SPHK2 — 136 ClinVar variants
All ClinVar germline SPHK2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 114 flagged for review →
5 Benign · 14 Likely benign · 117 Uncertain significance
Full SPHK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 114
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 95
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SPHK2 p.Ala141Ser Uncertain significance Single submitter
- SPHK2 p.Ala141Val Uncertain significance Single submitter
- SPHK2 p.Ala295Val Uncertain significance Single submitter
- SPHK2 p.Ala367Thr Uncertain significance Single submitter
- SPHK2 p.Ala38Thr Uncertain significance Single submitter
- SPHK2 p.Ala490Gly Uncertain significance Single submitter
- SPHK2 p.Ala490Val Uncertain significance Single submitter
- SPHK2 p.Ala605Thr Uncertain significance Single submitter
- SPHK2 p.Ala633Thr Uncertain significance Single submitter
- SPHK2 p.Ala85Val Uncertain significance Single submitter
- SPHK2 p.Arg104Gln Uncertain significance Single submitter
- SPHK2 p.Arg106Cys Uncertain significance Single submitter
- SPHK2 p.Arg106His Uncertain significance Single submitter
- SPHK2 p.Arg122Gln Uncertain significance Single submitter
- SPHK2 p.Arg125Cys Uncertain significance Single submitter
- SPHK2 p.Arg129His Uncertain significance Single submitter
- SPHK2 p.Arg133His Uncertain significance Single submitter
- SPHK2 p.Arg147Ser Uncertain significance Single submitter
- SPHK2 p.Arg152His Uncertain significance Single submitter
- SPHK2 p.Arg179Gln Uncertain significance Single submitter
- SPHK2 p.Arg193Gln Uncertain significance Single submitter
- SPHK2 p.Arg28Gly Uncertain significance Single submitter
- SPHK2 p.Arg328His Uncertain significance Single submitter
- SPHK2 p.Arg33Ser Uncertain significance Single submitter
- SPHK2 p.Arg357Cys Uncertain significance Single submitter
- SPHK2 p.Arg396Gly Uncertain significance Single submitter
- SPHK2 p.Arg396Leu Uncertain significance Single submitter
- SPHK2 p.Arg572His Uncertain significance Single submitter
- SPHK2 p.Arg61Gln Uncertain significance Single submitter
- SPHK2 p.Arg64His Uncertain significance Single submitter
- SPHK2 p.Arg78Gln Uncertain significance Single submitter
- SPHK2 p.Arg88Gln Uncertain significance Single submitter
- SPHK2 p.Arg88Trp Uncertain significance Single submitter
- SPHK2 p.Asn216Ser Uncertain significance Single submitter
- SPHK2 p.Asp299Asn Uncertain significance Single submitter
- SPHK2 p.Cys276Ser Uncertain significance Single submitter
- SPHK2 p.Gln288His Uncertain significance Single submitter
- SPHK2 p.Glu144Lys Uncertain significance Single submitter
- SPHK2 p.Glu18Gln Uncertain significance Single submitter
- SPHK2 p.Glu265Asp Uncertain significance Single submitter
- SPHK2 p.Glu384Gln Uncertain significance Single submitter
- SPHK2 p.Glu8Gln Uncertain significance Single submitter
- SPHK2 p.Gly168Arg Uncertain significance Single submitter
- SPHK2 p.Gly24Ser Uncertain significance Single submitter
- SPHK2 p.Gly256Arg Uncertain significance Single submitter
- SPHK2 p.Gly26Ala Uncertain significance Single submitter
- SPHK2 p.Gly448Asp Uncertain significance Single submitter
- SPHK2 p.Gly489Ala Uncertain significance Single submitter
- SPHK2 p.Gly509Arg Uncertain significance Single submitter
- SPHK2 p.Gly514Cys Uncertain significance Single submitter
- SPHK2 p.Gly536Ala Uncertain significance Single submitter
- SPHK2 p.Gly550Ser Uncertain significance Single submitter
- SPHK2 p.Gly62Ser Uncertain significance Single submitter
- SPHK2 p.Gly640Cys Uncertain significance Single submitter
- SPHK2 p.His417Leu Uncertain significance Single submitter
- SPHK2 p.His417Tyr Uncertain significance Single submitter
- SPHK2 p.His4Asn Uncertain significance Single submitter
- SPHK2 p.Ile76Leu Uncertain significance Single submitter
- SPHK2 p.Leu250Phe Uncertain significance Single submitter
- SPHK2 p.Leu318Pro Uncertain significance Single submitter
