AKT1

protein-coding

AKT serine/threonine kinase 1, the group of Pleckstrin homology domain containing|AKT kinases

Gene summary

This gene encodes one of the three members of the human AKT serine-threonine protein kinase family which are often referred to as protein kinase B alpha, beta, and gamma. These highly similar AKT proteins all have an N-terminal pleckstrin homology domain, a serine/threonine-specific kinase domain and a C-terminal regulatory domain. These proteins are phosphorylated by phosphoinositide 3-kinase (PI3K). AKT/PI3K forms a key component of many signalling pathways that involve the binding of membrane-bound ligands such as receptor tyrosine kinases, G-protein coupled receptors, and integrin-linked kinase. These AKT proteins therefore regulate a wide variety of cellular functions including cell proliferation, survival, metabolism, and angiogenesis in both normal and malignant cells. AKT proteins are recruited to the cell membrane by phosphatidylinositol 3,4,5-trisphosphate (PIP3) after phosphorylation of phosphatidylinositol 4,5-bisphosphate (PIP2) by PI3K. Subsequent phosphorylation of both threonine residue 308 and serine residue 473 is required for full activation of the AKT1 protein encoded by this gene. Phosphorylation of additional residues also occurs, for example, in response to insulin growth factor-1 and epidermal growth factor. Protein phosphatases act as negative regulators of AKT proteins by dephosphorylating AKT or PIP3. The PI3K/AKT signalling pathway is crucial for tumor cell survival. Survival factors can suppress apoptosis in a transcription-independent manner by activating AKT1 which then phosphorylates and inactivates components of the apoptotic machinery. AKT proteins also participate in the mammalian target of rapamycin (mTOR) signalling pathway which controls the assembly of the eukaryotic translation initiation factor 4F (eIF4E) complex and this pathway, in addition to responding to extracellular signals from growth factors and cytokines, is disregulated in many cancers. Mutations in this gene are associated with multiple types of cancer and excessive tissue growth including Proteus syndrome and Cowden syndrome 6, and breast, colorectal, and ovarian cancers. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2020]

MANE transcript

NM_001382430.1

Inheritance

AD

ClinVar variants

P:6U:373B:363

Top phenotype

Cowden syndrome 6; Proteus syndrome

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr14:104,769,349-104,795,759

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~26.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Cowden syndrome 6LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014048

Submitter: PanelApp Australia

Proteus syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008318

Submitter: Labcorp Genetics (formerly Invitae)

Cowden syndrome 6LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0014048

Submitter: Labcorp Genetics (formerly Invitae)

Proteus syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008318

Submitter: PanelApp Australia

Cowden diseaseSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016063

Submitter: Orphanet

Proteus syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008318

Submitter: G2P

Cowden syndrome 6LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014048

Submitter: ClinGen

AKT1 was first reported in relation to autosomal dominant Cowden syndrome in 2013 (Orloff et al., PMID: 23246288). AKT1 has been noted to be associated with Cowden syndrome and Proteus syndrome. Cowden syndrome is characterized by macrocephaly, trichilemmomas, and papillomatous papules, and benign and malignant tumors of the thyroid, breast, kidney and endometrium. Most people with Cowden syndrome carry a variant in the PTEN gene. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in the molecular mechanism and inheritance pattern of AKT1-associated Cowden syndrome and Proteus syndrome. Therefore, the disease entities have been split into separate curations. The Proteus syndrome assertion will be curated separately by the ClinGen Brain Malformations GCEP. Two missense variants in AKT1 that have been reported in two probands in one publication (PMID: 23246288) are included in this curation. This gene-disease relationship is also supported by in vitro functional assays demonstrating the effects of PTEN signaling on AKT1 activity in Cowden syndrome patients (PMIDs: 21194675, 22962422). In summary, there is limited evidence supporting the relationship between AKT1 and autosomal dominant Cowden syndrome. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen Childhood, Adolescent, and Young Adult Cancer Predisposition GCEP on November 12, 2024 (SOP Version 11).

