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AKT1
Final classification
Likely Pathogenic
AKT1 c.49G>A · p.Glu17Lys
AKT1

The AKT1 c.49G>A (p.Glu17Lys) variant resides in the pleckstrin homology (PH) domain, a critical functional domain, and lies within a statistically significant mutational hotspot where benign missense variation is notably absent (PM1_Moderate).

Gene
AKT1
Transcript
NM_001014431.1
HGVS · transcript:coding
NM_001014431.1:c.49G>A
Consequence
N/A
GRCh38
chr14:104780214 C>T
GRCh37
chr14:105246551 C>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PM1 moderate, PM2 supporting, PP5 supporting; combination = 1 strong + 1 moderate + 2 supporting, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PM1 moderate, PM2 supporting, PP5 supporting; combination = 1 strong + 1 moderate + 2 supporting, which maps to Likely Pathogenic.
Classification rationale
PS3PM1PM2PP5 Likely Pathogenic
AKT1 c.49G>A

The AKT1 c.49G>A (p.Glu17Lys) variant resides in the pleckstrin homology (PH) domain, a critical functional domain, and lies within a statistically significant mutational hotspot where benign missense variation is notably absent (PM1_Moderate).1 This variant is present in gnomAD v2.1 at an extremely low allele frequency of 0.0004% (1/250,006 alleles) and is absent from gnomAD v4.1, meeting the PM2 threshold for absence from population databases (PM2_Supporting).2 Well-established functional studies from multiple independent laboratories demonstrate that the E17K substitution results in constitutive AKT1 kinase activation, altered lipid-binding specificity, enhanced downstream signaling, transformation in cell-based assays, and oncogenesis in murine models (PS3_Strong).3 ClinVar reports this variant as Pathogenic by 4 clinical laboratories including Labcorp Genetics/Invitae and Variantyx (PP5_Supporting).4 The computational in silico predictors are equivocal (REVEL 0.51, BayesDel 0.116); PP3 is not met. BS3 is contradicted by overwhelming functional evidence of a damaging gain-of-function effect. BA1 and BS1 are not met given the extremely low population frequency.5 Under the generic ACMG/AMP 2015 framework (PMID:25741868), the criteria met are: PS3_Strong + PM1_Moderate + PM2_Supporting + PP5_Supporting. This combination (1 Strong + 1 Moderate + 2 Supporting) meets the threshold for Likely Pathogenic per Richards et al. 2015 (1 Strong AND ≥1 Moderate AND ≥2 Supporting qualifies as Likely Pathogenic).6

