AKT3 — 212 ClinVar variants

All ClinVar germline AKT3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 67 flagged for review →

6 Pathogenic · 2 Pathogenic/Likely pathogenic · 5 Likely pathogenic · 10 Conflicting · 25 Benign · 3 Benign/Likely benign · 96 Likely benign · 65 Uncertain significance

Full AKT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 67

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 8

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

Predictors lean, ClinVar uncertain 36

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

Predictors split 22

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

All AKT3 variants

Pathogenic 6

  • p.Glu17Lys Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Asn229Ile Single submitter
  • p.Asn229Ser Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠
  • p.Glu114Ter Single submitter AKT3 related microcephaly
  • p.Lys180Glu Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Asn321Lys No assertion criteria megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠

Pathogenic/Likely pathogenic 2

  • p.Arg465Trp Multiple submitters AKT3-related disorder
  • p.Asp322Asn Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠

Likely pathogenic 5

  • p.Asp322Tyr Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Lys161Gln Single submitter
  • p.Trp79Cys Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Val183Asp Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Leu77His No assertion criteria megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2

Conflicting classifications of pathogenicity 10

  • c.820-10T>G Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.*5462G>A Single submitter
  • p.Arg108Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg401Lys Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠
  • p.Asn229His Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠
  • p.Ile444Val Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠
  • p.Ile6Val Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠
  • p.Pro466Leu Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠
  • p.Thr137Ala Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠
  • p.Val268Ala Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 ⚠

Benign 25

  • c.285-13C>T Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.628-25C>T Multiple submitters
  • c.696+147G>A Multiple submitters
  • p.Asn348= Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.1163+16C>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.1164-172C>T Single submitter
  • c.1251+15T>C Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.173-121A>T Single submitter
  • c.173-23_173-20del Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.285-149G>A Single submitter
  • c.430-141A>G Single submitter
  • c.430-146A>G Single submitter
  • c.430-17dup Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.430-239C>G Single submitter
  • c.46+11C>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.46+12G>A Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.627+159G>T Single submitter
  • c.628-9dup Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.819+17del Single submitter
  • c.-112-388dup Single submitter
  • c.*5155_*5159dup Single submitter
  • c.*6+266A>G Single submitter
  • c.*6+96dup Single submitter
  • p.Pro466= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Ser264= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2

Benign/Likely benign 3

  • p.Asp453= Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Tyr269= Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.819+2T>A No assertion criteria

Likely benign 96

  • p.Glu361Gly Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes ⚠
  • p.Lys168= Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • c.1163+17G>A Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.1252-120G>A Multiple submitters
  • c.172+70T>C Multiple submitters
  • c.562-95C>T Multiple submitters
  • c.820-18A>G Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.948+105A>G Multiple submitters
  • c.*6+147T>C Multiple submitters
  • p.Asp280= Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Lys294= Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Ser55= Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Thr302= Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Thr91= Multiple submitters megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.1164-7C>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.1251+49A>G Single submitter
  • c.1252-10C>G Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.1252-12185A>C Single submitter
  • c.1252-20_1252-19del Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.1252-20C>G Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.172+132T>G Single submitter
  • c.172+13T>A Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.172+19T>C Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.173-121A>G Single submitter
  • c.173-177G>A Single submitter
  • c.173-207_173-203dup Single submitter
  • c.284+10T>C Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.284+211T>C Single submitter
  • c.284+253T>G Single submitter
  • c.429+15C>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.429+8A>G Single submitter
  • c.430-11G>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.430-19T>C Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.430-9del Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.46+139GT[2] Single submitter
  • c.46+18C>G Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.46+212_46+216del Single submitter
  • c.47-10C>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.47-17G>A Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.47-18C>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.47-4G>A Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.562-17C>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.562-6T>C Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.627+114G>A Single submitter
  • c.627+123G>A Single submitter
  • c.627+7G>A Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.628-18dup Single submitter
  • c.628-220_628-215del Single submitter
  • c.628-227A>G Single submitter
  • c.628-52_628-47del Single submitter
  • c.696+209C>T Single submitter
  • c.819+189G>A Single submitter
  • c.820-10T>A Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.820-12C>G Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.820-466G>C Single submitter
  • c.948+14C>G Single submitter
  • c.948+9C>A Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.948+9C>T Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.949-18T>C Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.949-222dup Single submitter
  • c.949-237del Single submitter
  • c.-112-173G>T Single submitter
  • c.-112-325C>T Single submitter
  • c.-43A>G Single submitter
  • c.*5398_*5402dup Single submitter
  • c.*7T>C Single submitter
  • p.Arg367= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Asn462= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Asp188= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Asp350= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Gln425= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Glu115= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Glu132= Single submitter
  • p.Glu240= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Glu311= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Glu65= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Gly231= Single submitter
  • p.His139= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Ile102= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Ile184= Single submitter
  • p.Leu332= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Lys180= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Lys58= Single submitter
  • p.Phe243= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Phe365= Single submitter
  • p.Phe405= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Pro121= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Pro448Thr Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Ser2= Single submitter
  • p.Ser472= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Thr368= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • p.Val242= Single submitter megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
  • c.*5453T>G No assertion criteria AKT3-related disorder
  • c.*5510_*5512del No assertion criteria AKT3-related disorder
  • p.Pro448= No assertion criteria AKT3-related disorder
  • p.Tyr174= No assertion criteria AKT3-related disorder

Uncertain significance 65