Clinical Genomic Database (CGD)

Cowden syndrome 6; Proteus syndromeAD

Manifestation: Cardiovascular; Dermatologic; Craniofacial; Hematologic; Musculoskeletal; Neurologic; Oncologic; Pulmonary

Intervention: Cardiovascular; Hematologic; Oncologic; Pulmonary

Rationale: In Cowden syndrome, individuals have been described with manifestations including breast, renal, and thyroid cancer, and surveillance may allow early detection and management of neoplasms; In Proteus syndrome, individuals may be at risk for a variety of manifestations, some of which may be occult; Surveillance for hematologic/vascular manifestations (eg, deep vein thrombosis and pulmonary embolism) can allow early detection and treatment; Surveillance for pulmonary disease (as patients are at risk for restrictive lung disease) can allow early detection and treatment; As individuals may be at increased risk for neoplastic processes, routine monitoring by history and physical examination (without separate imaging) may allow early detection of neoplasms

Comments: In Proteus syndrome, variants may be found on peripheral blood testing, but affected tissue must typically be tested for molecular diagnosis

Refs: 21793738; 22876373; 23246288Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AKT1 variants in ClinVar

17 Conditions Cataloged
Inborn genetic diseasesTotal: 566
Cowden syndrome 6Total: 491
not providedTotal: 88
Proteus syndromeTotal: 18
AKT1-related disorderTotal: 18
Familial cancer of breastTotal: 17
not specifiedTotal: 16
Colorectal cancerTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001382430.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
356
clinvar
3
clinvar
360
missense
4
clinvar
2
clinvar
362
clinvar
4
clinvar
372
nonsense
1
clinvar
1
start loss
0
frameshift
4
clinvar
4
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total423733603742

Highest pathogenic variant AF is 0.0000018594941

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 196 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001382430.1RefSeqNP_001369359.113MANE Select
ENST00000649815.2EnsemblENSP00000497822.113MANE Select
NM_001014431.2RefSeqNP_001014431.113Standard
NM_001014432.2RefSeqNP_001014432.113Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
akt1Danio rerio

Structure: neuron

Quality: apoptotic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • PI3K-Akt signaling pathway - Homo sapiens (human)
  • Non-small cell lung cancer - Homo sapiens (human)
  • Platelet activation - Homo sapiens (human)
  • Chronic myeloid leukemia - Homo sapiens (human)
  • Gastric cancer - Homo sapiens (human)

Biological Process

  • obsolete protein import into nucleus, translocation
  • osteoblast differentiation
  • maternal placenta development
  • positive regulation of protein phosphorylation
  • positive regulation of endothelial cell proliferation

Molecular Function

  • protein kinase activity
  • protein serine/threonine kinase activity
  • protein serine/threonine/tyrosine kinase activity
  • protein kinase C binding
  • protein binding

Cellular Component

  • nucleus
  • nucleoplasm
  • cytoplasm
  • mitochondrion
  • spindle

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000554581
Coding exons
13
Length
26403
Individuals with no LoFs
125732
Homozygous LoFs
0
Heterozygous LoFs
8
Defined
125740
p
0.0000318
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.481523300.4610.00002233175
Missense (PolyPhen)34128.930.263711379
Synonymous-0.4241381321.050.00000974882
Loss of Function4.31429.10.1380.00000150311