PS3 + PM1 + PM2 + PP5 Likely Pathogenic
Gene diagram · NM_001014431.1 · variants mapped to exon structure
AKT1 NM_001014431.1
Fetching transcript structure from UCSC…
Applied criteria · 4 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.9999e-06; MAF= 0.00040%, 1/250006 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.87185e-06; MAF= 0.00089%, 1/112716 alleles, homozygotes = 0).
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      0.0004% · 1 / 250,006
      0 hom
      European (non-Finnish)
      1 / 112,716
      0.00089%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (4 clinical laboratories). (ClinVarID = 13983)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.51. BayesDel score = 0.115701.
      Functional / OncoKB screenshot
      Functional Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV62571334, n = 894 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      4papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 6 further PMIDs triaged but not cited — see Sources & References.
      A transforming mutation in the pleckstrin homology domain of AKT1 in cancer.
      Searched
      c.49G>Ap.Glu17LysE17KGlu17Lys
      Found
      Identified AKT1 E17K as a somatic gain-of-function mutation in breast, colorectal, and ovarian cancers. E17K constitutively activates AKT1 kinase, transforms NIH-3T3 cells, and induces leukemia in a murine model.
      Variant
      ✓ Names this variant
      Applied to
      PM1 supports · met PS3 supports · met
      Why
      Seminal discovery paper for the AKT1 E17K variant. Referenced in PS3 (strong) for constitutive kinase activation; PM1 (moderate) as evidence the PH domain is a mutational hotspot; BS3 contradicted by the functional data demonstrating a deleterious gain-of-function effect.
      Molecular mechanism of an oncogenic mutation that alters membrane targeting: Glu17Lys modifies the PIP lipid specificity of the AKT1 PH domain.
      Found
      Constitutive AKT1 kinase activation demonstrated (PMID:17611497 PMID:23134728) Altered PIP lipid specificity and pathological membrane association (PMID:18954143) Growth factor-independent BaF3 survival and elevated pAKT (PMID:23134728) Anchorage-independent growth and 3D acinar disruption (PMID:23134728) In vivo oncogenesis with reduced survival in murine model (PMID:23134728) Weakened PH-KD interdomain interaction by two-hybrid assay (PMID:23134728)
      Applied to
      PS3 supports · met
      A mosaic activating mutation in AKT1 associated with the Proteus syndrome.
      Searched
      c.49G>Ap.Glu17LysE17KGlu17Lys
      Found
      Identified AKT1 c.49G>A (E17K) as a somatic mosaic activating mutation in 26 of 29 patients with Proteus syndrome. The mutation was present in affected tissues but absent from unaffected tissues and parents, with mutant allele levels ranging from <1% to ~50%.
      Variant
      ✓ Names this variant
      Applied to
      PS3 supports · met
      Why
      Landmark paper establishing E17K as the cause of Proteus syndrome. Referenced in PS2 (not assessed — somatic mosaic, not germline de novo), PS3 (strong), PS4 (not met — somatic, no case-control), PM6 (not assessed — not germline de novo), PP4 (not assessed — phenotype data), and BP5 (not met — variant is sole molecular finding).
      Location Full-text file is ICMJE disclosure forms only; no paper text available
      Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancers.
      Searched
      c.49G>Ap.Glu17LysE17KGlu17Lysglutamic acid at codon 17
      Found
      Demonstrated that the E17K substitution weakens the PH-KD autoinhibitory interaction, leading to constitutive AKT1 phosphorylation (pT308, pS473). E17K promoted growth factor-independent BaF3 survival (>50× enrichment over WT), anchorage-independent growth (~20-fold colonies), disrupted 3D acinar morphogenesis in MCF10A cells, and reduced median survival to 19–20.5 days in a murine leukemia model. The E17K mutant showed reduced sensitivity to allosteric AKT inhibitors while retaining sensitivity to ATP-competitive inhibitors.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PM1 supports · met PS3 supports · met
      Why
      Comprehensive functional characterization of the E17K variant across multiple independent assays and model systems. Referenced in PS3 (strong) for constitutive kinase activation, cell transformation, and in vivo oncogenesis; PM1 (moderate) for PH domain hotspot and structural disruption; BS3 contradicted by overwhelming evidence of a deleterious gain-of-function effect.
      This mutation results in the substitution of glutamic acid at codon 17 of AKT1 with lysine (E17K) and alters the lipid-binding specificity of AKT, leading to pathological membrane association and constitutive signaling.
      Location Abstract; Results paragraphs 1, 5–7; Figures 1A–G, 2C–D, 3A–F, 4; Discussion  ·  Context BaF3 cell viability assay (IL-3 withdrawal); NIH 3T3 signaling and anchorage-independent growth; MCF10A 3D morphogenesis; mammalian two-hybrid (VP16/Gal4 luciferase); murine leukemia model (BaF3 xenograft); recombinant full-length AKT1 biochemical kinase assays with allosteric (Inhibitor VIII, GNE-929) and ATP-competitive (GNE-692, GSK690693) inhibitors  ·  full text
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 6 PMIDs not cited in assessment
      18256540 ↗ Activating E17K mutation in the gene encoding the protein kinase AKT1 in a subset of squamous cell carcinoma of the lung. ONCOKB
      20440266 ↗ Oncogenic E17K mutation in the pleckstrin homology domain of AKT1 promotes v-Abl-mediated pre-B-cell transformation and survival of Pim-deficient cells. ONCOKB
      23741320 ↗ Cancer associated E17K mutation causes rapid conformational drift in AKT1 pleckstrin homology (PH) domain. ONCOKB
      19042984 ↗ National Academy of Clinical Biochemistry laboratory medicine practice guidelines for use of tumor markers in testicular, prostate, colorectal, breast, and ovarian cancers. CLINVAR
      22964825 ↗ Screening for ovarian cancer: U.S. Preventive Services Task Force reaffirmation recommendation statement. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR