SHMT1 — 73 ClinVar variants
All ClinVar germline SHMT1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 56 flagged for review →
7 Benign · 8 Likely benign · 58 Uncertain significance
Full SHMT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 56
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 46
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SHMT1 p.Thr258Ile Uncertain significance Multiple submitters
- SHMT1 p.Ala319Val Uncertain significance Single submitter
- SHMT1 p.Ala379Ser Uncertain significance Single submitter
- SHMT1 p.Ala459Val Uncertain significance Single submitter
- SHMT1 p.Arg137His Uncertain significance Single submitter
- SHMT1 p.Arg191His Uncertain significance Single submitter
- SHMT1 p.Arg207Gln Uncertain significance Single submitter
- SHMT1 p.Arg215Trp Uncertain significance Single submitter
- SHMT1 p.Arg263Gln Uncertain significance Single submitter
- SHMT1 p.Arg397Gln Uncertain significance Single submitter
- SHMT1 p.Arg397Trp Uncertain significance Single submitter
- SHMT1 p.Arg402Trp Uncertain significance Single submitter
- SHMT1 p.Arg411Cys Uncertain significance Single submitter
- SHMT1 p.Arg411His Uncertain significance Single submitter
- SHMT1 p.Asn42Asp Uncertain significance Single submitter
- SHMT1 p.Asp156Glu Uncertain significance Single submitter
- SHMT1 p.Asp355His Uncertain significance Single submitter
- SHMT1 p.Asp362Gly Uncertain significance Single submitter
- SHMT1 p.Asp455Gly Uncertain significance Single submitter
- SHMT1 p.Gln80His Uncertain significance Single submitter
- SHMT1 p.Glu344Gln Uncertain significance Single submitter
- SHMT1 p.Glu447Asp Uncertain significance Single submitter
- SHMT1 p.Gly222Glu Uncertain significance Single submitter
- SHMT1 p.Gly234Arg Uncertain significance Single submitter
- SHMT1 p.Gly299Val Uncertain significance Single submitter
- SHMT1 p.Gly79Asp Uncertain significance Single submitter
- SHMT1 p.His256Gln Uncertain significance Single submitter
- SHMT1 p.Ile284Val Uncertain significance Single submitter
- SHMT1 p.Ile89Val Uncertain significance Single submitter
- SHMT1 p.Leu285Pro Uncertain significance Single submitter
- SHMT1 p.Leu474Arg Uncertain significance Single submitter
- SHMT1 p.Lys105Asn Uncertain significance Single submitter
- SHMT1 p.Lys216Glu Uncertain significance Single submitter
- SHMT1 p.Lys416Asn Uncertain significance Single submitter
- SHMT1 p.Met266Arg Uncertain significance Single submitter
- SHMT1 p.Met320Val Uncertain significance Single submitter
- SHMT1 p.Met3Val Uncertain significance Single submitter
- SHMT1 p.Phe245Ser Uncertain significance Single submitter
- SHMT1 p.Pro108Ser Uncertain significance Single submitter
- SHMT1 p.Pro195Leu Uncertain significance Single submitter
- SHMT1 p.Pro478Arg Uncertain significance Single submitter
- SHMT1 p.Ser206Pro Uncertain significance Single submitter
- SHMT1 p.Thr202Ser Uncertain significance Single submitter
- SHMT1 p.Val132Leu Uncertain significance Single submitter
- SHMT1 p.Val312Ile Uncertain significance Single submitter
-
SHMT1 p.Leu474Phe
Uncertain significance
No assertion criteria
gastrointestinal stromal tumor
Predictors split 10
The independent predictors disagree with each other — read with care.
