PTEN

phosphatase and tensin homolog, the group of Phosphoinositide phosphatases|C2 tensin-type domain containing|PTEN protein phosphatases

Basic information

Region (hg38): 10:87862562-87971930

Previous symbols: [ "BZS", "MHAM" ]

Links

ENSG00000171862 ∙ NCBI:5728 ∙ OMIM:601728 ∙ HGNC:9588 ∙ Uniprot:P60484 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Cowden syndrome 1 (Definitive), mode of inheritance: AD
• Proteus syndrome (Definitive), mode of inheritance: Somatic mosaicism
• macrocephaly-autism syndrome (Definitive), mode of inheritance: AD
• leiomyosarcoma (Moderate), mode of inheritance: AR
• renal cell carcinoma (Moderate), mode of inheritance: AD
• Cowden syndrome 1 (Moderate), mode of inheritance: AD
• Cowden syndrome 1 (Strong), mode of inheritance: AD
• macrocephaly-autism syndrome (Strong), mode of inheritance: AD
• Cowden syndrome 1 (Strong), mode of inheritance: AD
• Cowden syndrome 1 (Definitive), mode of inheritance: AD
• macrocephaly-autism syndrome (Strong), mode of inheritance: AD
• Cowden syndrome 1 (Moderate), mode of inheritance: AD
• glioma susceptibility 2 (Limited), mode of inheritance: AD
• Cowden disease (Supportive), mode of inheritance: AD
• Bannayan-Riley-Ruvalcaba syndrome (Supportive), mode of inheritance: AD
• Proteus-like syndrome (Supportive), mode of inheritance: AD
• Lhermitte-Duclos disease (Supportive), mode of inheritance: AD
• macrocephaly-autism syndrome (Supportive), mode of inheritance: AD
• activated PI3K-delta syndrome (Supportive), mode of inheritance: AD
• Proteus syndrome (Definitive), mode of inheritance: AD
• PTEN hamartoma tumor syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
PTEN hamartoma tumor syndrome; Cowden syndrome 1; Bannayan-Riley-Ruvalcaba syndrome; Lhermitte-Duclos syndrome; Glioma susceptibility 2; Meningioma, familial; Endometrial cancer	AD	Oncologic	Surveillance is indicated to screen for the presence of neoplasms (including regular thyroid ultrasound, dermatologic examinations, breast screening including mammogram and/or MRI, transvaginal ultrasound and/or endometrial biopsy, colonoscopy, renal imaging, and other screening as specifically indicated by family or personal medical history), which may allow early diagnosis and treatment, which may be beneficial related to morbidity and mortality	Craniofacial; Dermatologic; Neurologic; Oncologic	5345120; 5091590; 957004; 7449178; 7079022; 6881215; 6507473; 3707175; 3698331; 3340479; 1336932; 1350505; 8207516; 9140396; 9286463; 9399897; 9241266; 9259288; 9545417; 9662392; 9832032; 9832031; 9425889; 9445133; 9856571; 10353779; 10400993; 10234502; 11238682; 11748304; 12085208; 11875759; 12938083; 14518069; 12833416; 14566704; 15805158; 16704655; 16752378; 17286265; 17526800; 17526801; 17847000; 18781191; 21659347; 21633361; 20301661; 21956414; 22595938; 22970944; 23335809; 23344409
Evidence for association with some cancerous processes is unclear,and the division into many separate disorders is likely specious

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTEN gene.