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.000140.00014rare
European (Non-Finnish)0.0000350.000035rare
South Asian00.0absent
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: AKT1 is one of 3 closely related serine/threonine- protein kinases (AKT1, AKT2 and AKT3) called the AKT kinase, and which regulate many processes including metabolism, proliferation, cell survival, growth and angiogenesis. This is mediated through serine and/or threonine phosphorylation of a range of downstream substrates. Over 100 substrate candidates have been reported so far, but for most of them, no isoform specificity has been reported. AKT is responsible of the regulation of glucose uptake by mediating insulin-induced translocation of the SLC2A4/GLUT4 glucose transporter to the cell surface. Phosphorylation of PTPN1 at 'Ser-50' negatively modulates its phosphatase activity preventing dephosphorylation of the insulin receptor and the attenuation of insulin signaling. Phosphorylation of TBC1D4 triggers the binding of this effector to inhibitory 14-3-3 proteins, which is required for insulin-stimulated glucose transport. AKT regulates also the storage of glucose in the form of glycogen by phosphorylating GSK3A at 'Ser-21' and GSK3B at 'Ser-9', resulting in inhibition of its kinase activity. Phosphorylation of GSK3 isoforms by AKT is also thought to be one mechanism by which cell proliferation is driven. AKT regulates also cell survival via the phosphorylation of MAP3K5 (apoptosis signal-related kinase). Phosphorylation of 'Ser-83' decreases MAP3K5 kinase activity stimulated by oxidative stress and thereby prevents apoptosis. AKT mediates insulin-stimulated protein synthesis by phosphorylating TSC2 at 'Ser-939' and 'Thr-1462', thereby activating mTORC1 signaling and leading to both phosphorylation of 4E-BP1 and in activation of RPS6KB1. AKT is involved in the phosphorylation of members of the FOXO factors (Forkhead family of transcription factors), leading to binding of 14-3-3 proteins and cytoplasmic localization. In particular, FOXO1 is phosphorylated at 'Thr-24', 'Ser-256' and 'Ser-319'. FOXO3 and FOXO4 are phosphorylated on equivalent sites. AKT has an important role in the regulation of NF-kappa-B-dependent gene transcription and positively regulates the activity of CREB1 (cyclic AMP (cAMP)- response element binding protein). The phosphorylation of CREB1 induces the binding of accessory proteins that are necessary for the transcription of pro-survival genes such as BCL2 and MCL1. AKT phosphorylates 'Ser-454' on ATP citrate lyase (ACLY), thereby potentially regulating ACLY activity and fatty acid synthesis. Activates the 3B isoform of cyclic nucleotide phosphodiesterase (PDE3B) via phosphorylation of 'Ser-273', resulting in reduced cyclic AMP levels and inhibition of lipolysis. Phosphorylates PIKFYVE on 'Ser-318', which results in increased PI(3)P-5 activity. The Rho GTPase-activating protein DLC1 is another substrate and its phosphorylation is implicated in the regulation cell proliferation and cell growth. AKT plays a role as key modulator of the AKT-mTOR signaling pathway controlling the tempo of the process of newborn neurons integration during adult neurogenesis, including correct neuron positioning, dendritic development and synapse formation. Signals downstream of phosphatidylinositol 3-kinase (PI(3)K) to mediate the effects of various growth factors such as platelet-derived growth factor (PDGF), epidermal growth factor (EGF), insulin and insulin-like growth factor I (IGF-I). AKT mediates the antiapoptotic effects of IGF-I. Essential for the SPATA13-mediated regulation of cell migration and adhesion assembly and disassembly. May be involved in the regulation of the placental development. Phosphorylates STK4/MST1 at 'Thr-120' and 'Thr-387' leading to inhibition of its: kinase activity, nuclear translocation, autophosphorylation and ability to phosphorylate FOXO3. Phosphorylates STK3/MST2 at 'Thr- 117' and 'Thr-384' leading to inhibition of its: cleavage, kinase activity, autophosphorylation at Thr-180, binding to RASSF1 and nuclear translocation. Phosphorylates SRPK2 and enhances its kinase activity towards SRSF2 and ACIN1 and promotes its nuclear translocation. Phosphorylates RAF1 at 'Ser-259' and negatively regulates its activity. Phosphorylation of BAD stimulates its pro- apoptotic activity. Phosphorylates KAT6A at 'Thr-369' and this phosphorylation inhibits the interaction of KAT6A with PML and negatively regulates its acetylation activity towards p53/TP53.;
Disease
DISEASE: Breast cancer (BC) [MIM:114480]: A common malignancy originating from breast epithelial tissue. Breast neoplasms can be distinguished by their histologic pattern. Invasive ductal carcinoma is by far the most common type. Breast cancer is etiologically and genetically heterogeneous. Important genetic factors have been indicated by familial occurrence and bilateral involvement. Mutations at more than one locus can be involved in different families or even in the same case. {ECO:0000269|PubMed:17611497}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Colorectal cancer (CRC) [MIM:114500]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Note=Genetic variations in AKT1 may play a role in susceptibility to ovarian cancer.; DISEASE: Proteus syndrome (PROTEUSS) [MIM:176920]: A highly variable, severe disorder of asymmetric and disproportionate overgrowth of body parts, connective tissue nevi, epidermal nevi, dysregulated adipose tissue, and vascular malformations. Many features of Proteus syndrome overlap with other overgrowth syndromes. {ECO:0000269|PubMed:18954143, ECO:0000269|PubMed:21793738}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cowden syndrome 6 (CWS6) [MIM:615109]: A form of Cowden syndrome, a hamartomatous polyposis syndrome with age-related penetrance. Cowden syndrome is characterized by hamartomatous lesions affecting derivatives of ectodermal, mesodermal and endodermal layers, macrocephaly, facial trichilemmomas (benign tumors of the hair follicle infundibulum), acral keratoses, papillomatous papules, and elevated risk for development of several types of malignancy, particularly breast carcinoma in women and thyroid carcinoma in both men and women. Colon cancer and renal cell carcinoma have also been reported. Hamartomas can be found in virtually every organ, but most commonly in the skin, gastrointestinal tract, breast and thyroid. {ECO:0000269|PubMed:23246288}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
1.00

Intolerance Scores

LoFtool
0.357
RVIS EVS
-1
RVIS percentile EVS
8.32

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.994

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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