- SPHK2 p.Leu446Val Uncertain significance Single submitter
- SPHK2 p.Leu51Phe Uncertain significance Single submitter
- SPHK2 p.Leu568Pro Uncertain significance Single submitter
- SPHK2 p.Leu5Pro Uncertain significance Single submitter
- SPHK2 p.Leu610Pro Uncertain significance Single submitter
- SPHK2 p.Met37Thr Uncertain significance Single submitter
- SPHK2 p.Met635Thr Uncertain significance Single submitter
- SPHK2 p.Phe608Cys Uncertain significance Single submitter
- SPHK2 p.Pro121Leu Uncertain significance Single submitter
- SPHK2 p.Pro407Ser Uncertain significance Single submitter
- SPHK2 p.Pro409Leu Uncertain significance Single submitter
- SPHK2 p.Pro40Ser Uncertain significance Single submitter
- SPHK2 p.Pro42Leu Uncertain significance Single submitter
- SPHK2 p.Pro464Gln Uncertain significance Single submitter
- SPHK2 p.Pro464Leu Uncertain significance Single submitter
- SPHK2 p.Pro467Arg Uncertain significance Single submitter
- SPHK2 p.Pro495Leu Uncertain significance Single submitter
- SPHK2 p.Pro495Thr Uncertain significance Single submitter
- SPHK2 p.Pro49Leu Uncertain significance Single submitter
- SPHK2 p.Pro516His Uncertain significance Single submitter
- SPHK2 p.Pro647Ser Uncertain significance Single submitter
- SPHK2 p.Pro93Ala Uncertain significance Single submitter
- SPHK2 p.Ser22Arg Uncertain significance Single submitter
- SPHK2 p.Ser236Arg Uncertain significance Single submitter
- SPHK2 p.Ser327Phe Uncertain significance Single submitter
- SPHK2 p.Ser545Leu Uncertain significance Single submitter
- SPHK2 p.Ser57Cys Uncertain significance Single submitter
- SPHK2 p.Ser71Leu Uncertain significance Single submitter
- SPHK2 p.Ser98Thr Uncertain significance Single submitter
- SPHK2 p.Thr48Ile Uncertain significance Single submitter
- SPHK2 p.Thr503Ile Uncertain significance Single submitter
- SPHK2 p.Val271Leu Uncertain significance Single submitter
- SPHK2 p.Val271Met Uncertain significance Single submitter
- SPHK2 p.Val554Leu Uncertain significance Single submitter
- SPHK2 p.Val571Leu Uncertain significance Single submitter
Predictors split 19
The independent predictors disagree with each other — read with care.
- SPHK2 p.Ala281Thr Uncertain significance Single submitter
- SPHK2 p.Arg128Gln Uncertain significance Single submitter
- SPHK2 p.Arg128Trp Uncertain significance Single submitter
- SPHK2 p.Arg182Gln Uncertain significance Single submitter
- SPHK2 p.Arg182Trp Uncertain significance Single submitter
- SPHK2 p.Arg310Trp Uncertain significance Single submitter
- SPHK2 p.Arg375His Uncertain significance Single submitter
- SPHK2 p.Arg572Leu Uncertain significance Single submitter
- SPHK2 p.Arg606Cys Uncertain significance Single submitter
- SPHK2 p.Arg64Cys Uncertain significance Single submitter
- SPHK2 p.Asp239Glu Uncertain significance Single submitter
- SPHK2 p.Gln151Pro Uncertain significance Single submitter
- SPHK2 p.Gly326Val Uncertain significance Single submitter
- SPHK2 p.Leu176Pro Uncertain significance Single submitter
- SPHK2 p.Met587Ile Uncertain significance Single submitter
- SPHK2 p.Pro93Arg Uncertain significance Single submitter
- SPHK2 p.Thr142Ile Uncertain significance Single submitter
- SPHK2 p.Thr243Met Uncertain significance Single submitter
- SPHK2 p.Thr70Ile Uncertain significance Single submitter
All SPHK2 variants
Benign 5
- p.Ala506Ser Multiple submitters
- p.Glu149Lys Single submitter
- p.Leu249= Single submitter
- p.Pro380= Single submitter
- p.Pro654His Single submitter
Likely benign 14
- p.Asp530Glu Multiple submitters
- p.Ala141Thr Single submitter
- p.Arg507Pro Single submitter
- p.Asp406Ala Single submitter
- p.Asp530Gly Single submitter
- p.Gly313Ser Single submitter
- p.Met269Thr Single submitter
- p.Pro415= Single submitter
- p.Pro504Ser Single submitter
- p.Pro83= Single submitter
- p.Ser245= Single submitter
- p.Ser437= Single submitter
- p.Thr20= Single submitter
