SPHK1 — 75 ClinVar variants
All ClinVar germline SPHK1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 49 flagged for review →
4 Benign · 3 Likely benign · 68 Uncertain significance
Full SPHK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 49
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 34
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SPHK1 p.Ala43Val Uncertain significance Single submitter
- SPHK1 p.Arg144His Uncertain significance Single submitter
- SPHK1 p.Arg217Gly Uncertain significance Single submitter
- SPHK1 p.Arg279Cys Uncertain significance Single submitter
- SPHK1 p.Arg57Gly Uncertain significance Single submitter
- SPHK1 p.Asn131Ile Uncertain significance Single submitter
- SPHK1 p.Asn131Tyr Uncertain significance Single submitter
- SPHK1 p.Cys365Trp Uncertain significance Single submitter
- SPHK1 p.Gln231Arg Uncertain significance Single submitter
- SPHK1 p.Glu127Lys Uncertain significance Single submitter
- SPHK1 p.Glu132Lys Uncertain significance Single submitter
- SPHK1 p.Glu44Asp Uncertain significance Single submitter
- SPHK1 p.Glu98Gln Uncertain significance Single submitter
- SPHK1 p.Gly208Ser Uncertain significance Single submitter
- SPHK1 p.Gly82Arg Uncertain significance Single submitter
- SPHK1 p.His156Arg Uncertain significance Single submitter
- SPHK1 p.His156Tyr Uncertain significance Single submitter
- SPHK1 p.His248Tyr Uncertain significance Single submitter
- SPHK1 p.Leu134His Uncertain significance Single submitter
- SPHK1 p.Leu134Val Uncertain significance Single submitter
- SPHK1 p.Leu142Pro Uncertain significance Single submitter
- SPHK1 p.Leu169Gln Uncertain significance Single submitter
- SPHK1 p.Leu238Phe Uncertain significance Single submitter
- SPHK1 p.Phe197Leu Uncertain significance Single submitter
- SPHK1 p.Pro378Ser Uncertain significance Single submitter
- SPHK1 p.Pro95Thr Uncertain significance Single submitter
- SPHK1 p.Ser220Phe Uncertain significance Single submitter
- SPHK1 p.Thr157Met Uncertain significance Single submitter
- SPHK1 p.Thr99Ser Uncertain significance Single submitter
- SPHK1 p.Val227Ile Uncertain significance Single submitter
- SPHK1 p.Val251Leu Uncertain significance Single submitter
- SPHK1 p.Val320Ile Uncertain significance Single submitter
- SPHK1 p.Val337Ala Uncertain significance Single submitter
- SPHK1 p.Val366Met Uncertain significance Single submitter
Predictors split 15
The independent predictors disagree with each other — read with care.
- SPHK1 p.Arg145Trp Uncertain significance Single submitter
- SPHK1 p.Arg162Ser Uncertain significance Single submitter
- SPHK1 p.Arg199Gly Uncertain significance Single submitter
- SPHK1 p.Arg209Pro Uncertain significance Single submitter
- SPHK1 p.Arg35Trp Uncertain significance Single submitter
- SPHK1 p.Asn151Tyr Uncertain significance Single submitter
- SPHK1 p.Cys106Tyr Uncertain significance Single submitter
- SPHK1 p.Leu41Phe Uncertain significance Single submitter
- SPHK1 p.Met306Ile Uncertain significance Single submitter
- SPHK1 p.Phe197Ser Uncertain significance Single submitter
- SPHK1 p.Pro104Ala Uncertain significance Single submitter
- SPHK1 p.Pro12Ser Uncertain significance Single submitter
- SPHK1 p.Ser48Phe Uncertain significance Single submitter
- SPHK1 p.Thr136Pro Uncertain significance Single submitter
- SPHK1 p.Thr50Met Uncertain significance Single submitter
All SPHK1 variants
Benign 4
- p.Ala4= Multiple submitters
- p.Arg199= Multiple submitters
- p.His156= Multiple submitters
- p.Pro379Leu Multiple submitters
Likely benign 3
- c.-164C>A Single submitter
- p.Arg199fs Single submitter
- p.Lys332Glu Single submitter
Uncertain significance 68
- c.-105C>G Single submitter
- c.-114T>G Single submitter
- c.-117C>T Single submitter
- c.-147C>G Single submitter
- c.-162C>T Single submitter
- c.-164C>T Single submitter
- c.-194-291G>A Single submitter
- c.-194-300C>T Single submitter
- c.-194G>T Single submitter
- c.-195+309C>G Single submitter
- c.-66G>C Single submitter
- c.-95G>T Single submitter
- p.Ala43Val Single submitter ⚠
- p.Arg144His Single submitter ⚠
- p.Arg145Trp Single submitter ⚠
- p.Arg162Ser Single submitter ⚠
- p.Arg185Trp Single submitter
- p.Arg199Gly Single submitter ⚠
- p.Arg209Pro Single submitter ⚠
- p.Arg217Gly Single submitter ⚠
- p.Arg279Cys Single submitter ⚠
- p.Arg296Cys Single submitter
- p.Arg35Trp Single submitter ⚠
- p.Arg57Gly Single submitter ⚠
- p.Asn131Ile Single submitter ⚠
- p.Asn131Tyr Single submitter ⚠
- p.Asn151Tyr Single submitter ⚠
- p.Asp73Gly Single submitter
- p.Cys106Tyr Single submitter ⚠
- p.Cys365Trp Single submitter ⚠
- p.Gln231Arg Single submitter ⚠
- p.Glu127Lys Single submitter ⚠
- p.Glu132Lys Single submitter ⚠
- p.Glu44Asp Single submitter ⚠
- p.Glu98Gln Single submitter ⚠
- p.Gly208Ser Single submitter ⚠
- p.Gly82Arg Single submitter ⚠
- p.His156Arg Single submitter ⚠
- p.His156Tyr Single submitter ⚠
- p.His248Tyr Single submitter ⚠
- p.Leu134His Single submitter ⚠
- p.Leu134Val Single submitter ⚠
- p.Leu142Pro Single submitter ⚠
- p.Leu169Gln Single submitter ⚠
- p.Leu238Phe Single submitter ⚠
- p.Leu41Phe Single submitter ⚠
- p.Met1Val Single submitter
- p.Met306Ile Single submitter ⚠
- p.Phe197Leu Single submitter ⚠
- p.Phe197Ser Single submitter ⚠
- p.Pro104Ala Single submitter ⚠
- p.Pro104Leu Single submitter
- p.Pro12Ser Single submitter ⚠
- p.Pro276Thr Single submitter
- p.Pro378Ser Single submitter ⚠
- p.Pro95Thr Single submitter ⚠
- p.Ser220Phe Single submitter ⚠
- p.Ser48Phe Single submitter ⚠
- p.Thr136Pro Single submitter ⚠
- p.Thr157Met Single submitter ⚠
- p.Thr50Met Single submitter ⚠
- p.Thr99Ser Single submitter ⚠
- p.Val227Ile Single submitter ⚠
- p.Val251Leu Single submitter ⚠
- p.Val320Ile Single submitter ⚠
- p.Val324Met Single submitter
- p.Val337Ala Single submitter ⚠
- p.Val366Met Single submitter ⚠