- SHMT1 p.Arg213Trp Likely benign Multiple submitters
- SHMT1 p.Ala227Val Uncertain significance Single submitter
- SHMT1 p.Ile309Val Uncertain significance Single submitter
- SHMT1 p.Ile89Thr Uncertain significance Single submitter
- SHMT1 p.Met170Val Uncertain significance Single submitter
- SHMT1 p.Pro476Arg Uncertain significance Single submitter
- SHMT1 p.Tyr180His Uncertain significance Single submitter
- SHMT1 p.Tyr269Cys Uncertain significance Single submitter
- SHMT1 p.Val115Ile Uncertain significance Single submitter
- SHMT1 p.Val461Met Uncertain significance Single submitter
All SHMT1 variants
Benign 7
- c.242+10T>C Multiple submitters
- c.815-3C>T Multiple submitters
- p.Ala460= Multiple submitters
- p.Lys216Arg Multiple submitters
- p.Met1Lys Multiple submitters
- p.Val251= Multiple submitters
- p.Glu340Gln Single submitter
Likely benign 8
- p.Arg213Trp Multiple submitters ⚠
- c.1054+6G>A Single submitter
- c.520-6C>G Single submitter
- p.Ala237Val Single submitter
- p.Arg393Lys Single submitter
- p.Leu14= Single submitter
- p.Met1Arg Single submitter
- p.Thr439Ile Single submitter
Uncertain significance 58
- p.Thr258Ile Multiple submitters ⚠
- p.Ala227Val Single submitter ⚠
- p.Ala319Val Single submitter ⚠
- p.Ala379Ser Single submitter ⚠
- p.Ala459Val Single submitter ⚠
- p.Arg137His Single submitter ⚠
- p.Arg191His Single submitter ⚠
- p.Arg207Gln Single submitter ⚠
- p.Arg215Trp Single submitter ⚠
- p.Arg263Gln Single submitter ⚠
- p.Arg397Gln Single submitter ⚠
- p.Arg397Trp Single submitter ⚠
- p.Arg402Trp Single submitter ⚠
- p.Arg411Cys Single submitter ⚠
- p.Arg411His Single submitter ⚠
- p.Asn42Asp Single submitter ⚠
- p.Asp156Glu Single submitter ⚠
- p.Asp355His Single submitter ⚠
- p.Asp362Gly Single submitter ⚠
- p.Asp455Gly Single submitter ⚠
- p.Gln80His Single submitter ⚠
- p.Gln97Leu Single submitter
- p.Glu344Gln Single submitter ⚠
- p.Glu447Asp Single submitter ⚠
- p.Gly222Glu Single submitter ⚠
- p.Gly234Arg Single submitter ⚠
- p.Gly299Val Single submitter ⚠
- p.Gly79Asp Single submitter ⚠
- p.His256Gln Single submitter ⚠
- p.Ile284Val Single submitter ⚠
- p.Ile309Val Single submitter ⚠
- p.Ile349Thr Single submitter
- p.Ile89Thr Single submitter ⚠
- p.Ile89Val Single submitter ⚠
- p.Leu285Pro Single submitter ⚠
- p.Leu474Arg Single submitter ⚠
- p.Lys105Asn Single submitter ⚠
- p.Lys216Glu Single submitter ⚠
- p.Lys416Asn Single submitter ⚠
- p.Met170Val Single submitter ⚠
- p.Met266Arg Single submitter ⚠
- p.Met320Val Single submitter ⚠
- p.Met3Val Single submitter ⚠
- p.Phe245Ser Single submitter ⚠
- p.Pro108Ser Single submitter ⚠
- p.Pro195Leu Single submitter ⚠
- p.Pro476Arg Single submitter ⚠
- p.Pro478Arg Single submitter ⚠
- p.Ser206Pro Single submitter ⚠
- p.Thr202Ser Single submitter ⚠
- p.Tyr180His Single submitter ⚠
- p.Tyr269Cys Single submitter ⚠
- p.Tyr286His Single submitter
- p.Val115Ile Single submitter ⚠
- p.Val132Leu Single submitter ⚠
- p.Val312Ile Single submitter ⚠
- p.Val461Met Single submitter ⚠
- p.Leu474Phe No assertion criteria gastrointestinal stromal tumor ⚠