- p.Phe561= No assertion criteria EBV-positive nodal T- and NK-cell lymphoma
Uncertain significance 117
- p.Ala141Ser Single submitter ⚠
- p.Ala141Val Single submitter ⚠
- p.Ala281Thr Single submitter ⚠
- p.Ala295Val Single submitter ⚠
- p.Ala367Thr Single submitter ⚠
- p.Ala38Thr Single submitter ⚠
- p.Ala490Gly Single submitter ⚠
- p.Ala490Val Single submitter ⚠
- p.Ala605Thr Single submitter ⚠
- p.Ala633Thr Single submitter ⚠
- p.Ala85Val Single submitter ⚠
- p.Arg104Gln Single submitter ⚠
- p.Arg106Cys Single submitter ⚠
- p.Arg106His Single submitter ⚠
- p.Arg122Gln Single submitter ⚠
- p.Arg125Cys Single submitter ⚠
- p.Arg128Gln Single submitter ⚠
- p.Arg128Trp Single submitter ⚠
- p.Arg129His Single submitter ⚠
- p.Arg133His Single submitter ⚠
- p.Arg147Ser Single submitter ⚠
- p.Arg152His Single submitter ⚠
- p.Arg179Gln Single submitter ⚠
- p.Arg182Gln Single submitter ⚠
- p.Arg182Trp Single submitter ⚠
- p.Arg193Gln Single submitter ⚠
- p.Arg28Gly Single submitter ⚠
- p.Arg310Trp Single submitter ⚠
- p.Arg328His Single submitter ⚠
- p.Arg33Ser Single submitter ⚠
- p.Arg357Cys Single submitter ⚠
- p.Arg375His Single submitter ⚠
- p.Arg396Gly Single submitter ⚠
- p.Arg396Leu Single submitter ⚠
- p.Arg572His Single submitter ⚠
- p.Arg572Leu Single submitter ⚠
- p.Arg606Cys Single submitter ⚠
- p.Arg61Gln Single submitter ⚠
- p.Arg64Cys Single submitter ⚠
- p.Arg64His Single submitter ⚠
- p.Arg78Gln Single submitter ⚠
- p.Arg88Gln Single submitter ⚠
- p.Arg88Trp Single submitter ⚠
- p.Asn216Ser Single submitter ⚠
- p.Asp239Glu Single submitter ⚠
- p.Asp239Tyr Single submitter
- p.Asp299Asn Single submitter ⚠
- p.Cys276Ser Single submitter ⚠
- p.Gln151Pro Single submitter ⚠
- p.Gln288His Single submitter ⚠
- p.Glu144Lys Single submitter ⚠
- p.Glu18Gln Single submitter ⚠
- p.Glu265Asp Single submitter ⚠
- p.Glu384Gln Single submitter ⚠
- p.Glu8Gln Single submitter ⚠
- p.Gly168Arg Single submitter ⚠
- p.Gly24Ser Single submitter ⚠
- p.Gly256Arg Single submitter ⚠
- p.Gly26Ala Single submitter ⚠
- p.Gly326Val Single submitter ⚠
- p.Gly448Asp Single submitter ⚠
- p.Gly489Ala Single submitter ⚠
- p.Gly509Arg Single submitter ⚠
- p.Gly514Cys Single submitter ⚠
- p.Gly536Ala Single submitter ⚠
- p.Gly550Ser Single submitter ⚠
- p.Gly617Ser Single submitter
- p.Gly62Ser Single submitter ⚠
- p.Gly640Cys Single submitter ⚠
- p.His417Leu Single submitter ⚠
- p.His417Tyr Single submitter ⚠
- p.His4Asn Single submitter ⚠
- p.Ile76Leu Single submitter ⚠
- p.Leu176Pro Single submitter ⚠
- p.Leu186Phe Single submitter
- p.Leu250Phe Single submitter ⚠
- p.Leu318Pro Single submitter ⚠
- p.Leu446Val Single submitter ⚠
- p.Leu51Phe Single submitter ⚠
- p.Leu568Pro Single submitter ⚠
- p.Leu5Pro Single submitter ⚠
- p.Leu610Pro Single submitter ⚠
- p.Met37Thr Single submitter ⚠
- p.Met587Ile Single submitter ⚠
- p.Met635Thr Single submitter ⚠
- p.Phe608Cys Single submitter ⚠
- p.Pro121Leu Single submitter ⚠
- p.Pro407Ser Single submitter ⚠
- p.Pro409Leu Single submitter ⚠
- p.Pro40Ser Single submitter ⚠
- p.Pro42Leu Single submitter ⚠
- p.Pro464Gln Single submitter ⚠
- p.Pro464Leu Single submitter ⚠
- p.Pro467Arg Single submitter ⚠
- p.Pro495Leu Single submitter ⚠
- p.Pro495Thr Single submitter ⚠
- p.Pro49Leu Single submitter ⚠
- p.Pro516His Single submitter ⚠
- p.Pro647Ser Single submitter ⚠
- p.Pro93Ala Single submitter ⚠
- p.Pro93Arg Single submitter ⚠
- p.Ser22Arg Single submitter ⚠
- p.Ser236Arg Single submitter ⚠
- p.Ser327Phe Single submitter ⚠
- p.Ser545Leu Single submitter ⚠
- p.Ser57Cys Single submitter ⚠
- p.Ser71Leu Single submitter ⚠
- p.Ser98Thr Single submitter ⚠
- p.Thr142Ile Single submitter ⚠
- p.Thr243Met Single submitter ⚠
- p.Thr48Ile Single submitter ⚠
- p.Thr503Ile Single submitter ⚠
- p.Thr70Ile Single submitter ⚠
- p.Val271Leu Single submitter ⚠
- p.Val271Met Single submitter ⚠
- p.Val554Leu Single submitter ⚠
- p.Val571Leu Single submitter ⚠