SMPD3 — 103 ClinVar variants
All ClinVar germline SMPD3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 99 flagged for review →
2 Likely benign · 101 Uncertain significance
Full SMPD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 99
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 lean, ClinVar uncertain 87
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SMPD3 p.Ala127Val Uncertain significance Single submitter
- SMPD3 p.Ala15Thr Uncertain significance Single submitter
- SMPD3 p.Ala15Val Uncertain significance Single submitter
- SMPD3 p.Ala163Thr Uncertain significance Single submitter
- SMPD3 p.Ala242Asp Uncertain significance Single submitter
- SMPD3 p.Ala242Ser Uncertain significance Single submitter
- SMPD3 p.Ala335Thr Uncertain significance Single submitter
- SMPD3 p.Ala35Ser Uncertain significance Single submitter
- SMPD3 p.Ala35Thr Uncertain significance Single submitter
- SMPD3 p.Ala458Thr Uncertain significance Single submitter
- SMPD3 p.Ala496Val Uncertain significance Single submitter
- SMPD3 p.Ala583Val Uncertain significance Single submitter
- SMPD3 p.Ala643Thr Uncertain significance Single submitter
- SMPD3 p.Arg159Cys Uncertain significance Single submitter
- SMPD3 p.Arg159His Uncertain significance Single submitter
- SMPD3 p.Arg198Gln Uncertain significance Single submitter
- SMPD3 p.Arg218Gln Uncertain significance Single submitter
- SMPD3 p.Arg218Pro Uncertain significance Single submitter
- SMPD3 p.Arg246His Uncertain significance Single submitter
- SMPD3 p.Arg254Gln Uncertain significance Single submitter
- SMPD3 p.Arg254Trp Uncertain significance Single submitter
- SMPD3 p.Arg299Trp Uncertain significance Single submitter
- SMPD3 p.Arg336His Uncertain significance Single submitter
- SMPD3 p.Arg339Gln Uncertain significance Single submitter
- SMPD3 p.Arg33Gln Uncertain significance Single submitter
- SMPD3 p.Arg46His Uncertain significance Single submitter
- SMPD3 p.Arg472Gln Uncertain significance Single submitter
- SMPD3 p.Arg48Gln Uncertain significance Single submitter
- SMPD3 p.Arg595Gln Uncertain significance Single submitter
- SMPD3 p.Arg605His Uncertain significance Single submitter
- SMPD3 p.Arg99Gln Uncertain significance Single submitter
- SMPD3 p.Asp260Asn Uncertain significance Single submitter
- SMPD3 p.Asp346Asn Uncertain significance Single submitter
- SMPD3 p.Asp429Asn Uncertain significance Single submitter
- SMPD3 p.Asp477His Uncertain significance Single submitter
- SMPD3 p.Asp553Glu Uncertain significance Single submitter
- SMPD3 p.Asp559Asn Uncertain significance Single submitter
- SMPD3 p.Cys427Tyr Uncertain significance Single submitter
- SMPD3 p.Cys54Ser Uncertain significance Single submitter
- SMPD3 p.Gln278His Uncertain significance Single submitter
- SMPD3 p.Glu223Lys Uncertain significance Single submitter
- SMPD3 p.Glu250Lys Uncertain significance Single submitter
- SMPD3 p.Glu343Lys Uncertain significance Single submitter
- SMPD3 p.Glu597Gln Uncertain significance Single submitter
- SMPD3 p.Glu652Gln Uncertain significance Single submitter
- SMPD3 p.Glu654Ala Uncertain significance Single submitter
- SMPD3 p.Gly107Ser Uncertain significance Single submitter
- SMPD3 p.Gly202Arg Uncertain significance Single submitter
