Sugi Variant

Sugi Variant/PSAT1

PSAT1 — 371 ClinVar variants

All ClinVar germline PSAT1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 127 flagged for review →

18 Pathogenic · 6 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 13 Conflicting · 38 Benign · 4 Benign/Likely benign · 137 Likely benign · 146 Uncertain significance

Full PSAT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 127

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 vs ClinVar 1

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 5

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 98

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 23

The independent predictors disagree with each other — read with care.

All PSAT1 variants

Pathogenic 18

Pathogenic/Likely pathogenic 6

  • c.870-1G>T Multiple submitters PSAT1-related disorder
  • p.Arg222Ter Multiple submitters Neu-Laxova syndrome 2
  • p.Asp100Ala Multiple submitters PSAT1-related disorder
  • p.Glu280Ter Multiple submitters PSAT1-related disorder
  • p.Glu28fs Multiple submitters PSAT deficiency
  • p.Glu317Ter Multiple submitters PSAT1-related disorder

Likely pathogenic 9

Conflicting classifications of pathogenicity 13

Benign 38

Benign/Likely benign 4

  • c.1008-11G>T Multiple submitters Neu-Laxova syndrome 2
  • c.122-17T>C Multiple submitters Neu-Laxova syndrome 2
  • c.571-4dup Multiple submitters Neu-Laxova syndrome 2
  • p.Asp353= Multiple submitters Neu-Laxova syndrome 2

