GPAT2 — 118 ClinVar variants

All ClinVar germline GPAT2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 98 flagged for review →

3 Likely pathogenic · 1 Benign · 10 Likely benign · 104 Uncertain significance

Full GPAT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 98

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.

GPAT2 p.Arg627Trp Likely pathogenic Single submitter
male infertility

Predictors lean, ClinVar uncertain 77

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

Predictors split 20

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

All GPAT2 variants

Likely pathogenic 3

c.1156-1G>A Single submitter male infertility
p.Arg627Trp Single submitter male infertility ⚠
p.Arg652Ter Single submitter male infertility

Benign 1

p.Pro45= Multiple submitters

Likely benign 10

p.Ala712Thr Single submitter
p.Arg365His Single submitter
p.His688Arg Single submitter
p.Ile494Thr Single submitter
p.Lys42= Single submitter
p.Ser26= Single submitter
p.Ser346Leu Single submitter
p.Ser452Asn Single submitter
p.Thr768Met Single submitter
p.Val161Leu Single submitter

Uncertain significance 104

p.Ala459Val Single submitter
p.Ala636Thr Single submitter ⚠
p.Ala736Thr Single submitter ⚠
p.Ala738Thr Single submitter ⚠
p.Ala747Val Single submitter ⚠
p.Ala752Thr Single submitter ⚠
p.Arg127Gly Single submitter ⚠
p.Arg147His Single submitter ⚠
p.Arg157His Single submitter ⚠
p.Arg360Cys Single submitter ⚠
p.Arg371Trp Single submitter ⚠
p.Arg44Cys Single submitter ⚠
p.Arg49Cys Single submitter ⚠
p.Arg49His Single submitter male infertility ⚠
p.Arg508Trp Single submitter ⚠
p.Arg519Pro Single submitter ⚠
p.Arg519Trp Single submitter ⚠
p.Arg526His Single submitter ⚠
p.Arg528Cys Single submitter ⚠
p.Arg567Gln Single submitter ⚠
p.Arg567Trp Single submitter ⚠
p.Arg595His Single submitter ⚠
p.Arg627Gln Single submitter ⚠
p.Arg643Gln Single submitter ⚠
p.Arg679Gln Single submitter ⚠
p.Arg679Trp Single submitter ⚠
p.Arg682Thr Single submitter ⚠
p.Arg715Cys Single submitter ⚠
p.Arg760Thr Single submitter ⚠
p.Arg796Gln Single submitter ⚠
p.Arg796Pro Single submitter ⚠
p.Arg796Trp Single submitter ⚠
p.Asp647Gly Single submitter
p.Asp667His Single submitter ⚠
p.Cys621Arg Single submitter ⚠
p.Gln10Glu Single submitter ⚠
p.Gln10Pro Single submitter ⚠
p.Gln12His Single submitter ⚠
p.Gln423His Single submitter ⚠
p.Gln630Arg Single submitter ⚠
p.Gln718His Single submitter ⚠
p.Gln767Arg Single submitter ⚠
p.Gln797Arg Single submitter ⚠
p.Gln797Pro Single submitter
p.Glu144Ala Single submitter ⚠
p.Glu386Gly Single submitter ⚠
p.Glu422Lys Single submitter ⚠
p.Glu437Lys Single submitter ⚠
p.Glu559Lys Single submitter ⚠
p.Glu745Ala Single submitter ⚠
p.Gly119Arg Single submitter ⚠
p.Gly131Val Single submitter ⚠
p.Gly350Arg Single submitter ⚠
p.Gly397Arg Single submitter ⚠
p.Gly485Glu Single submitter ⚠
p.Gly632Arg Single submitter ⚠
p.Gly641Asp Single submitter ⚠
p.Gly674Arg Single submitter ⚠
p.Gly678Ser Single submitter ⚠
p.His377Arg Single submitter male infertility ⚠
p.His449Pro Single submitter ⚠
p.Leu470Met Single submitter ⚠
p.Leu495Arg Single submitter ⚠
p.Leu593Arg Single submitter ⚠
p.Leu598Pro Single submitter ⚠
p.Leu696Phe Single submitter ⚠
p.Leu700Pro Single submitter ⚠
p.Lys473Gln Single submitter ⚠
p.Lys660Asn Single submitter ⚠
p.Lys705Glu Single submitter ⚠
p.Lys750Gln Single submitter ⚠
p.Lys790Gln Single submitter ⚠
p.Met4Ile Single submitter ⚠
p.Met601Ile Single submitter ⚠
p.Phe556Ser Single submitter ⚠
p.Phe692Leu Single submitter ⚠
p.Phe695Leu Single submitter ⚠
p.Phe733Cys Single submitter ⚠
p.Pro45Leu Single submitter ⚠
p.Pro536Leu Single submitter ⚠
p.Pro575Leu Single submitter ⚠
p.Pro605Leu Single submitter ⚠
p.Pro702Leu Single submitter ⚠
p.Pro769Leu Single submitter ⚠
p.Ser26Leu Single submitter ⚠
p.Ser452Thr Single submitter ⚠
p.Ser462Asn Single submitter ⚠
p.Ser558Arg Single submitter
p.Ser779Cys Single submitter ⚠
p.Ser779Thr Single submitter ⚠
p.Thr463Met Single submitter male infertility ⚠
p.Thr722Ile Single submitter ⚠
p.Thr758Ile Single submitter ⚠
p.Trp352Arg Single submitter ⚠
p.Tyr680Cys Single submitter ⚠
p.Tyr726His Single submitter ⚠
p.Val443Asp Single submitter ⚠
p.Val455Ala Single submitter ⚠
p.Val501Ala Single submitter
p.Val522Leu Single submitter ⚠
p.Val522Met Single submitter
p.Val555Ile Single submitter ⚠
p.Val566Ala Single submitter
p.Val764Gly Single submitter ⚠