- SMPD3 p.Gly221Cys Uncertain significance Single submitter
- SMPD3 p.Gly227Arg Uncertain significance Single submitter
- SMPD3 p.Gly248Asp Uncertain significance Single submitter
- SMPD3 p.Gly265Cys Uncertain significance Single submitter
- SMPD3 p.Gly274Ser Uncertain significance Single submitter
- SMPD3 p.Gly305Arg Uncertain significance Single submitter
- SMPD3 p.Gly393Ser Uncertain significance Single submitter
- SMPD3 p.Gly396Asp Uncertain significance Single submitter
- SMPD3 p.Gly406Ser Uncertain significance Single submitter
- SMPD3 p.Gly556Ser Uncertain significance Single submitter
- SMPD3 p.His421Arg Uncertain significance Single submitter
- SMPD3 p.Ile606Leu Uncertain significance Single submitter
- SMPD3 p.Leu100Arg Uncertain significance Single submitter
- SMPD3 p.Leu582Val Uncertain significance Single submitter
- SMPD3 p.Leu83Ile Uncertain significance Single submitter
- SMPD3 p.Lys331Arg Uncertain significance Single submitter
- SMPD3 p.Lys45Thr Uncertain significance Single submitter
- SMPD3 p.Met416Ile Uncertain significance Single submitter
- SMPD3 p.Met609Ile Uncertain significance Single submitter
- SMPD3 p.Pro233Arg Uncertain significance Single submitter
- SMPD3 p.Pro239Arg Uncertain significance Single submitter
- SMPD3 p.Pro256Ser Uncertain significance Single submitter
- SMPD3 p.Pro261Ser Uncertain significance Single submitter
- SMPD3 p.Pro275Arg Uncertain significance Single submitter
- SMPD3 p.Pro52Leu Uncertain significance Single submitter
- SMPD3 p.Ser185Thr Uncertain significance Single submitter
- SMPD3 p.Ser289Leu Uncertain significance Single submitter
- SMPD3 p.Ser291Asn Uncertain significance Single submitter
- SMPD3 p.Ser321Asn Uncertain significance Single submitter
- SMPD3 p.Ser489Pro Uncertain significance Single submitter
- SMPD3 p.Thr279Met Uncertain significance Single submitter
- SMPD3 p.Thr554Met Uncertain significance Single submitter
- SMPD3 p.Thr64Met Uncertain significance Single submitter
- SMPD3 p.Tyr212Cys Uncertain significance Single submitter
- SMPD3 p.Val141Ala Uncertain significance Single submitter
- SMPD3 p.Val210Ala Uncertain significance Single submitter
- SMPD3 p.Val210Leu Uncertain significance Single submitter
- SMPD3 p.Val330Leu Uncertain significance Single submitter
- SMPD3 p.Val454Ile Uncertain significance Single submitter
Predictors split 12
The independent predictors disagree with each other — read with care.
- SMPD3 p.Arg246Ser Uncertain significance Single submitter
- SMPD3 p.Arg46Cys Uncertain significance Single submitter
- SMPD3 p.Arg487Gln Uncertain significance Single submitter
- SMPD3 p.Arg48Trp Uncertain significance Single submitter
- SMPD3 p.Arg537His Uncertain significance Single submitter
- SMPD3 p.Arg578Cys Uncertain significance Single submitter
- SMPD3 p.Arg595Trp Uncertain significance Single submitter
- SMPD3 p.Arg99Trp Uncertain significance Single submitter
- SMPD3 p.Gly445Glu Uncertain significance Single submitter
- SMPD3 p.Gly635Ser Uncertain significance Single submitter
- SMPD3 p.Met644Ile Uncertain significance Single submitter
- SMPD3 p.Met644Thr Uncertain significance Single submitter
All SMPD3 variants
Likely benign 2
- p.Gly253Ser Single submitter
- p.Val262Ala Single submitter
Uncertain significance 101
- p.Ala127Val Single submitter ⚠
