uncertain significance Single submitter
- PDXK p.Val135Ile Uncertain significance Single submitter
- PDXK p.Val183Met Uncertain significance Single submitter
- PDXK p.Val215Met Uncertain significance Single submitter
Predictors split 5
The independent predictors disagree with each other — read with care.
-
PDXK p.Gly281Glu
Uncertain significance
Multiple submitters
neuropathy, hereditary motor and sensory, type VIc, with optic atrophy
- PDXK p.Arg292Gln Uncertain significance Single submitter
- PDXK p.Gly281Arg Uncertain significance Single submitter
- PDXK p.Thr148Met Uncertain significance Single submitter
- PDXK p.Thr85Met Uncertain significance Single submitter
All PDXK variants
Pathogenic 3
- p.Ala228Thr Multiple submitters PDXK-related disorder ⚠
- c.465-15_489delinsGCA Single submitter
- p.Arg220Gln No assertion criteria neuropathy, hereditary motor and sensory, type VIc, with optic atrophy ⚠
Likely pathogenic 1
- p.Asn75Lys Single submitter neuropathy, hereditary motor and sensory, type VIc, with optic atrophy ⚠
Benign 25
- c.143-116A>G Multiple submitters
- c.143-202G>A Multiple submitters
- c.331+26T>G Multiple submitters neuropathy, hereditary motor and sensory, type VIc, with optic atrophy
- c.331+78G>A Multiple submitters
- c.464+44A>G Multiple submitters
- c.465-96A>G Multiple submitters
- c.510+154A>G Multiple submitters
- c.511-20G>A Multiple submitters
- c.622+118G>A Multiple submitters
- c.759+105T>C Multiple submitters
- c.760-209G>A Multiple submitters
- c.760-8C>A Multiple submitters
- c.88-199A>G Multiple submitters
- c.*14T>C Multiple submitters neuropathy, hereditary motor and sensory, type VIc, with optic atrophy
- p.Pro129= Multiple submitters neuropathy, hereditary motor and sensory, type VIc, with optic atrophy
- p.Ser213= Multiple submitters
- c.142+140C>T Single submitter
- c.142+171_142+172del Single submitter
- c.247+198T>C Single submitter
- c.331+179G>T Single submitter
- c.379-167T>C Single submitter
- c.510+189TG[9] Single submitter
- c.623-233C>A Single submitter
- c.*8G>A No assertion criteria PDXK-related disorder
- p.Pro142= No assertion criteria PDXK-related disorder
Likely benign 26
- c.142+3058C>T Multiple submitters
- p.Lys139= Multiple submitters
- p.Ser125Leu Multiple submitters neuropathy, hereditary motor and sensory, type VIc, with optic atrophy
- c.142+3078C>T Single submitter
- c.142+3164C>T Single submitter
- c.142+3165G>A Single submitter
- c.142+3197C>T Single submitter
- c.142+3261C>T Single submitter
- c.142+3323G>T Single submitter
- c.142+8G>A Single submitter
- c.143-102T>C Single submitter
- c.143-115T>C Single submitter
- c.511-15C>T Single submitter
- c.622+23G>A Single submitter
- c.88-1631A>T Single submitter
- c.88-1657C>T Single submitter
- c.88-1682C>T Single submitter
- c.88-1702C>T Single submitter
- p.Ala278= Single submitter
- p.Gly117= Single submitter
- p.Leu267= Single submitter
- p.Met74Val Single submitter
- p.Ser89= Single submitter
- p.Thr85= Single submitter
- p.Val41= Single submitter
- p.Val80= Single submitter
Uncertain significance 30
- p.Ala211Thr Multiple submitters ⚠
- p.Ala37Val Multiple submitters ⚠
- p.Gly281Glu Multiple submitters neuropathy, hereditary motor and sensory, type VIc, with optic atrophy ⚠
- p.Met126Thr Multiple submitters ⚠
- c.142+7C>T Single submitter
- p.Ala276Val Single submitter ⚠
- p.Ala50Thr Single submitter ⚠
- p.Arg170Gln Single submitter neuropathy, hereditary motor and sensory, type VIc, with optic atrophy ⚠
- p.Arg292Gln Single submitter ⚠
- p.Arg86Lys Single submitter ⚠
- p.Asn197Lys Single submitter ⚠
- p.Asn250Ser Single submitter ⚠
- p.Asp181Glu Single submitter ⚠
- p.Gln63Leu Single submitter ⚠
- p.Glu304Ala Single submitter ⚠
- p.Gly281Arg Single submitter ⚠
- p.Ile97Val Single submitter ⚠
- p.Leu263Val Single submitter ⚠
- p.Lys88Asn Single submitter
- p.Met293Leu Single submitter ⚠
- p.Pro129Leu Single submitter ⚠
- p.Ser213Cys Single submitter ⚠
- p.Thr148Met Single submitter ⚠
- p.Thr47Ile Single submitter ⚠
- p.Thr85Met Single submitter ⚠
- p.Tyr136Cys Single submitter ⚠
- p.Val135Ile Single submitter ⚠
- p.Val183Met Single submitter ⚠
- p.Val215Met Single submitter ⚠
- c.143-100C>T No assertion criteria PDXK-related disorder