SPTLC3 — 73 ClinVar variants
All ClinVar germline SPTLC3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 70 flagged for review →
1 Likely pathogenic · 2 Likely benign · 70 Uncertain significance
Full SPTLC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 70
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 50
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SPTLC3 p.Ala133Val Uncertain significance Single submitter
- SPTLC3 p.Ala262Ser Uncertain significance Single submitter
- SPTLC3 p.Ala38Thr Uncertain significance Single submitter
- SPTLC3 p.Ala519Val Uncertain significance Single submitter
- SPTLC3 p.Ala93Thr Uncertain significance Single submitter
- SPTLC3 p.Arg128Gln Uncertain significance Single submitter
- SPTLC3 p.Arg157Thr Uncertain significance Single submitter
- SPTLC3 p.Arg296Cys Uncertain significance Single submitter
- SPTLC3 p.Arg296His Uncertain significance Single submitter
- SPTLC3 p.Arg349Pro Uncertain significance Single submitter
- SPTLC3 p.Arg499Gln Uncertain significance Single submitter
- SPTLC3 p.Arg499Pro Uncertain significance Single submitter
- SPTLC3 p.Arg501Gln Uncertain significance Single submitter
- SPTLC3 p.Arg501Trp Uncertain significance Single submitter
- SPTLC3 p.Arg539His Uncertain significance Single submitter
- SPTLC3 p.Asn149Ile Uncertain significance Single submitter
- SPTLC3 p.Asn220Lys Uncertain significance Single submitter
- SPTLC3 p.Asp358Glu Uncertain significance Single submitter
- SPTLC3 p.Asp363Glu Uncertain significance Single submitter
- SPTLC3 p.Cys91Gly Uncertain significance Single submitter
- SPTLC3 p.Gln443Lys Uncertain significance Single submitter
- SPTLC3 p.Glu551Ala Uncertain significance Single submitter
- SPTLC3 p.Glu551Lys Uncertain significance Single submitter
- SPTLC3 p.His200Arg Uncertain significance Single submitter
- SPTLC3 p.His208Tyr Uncertain significance Single submitter
- SPTLC3 p.His318Tyr Uncertain significance Single submitter
- SPTLC3 p.Ile159Met Uncertain significance Single submitter
- SPTLC3 p.Ile159Thr Uncertain significance Single submitter
- SPTLC3 p.Ile335Val Uncertain significance Single submitter
- SPTLC3 p.Ile34Lys Uncertain significance Single submitter
- SPTLC3 p.Ile380Val Uncertain significance Single submitter
- SPTLC3 p.Ile51Thr Uncertain significance Single submitter
- SPTLC3 p.Leu305Val Uncertain significance Single submitter
- SPTLC3 p.Lys209Thr Uncertain significance Single submitter
- SPTLC3 p.Lys530Arg Uncertain significance Single submitter
- SPTLC3 p.Met202Ile Uncertain significance Single submitter
- SPTLC3 p.Pro44Ala Uncertain significance Single submitter
- SPTLC3 p.Ser265Pro Uncertain significance Single submitter
- SPTLC3 p.Ser396Thr Uncertain significance Single submitter
- SPTLC3 p.Thr183Lys Uncertain significance Single submitter
- SPTLC3 p.Thr277Ala Uncertain significance Single submitter
- SPTLC3 p.Thr368Ile Uncertain significance Single submitter
- SPTLC3 p.Thr515Met Uncertain significance Single submitter
- SPTLC3 p.Thr546Met Uncertain significance Single submitter
- SPTLC3 p.Val226Ile Uncertain significance Single submitter
- SPTLC3 p.Val344Met Uncertain significance Single submitter
- SPTLC3 p.Val35Met Uncertain significance Single submitter
- SPTLC3 p.Val485Gly Uncertain significance Single submitter
- SPTLC3 p.Val488Met Uncertain significance Single submitter
- SPTLC3 p.Val516Asp Uncertain significance Single submitter
Predictors split 20
The independent predictors disagree with each other — read with care.