- p.Ala15Thr Single submitter ⚠
- p.Ala15Val Single submitter ⚠
- p.Ala163Thr Single submitter ⚠
- p.Ala242Asp Single submitter ⚠
- p.Ala242Ser Single submitter ⚠
- p.Ala335Thr Single submitter ⚠
- p.Ala35Ser Single submitter ⚠
- p.Ala35Thr Single submitter ⚠
- p.Ala458Thr Single submitter ⚠
- p.Ala496Val Single submitter ⚠
- p.Ala583Val Single submitter ⚠
- p.Ala643Thr Single submitter ⚠
- p.Arg159Cys Single submitter ⚠
- p.Arg159His Single submitter ⚠
- p.Arg198Gln Single submitter ⚠
- p.Arg218Gln Single submitter ⚠
- p.Arg218Pro Single submitter ⚠
- p.Arg246His Single submitter ⚠
- p.Arg246Ser Single submitter ⚠
- p.Arg254Gln Single submitter ⚠
- p.Arg254Trp Single submitter ⚠
- p.Arg299Trp Single submitter ⚠
- p.Arg336His Single submitter ⚠
- p.Arg339Gln Single submitter ⚠
- p.Arg33Gln Single submitter ⚠
- p.Arg46Cys Single submitter ⚠
- p.Arg46His Single submitter ⚠
- p.Arg472Gln Single submitter ⚠
- p.Arg487Gln Single submitter ⚠
- p.Arg48Gln Single submitter ⚠
- p.Arg48Trp Single submitter ⚠
- p.Arg537His Single submitter ⚠
- p.Arg578Cys Single submitter ⚠
- p.Arg595Gln Single submitter ⚠
- p.Arg595Trp Single submitter ⚠
- p.Arg605His Single submitter ⚠
- p.Arg99Gln Single submitter ⚠
- p.Arg99Trp Single submitter ⚠
- p.Asp260Asn Single submitter ⚠
- p.Asp346Asn Single submitter ⚠
- p.Asp429Asn Single submitter ⚠
- p.Asp430Asn Single submitter
- p.Asp477His Single submitter ⚠
- p.Asp553Glu Single submitter ⚠
- p.Asp559Asn Single submitter ⚠
- p.Cys427Tyr Single submitter ⚠
- p.Cys54Ser Single submitter ⚠
- p.Gln278His Single submitter ⚠
- p.Glu223Lys Single submitter ⚠
- p.Glu250Lys Single submitter ⚠
- p.Glu343Lys Single submitter ⚠
- p.Glu597Gln Single submitter ⚠
- p.Glu652Gln Single submitter ⚠
- p.Glu654Ala Single submitter ⚠
- p.Gly107Ser Single submitter ⚠
- p.Gly202Arg Single submitter ⚠
- p.Gly221Cys Single submitter ⚠
- p.Gly227Arg Single submitter ⚠
- p.Gly248Asp Single submitter ⚠
- p.Gly265Cys Single submitter ⚠
- p.Gly274Ser Single submitter ⚠
- p.Gly305Arg Single submitter ⚠
- p.Gly393Ser Single submitter ⚠
- p.Gly396Asp Single submitter ⚠
- p.Gly406Ser Single submitter ⚠
- p.Gly445Glu Single submitter ⚠
- p.Gly556Ser Single submitter ⚠
- p.Gly635Ser Single submitter ⚠
- p.His421Arg Single submitter ⚠
- p.Ile606Leu Single submitter ⚠
- p.Leu100Arg Single submitter ⚠
- p.Leu582Val Single submitter ⚠
- p.Leu83Ile Single submitter ⚠
- p.Lys331Arg Single submitter ⚠
- p.Lys45Thr Single submitter ⚠
- p.Met416Ile Single submitter ⚠
- p.Met609Ile Single submitter ⚠
- p.Met644Ile Single submitter ⚠
- p.Met644Thr Single submitter ⚠
- p.Pro233Arg Single submitter ⚠
- p.Pro239Arg Single submitter ⚠
- p.Pro256Ser Single submitter ⚠
- p.Pro261Ser Single submitter ⚠
- p.Pro275Arg Single submitter ⚠
- p.Pro52Leu Single submitter ⚠
- p.Ser185Thr Single submitter ⚠
- p.Ser289Leu Single submitter ⚠
- p.Ser291Asn Single submitter ⚠
- p.Ser321Asn Single submitter ⚠
- p.Ser489Pro Single submitter ⚠
- p.Thr147Pro Single submitter
- p.Thr279Met Single submitter ⚠
- p.Thr554Met Single submitter ⚠
- p.Thr64Met Single submitter ⚠
- p.Tyr212Cys Single submitter ⚠
- p.Val141Ala Single submitter ⚠
- p.Val210Ala Single submitter ⚠
- p.Val210Leu Single submitter ⚠
- p.Val330Leu Single submitter ⚠
- p.Val454Ile Single submitter ⚠