Likely benign 137

  • c.571-19A>T Multiple submitters Neu-Laxova syndrome 2
  • c.60+8C>G Multiple submitters Neu-Laxova syndrome 2
  • p.Ala264= Multiple submitters Neu-Laxova syndrome 2
  • p.Asp167= Multiple submitters Neu-Laxova syndrome 2
  • p.Ile123Val Multiple submitters Neu-Laxova syndrome 2
  • p.Leu75= Multiple submitters Neu-Laxova syndrome 2
  • p.Pro166= Multiple submitters Neu-Laxova syndrome 2
  • p.Tyr131= Multiple submitters Neu-Laxova syndrome 2
  • p.Tyr148= Multiple submitters Neu-Laxova syndrome 2
  • p.Tyr289= Multiple submitters Neu-Laxova syndrome 2
  • p.Val254= Multiple submitters Neu-Laxova syndrome 2
  • c.1007+11C>T Single submitter Neu-Laxova syndrome 2
  • c.1007+12T>G Single submitter Neu-Laxova syndrome 2
  • c.1007+16A>G Single submitter Neu-Laxova syndrome 2
  • c.1008-16T>C Single submitter Neu-Laxova syndrome 2
  • c.1008-17A>G Single submitter Neu-Laxova syndrome 2
  • c.1008-18G>C Single submitter Neu-Laxova syndrome 2
  • c.1008-7A>G Single submitter Neu-Laxova syndrome 2
  • c.121+16G>A Single submitter Neu-Laxova syndrome 2
  • c.122-11T>C Single submitter Neu-Laxova syndrome 2
  • c.122-15T>C Single submitter Neu-Laxova syndrome 2
  • c.122-9_122-5del Single submitter Neu-Laxova syndrome 2
  • c.122-9C>G Single submitter Neu-Laxova syndrome 2
  • c.191+20A>G Single submitter Neu-Laxova syndrome 2
  • c.191+8T>A Single submitter Neu-Laxova syndrome 2
  • c.192-14A>C Single submitter Neu-Laxova syndrome 2
  • c.192-16C>G Single submitter Neu-Laxova syndrome 2
  • c.192-17C>T Single submitter Neu-Laxova syndrome 2
  • c.398-12C>T Single submitter Neu-Laxova syndrome 2
  • c.398-19A>G Single submitter Neu-Laxova syndrome 2
  • c.398-9C>G Single submitter Neu-Laxova syndrome 2
  • c.570+13A>G Single submitter Neu-Laxova syndrome 2
  • c.571-11C>G Single submitter Neu-Laxova syndrome 2
  • c.571-15C>A Single submitter Neu-Laxova syndrome 2
  • c.571-4T>A Single submitter Neu-Laxova syndrome 2
  • c.571-6T>C Single submitter Neu-Laxova syndrome 2
  • c.60+10C>A Single submitter Neu-Laxova syndrome 2
  • c.60+10C>T Single submitter Neu-Laxova syndrome 2
  • c.60+13G>A Single submitter Neu-Laxova syndrome 2
  • c.60+20C>A Single submitter Neu-Laxova syndrome 2
  • c.60+20C>T Single submitter Neu-Laxova syndrome 2
  • c.60+9C>G Single submitter Neu-Laxova syndrome 2
  • c.61-17C>G Single submitter Neu-Laxova syndrome 2
  • c.61-7T>A Single submitter Neu-Laxova syndrome 2
  • c.740+10G>A Single submitter Neu-Laxova syndrome 2
  • c.740+8T>C Single submitter Neu-Laxova syndrome 2
  • c.740+9G>T Single submitter Neu-Laxova syndrome 2
  • c.741-18_741-17delinsAC Single submitter Neu-Laxova syndrome 2
  • c.741-19_741-18insA Single submitter Neu-Laxova syndrome 2
  • c.741-7A>C Single submitter Neu-Laxova syndrome 2
  • c.741-7A>G Single submitter Neu-Laxova syndrome 2
  • c.741-8C>G Single submitter Neu-Laxova syndrome 2
  • c.741-8C>T Single submitter Neu-Laxova syndrome 2
  • c.869+11G>A Single submitter Neu-Laxova syndrome 2
  • c.869+12G>C Single submitter Neu-Laxova syndrome 2
  • c.869+14T>C Single submitter Neu-Laxova syndrome 2
  • c.869+8A>C Single submitter Neu-Laxova syndrome 2
  • c.869+9A>G Single submitter Neu-Laxova syndrome 2
  • c.870-15A>G Single submitter Neu-Laxova syndrome 2
  • c.870-16T>C Single submitter Neu-Laxova syndrome 2
  • c.870-4T>C Single submitter
  • c.*592A>C Single submitter
  • c.*865C>G Single submitter PSAT deficiency
  • p.Ala111= Single submitter Neu-Laxova syndrome 2
  • p.Ala196= Single submitter Neu-Laxova syndrome 2
  • p.Ala220= Single submitter Neu-Laxova syndrome 2
  • p.Ala265= Single submitter Neu-Laxova syndrome 2
  • p.Ala3= Single submitter Neu-Laxova syndrome 2
  • p.Ala359= Single submitter Neu-Laxova syndrome 2
  • p.Ala50= Single submitter Neu-Laxova syndrome 2
  • p.Ala99= Single submitter Neu-Laxova syndrome 2
  • p.Arg319= Single submitter Neu-Laxova syndrome 2
  • p.Arg342= Single submitter Neu-Laxova syndrome 2
  • p.Arg45= Single submitter Neu-Laxova syndrome 2
  • p.Arg61= Single submitter Neu-Laxova syndrome 2
  • p.Arg97= Single submitter Neu-Laxova syndrome 2
  • p.Asn54= Single submitter Neu-Laxova syndrome 2
  • p.Asn89= Single submitter Neu-Laxova syndrome 2
  • p.Asn9= Single submitter Neu-Laxova syndrome 2
  • p.Asp100= Single submitter Neu-Laxova syndrome 2
  • p.Asp145= Single submitter Neu-Laxova syndrome 2
  • p.Asp215= Single submitter Neu-Laxova syndrome 2
  • p.Asp322= Single submitter Neu-Laxova syndrome 2
  • p.Cys152= Single submitter Neu-Laxova syndrome 2
  • p.Cys80= Single submitter Neu-Laxova syndrome 2
  • p.Cys98= Single submitter Neu-Laxova syndrome 2
  • p.Glu223= Single submitter Neu-Laxova syndrome 2
  • p.Glu229= Single submitter Neu-Laxova syndrome 2
  • p.Glu317= Single submitter Neu-Laxova syndrome 2
  • p.Gly11= Single submitter Neu-Laxova syndrome 2
  • p.Gly119= Single submitter Neu-Laxova syndrome 2
  • p.Gly206= Single submitter Neu-Laxova syndrome 2
  • p.Gly287= Single submitter Neu-Laxova syndrome 2
  • p.Gly334= Single submitter Neu-Laxova syndrome 2
  • p.Gly340= Single submitter Neu-Laxova syndrome 2
  • p.Gly36= Single submitter Neu-Laxova syndrome 2
  • p.Gly79= Single submitter Neu-Laxova syndrome 2
  • p.His335= Single submitter Neu-Laxova syndrome 2
  • p.Ile123= Single submitter Neu-Laxova syndrome 2
  • p.Leu17= Single submitter Neu-Laxova syndrome 2
  • p.Leu182= Single submitter Neu-Laxova syndrome 2
  • p.Leu216= Single submitter Neu-Laxova syndrome 2
  • p.Leu217= Single submitter Neu-Laxova syndrome 2
  • p.Leu30= Single submitter
  • p.Leu330= Single submitter Neu-Laxova syndrome 2
  • p.Leu357= Single submitter Neu-Laxova syndrome 2
  • p.Leu370= Single submitter Neu-Laxova syndrome 2
  • p.Leu59= Single submitter Neu-Laxova syndrome 2
  • p.Leu90= Single submitter Neu-Laxova syndrome 2
  • p.Lys200= Single submitter Neu-Laxova syndrome 2
  • p.Lys33= Single submitter Neu-Laxova syndrome 2
  • p.Phe181= Single submitter Neu-Laxova syndrome 2
  • p.Phe305= Single submitter Neu-Laxova syndrome 2
  • p.Pro18= Single submitter Neu-Laxova syndrome 2
  • p.Pro295Arg Single submitter Neu-Laxova syndrome 2
  • p.Pro304= Single submitter Neu-Laxova syndrome 2
  • p.Pro87= Single submitter Neu-Laxova syndrome 2
  • p.Ser108= Single submitter Neu-Laxova syndrome 2
  • p.Ser226= Single submitter Neu-Laxova syndrome 2
  • p.Ser271= Single submitter Neu-Laxova syndrome 2
  • p.Ser272= Single submitter Neu-Laxova syndrome 2
  • p.Ser38= Single submitter Neu-Laxova syndrome 2
  • p.Ser43= Single submitter Neu-Laxova syndrome 2
  • p.Thr104= Single submitter Neu-Laxova syndrome 2
  • p.Thr156= Single submitter Neu-Laxova syndrome 2
  • p.Thr208= Single submitter Neu-Laxova syndrome 2
  • p.Thr242= Single submitter Neu-Laxova syndrome 2
  • p.Thr277= Single submitter Neu-Laxova syndrome 2
  • p.Thr350= Single submitter Neu-Laxova syndrome 2
  • p.Tyr240= Single submitter Neu-Laxova syndrome 2
  • p.Tyr249= Single submitter Neu-Laxova syndrome 2
  • p.Val149= Single submitter Neu-Laxova syndrome 2
  • p.Val172= Single submitter Neu-Laxova syndrome 2
  • p.Val174= Single submitter Neu-Laxova syndrome 2
  • p.Val227= Single submitter Neu-Laxova syndrome 2
  • p.Val293= Single submitter Neu-Laxova syndrome 2
  • p.Val66= Single submitter Neu-Laxova syndrome 2

Uncertain significance 146