- SPTLC3 p.Ala500Ser Uncertain significance Single submitter
- SPTLC3 p.Arg349Gln Uncertain significance Single submitter
- SPTLC3 p.Arg430Ile Uncertain significance Single submitter
- SPTLC3 p.Arg533Trp Uncertain significance Single submitter
- SPTLC3 p.Asp161Tyr Uncertain significance Single submitter
- SPTLC3 p.Asp358Tyr Uncertain significance Single submitter
- SPTLC3 p.Asp525Val Uncertain significance Single submitter
- SPTLC3 p.Ile322Phe Uncertain significance Single submitter
- SPTLC3 p.Ile323Arg Uncertain significance Single submitter
- SPTLC3 p.Leu283Phe Uncertain significance Single submitter
- SPTLC3 p.Leu365Ile Uncertain significance Single submitter
- SPTLC3 p.Phe354Leu Uncertain significance Single submitter
- SPTLC3 p.Pro406Leu Uncertain significance Single submitter
- SPTLC3 p.Thr268Ile Uncertain significance Single submitter
- SPTLC3 p.Thr295Asn Uncertain significance Single submitter
- SPTLC3 p.Thr352Met Uncertain significance Single submitter
-
SPTLC3 p.Trp150Arg
Likely pathogenic
Single submitter
peripheral neuropathy
- SPTLC3 p.Val317Met Uncertain significance Single submitter
- SPTLC3 p.Val387Met Uncertain significance Single submitter
- SPTLC3 p.Val485Met Uncertain significance Single submitter
All SPTLC3 variants
Likely pathogenic 1
- p.Trp150Arg Single submitter peripheral neuropathy ⚠
Likely benign 2
- p.Met478Leu Single submitter
- p.Val288Ile Single submitter
Uncertain significance 70
- p.Ala133Val Single submitter ⚠
- p.Ala262Ser Single submitter ⚠
- p.Ala38Thr Single submitter ⚠
- p.Ala500Ser Single submitter ⚠
- p.Ala519Val Single submitter ⚠
- p.Ala93Thr Single submitter ⚠
- p.Arg128Gln Single submitter ⚠
- p.Arg157Thr Single submitter ⚠
- p.Arg296Cys Single submitter ⚠
- p.Arg296His Single submitter ⚠
- p.Arg349Gln Single submitter ⚠
- p.Arg349Pro Single submitter ⚠
- p.Arg430Ile Single submitter ⚠
- p.Arg499Gln Single submitter ⚠
- p.Arg499Pro Single submitter ⚠
- p.Arg501Gln Single submitter ⚠
- p.Arg501Trp Single submitter ⚠
- p.Arg533Trp Single submitter ⚠
- p.Arg539His Single submitter ⚠
- p.Asn149Ile Single submitter ⚠
- p.Asn220Lys Single submitter ⚠
- p.Asp161Tyr Single submitter ⚠
- p.Asp358Glu Single submitter ⚠
- p.Asp358Tyr Single submitter ⚠
- p.Asp363Glu Single submitter ⚠
- p.Asp525Val Single submitter ⚠
- p.Cys91Gly Single submitter ⚠
- p.Gln443Lys Single submitter ⚠
- p.Glu551Ala Single submitter ⚠
- p.Glu551Lys Single submitter ⚠
- p.Gly12Arg Single submitter
- p.His200Arg Single submitter ⚠
- p.His208Tyr Single submitter ⚠
- p.His318Tyr Single submitter ⚠
- p.Ile159Met Single submitter ⚠
- p.Ile159Thr Single submitter ⚠
- p.Ile322Phe Single submitter ⚠
- p.Ile323Arg Single submitter ⚠
- p.Ile335Val Single submitter ⚠
- p.Ile34Lys Single submitter ⚠
- p.Ile380Val Single submitter ⚠
- p.Ile51Thr Single submitter ⚠
- p.Leu283Phe Single submitter ⚠
- p.Leu305Val Single submitter ⚠
- p.Leu365Ile Single submitter ⚠
- p.Lys209Thr Single submitter ⚠
- p.Lys530Arg Single submitter ⚠
- p.Met202Ile Single submitter ⚠
- p.Phe354Leu Single submitter ⚠
- p.Pro406Leu Single submitter ⚠
- p.Pro44Ala Single submitter ⚠
- p.Ser265Pro Single submitter ⚠
- p.Ser396Thr Single submitter ⚠
- p.Thr183Lys Single submitter ⚠
- p.Thr268Ile Single submitter ⚠
- p.Thr277Ala Single submitter ⚠
- p.Thr295Asn Single submitter ⚠
- p.Thr352Met Single submitter ⚠
- p.Thr368Ile Single submitter ⚠
- p.Thr515Met Single submitter ⚠
- p.Thr546Met Single submitter ⚠
- p.Val226Ile Single submitter ⚠
- p.Val317Met Single submitter ⚠
- p.Val344Met Single submitter ⚠
- p.Val35Met Single submitter ⚠
- p.Val387Met Single submitter ⚠
- p.Val485Gly Single submitter ⚠
- p.Val485Met Single submitter ⚠
- p.Val488Met Single submitter ⚠
- p.Val516Asp Single submitter ⚠