• PTEN hamartoma tumor syndrome (1633 variants)
• Hereditary cancer-predisposing syndrome (1382 variants)
• not provided (859 variants)
• Cowden syndrome 1 (548 variants)
• not specified (300 variants)
• Macrocephaly-autism syndrome (55 variants)
• Glioma susceptibility 2 (50 variants)
• Cowden syndrome (29 variants)
• Breast and/or ovarian cancer (28 variants)
• PTEN-related condition (22 variants)
• Prostate cancer, hereditary, 1 (21 variants)
• Inborn genetic diseases (18 variants)
• Neoplasm of ovary (16 variants)
• 7 conditions (11 variants)
• Malignant tumor of breast (11 variants)
• Neoplasm of the large intestine (8 variants)
• Familial meningioma (8 variants)
• Breast neoplasm (8 variants)
• Gastric cancer (7 variants)
• Glioblastoma (6 variants)
• See cases (5 variants)
• Hereditary breast ovarian cancer syndrome (5 variants)
• Uterine carcinosarcoma (5 variants)
• PTEN-related disorder (5 variants)
• Macrocephaly-autism syndrome;Familial meningioma;Malignant tumor of prostate;Cowden syndrome 1;Glioma susceptibility 2 (5 variants)
• Gastric adenocarcinoma (5 variants)
• Prostate adenocarcinoma (5 variants)
• Malignant neoplasm of body of uterus (5 variants)
• Neoplasm of uterine cervix (5 variants)
• Familial cancer of breast (4 variants)
• Endometrial carcinoma (4 variants)
• Cowden syndrome 1;Macrocephaly-autism syndrome (4 variants)
• Malignant melanoma of skin (4 variants)
• Papillary renal cell carcinoma type 1 (4 variants)
• Neoplasm of brain (4 variants)
• Small cell lung carcinoma (4 variants)
• Macrocephaly-autism syndrome;Cowden syndrome 1 (4 variants)
• Squamous cell carcinoma of the head and neck (4 variants)
• Squamous cell lung carcinoma (4 variants)
• Intellectual disability (3 variants)
• PTEN hamartoma tumor syndromes (3 variants)
• Malignant tumor of urinary bladder (3 variants)
• Carcinoma of colon (3 variants)
• Melanoma (3 variants)
• Malignant lymphoma, large B-cell, diffuse (3 variants)
• Breast carcinoma (2 variants)
• Lhermitte-Duclos disease (2 variants)
• - (2 variants)
• Malignant tumor of prostate;Cowden syndrome 1;Macrocephaly-autism syndrome;Familial meningioma;Glioma susceptibility 2 (2 variants)
• Glioma susceptibility 2;Malignant tumor of prostate;Familial meningioma;Cowden syndrome 1;Macrocephaly-autism syndrome (2 variants)
• Global developmental delay (2 variants)
• Familial meningioma;Glioma susceptibility 2;Cowden syndrome 1;Macrocephaly-autism syndrome;Malignant tumor of prostate (2 variants)
• Hemimegalencephaly (2 variants)
• Bannayan-Riley-Ruvalcaba syndrome (2 variants)
• Prostate cancer, somatic (2 variants)
• Glioma susceptibility 2;Macrocephaly-autism syndrome;Familial meningioma;Cowden syndrome 1;Malignant tumor of prostate (2 variants)
• Seizure (2 variants)
• Neoplasm (2 variants)
• Abnormal cardiovascular system morphology (2 variants)
• Hereditary cancer (2 variants)
• Neurodevelopmental delay (2 variants)
• Proteus-like syndrome (2 variants)
• Macrocephaly-autism syndrome;Familial meningioma;Malignant tumor of prostate;Glioma susceptibility 2;Cowden syndrome 1 (2 variants)
• Autism spectrum disorder (2 variants)
• Cowden syndrome 4 (2 variants)
• Macrocephaly-autism syndrome;Familial meningioma;Glioma susceptibility 2;Cowden syndrome 1;Malignant tumor of prostate (2 variants)
• Glioma susceptibility 2;Cowden syndrome 1;Macrocephaly-autism syndrome;Familial meningioma;Malignant tumor of prostate (1 variants)
• Thyroid cancer, nonmedullary, 2 (1 variants)
• Transitional cell carcinoma of the bladder (1 variants)
• Familial ovarian cancer (1 variants)
• Ovarian cancer (1 variants)
• Acute megakaryoblastic leukemia;Mediastinal germ cell tumor (1 variants)
• Macrocephaly-autism syndrome;Glioma susceptibility 2;Familial meningioma;Malignant tumor of prostate;Cowden syndrome 1 (1 variants)
• Vater association with macrocephaly and ventriculomegaly (1 variants)
• Uterine corpus cancer (1 variants)
• PTEN hamartoma tumor syndrome;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome (1 variants)
• Macrocephaly (1 variants)
• Bannayan-Riley-Ruvalcaba syndrome;Cowden syndrome;PTEN hamartoma tumor syndrome;Macrocephaly-autism syndrome (1 variants)
• Malignant tumor of prostate;Macrocephaly-autism syndrome;Familial meningioma;Cowden syndrome 1;Glioma susceptibility 2 (1 variants)
• Abnormality of the nervous system (1 variants)
• Papillary tumor of the pineal region (1 variants)
• 8 conditions (1 variants)
• Malignant tumor of prostate;Cowden syndrome 1;Glioma susceptibility 2;Macrocephaly-autism syndrome;Familial meningioma (1 variants)
• developmental delay with seizures (1 variants)
• Macrocephaly-autism syndrome;Cowden syndrome 1;Glioma susceptibility 2;Malignant tumor of prostate;Familial meningioma (1 variants)
• Hemangioma (1 variants)
• PTEN hamartoma tumor syndrome;Bannayan-Riley-Ruvalcaba syndrome;Cowden syndrome (1 variants)
• Malignant tumor of prostate;Macrocephaly-autism syndrome;Cowden syndrome 1;Glioma susceptibility 2;Familial meningioma (1 variants)
• Meningioma (1 variants)
• Cowden syndrome 1;Malignant tumor of prostate;Familial meningioma;Glioma susceptibility 2;Macrocephaly-autism syndrome (1 variants)
• Lung adenocarcinoma (1 variants)
• 11 conditions (1 variants)
• Bannayan-Riley-Ruvalcaba syndrome;Macrocephaly-autism syndrome;Cowden syndrome 1 (1 variants)
• Atypical endometrial hyperplasia (1 variants)
• Squamous cell carcinoma (1 variants)
• Loss of consciousness;Macrocephaly;Large for gestational age (1 variants)
• Malignant tumor of prostate;Cowden syndrome 1;Glioma susceptibility 2;Familial meningioma;Macrocephaly-autism syndrome (1 variants)
• PTEN hamartoma tumor syndrome;Macrocephaly-autism syndrome;Cowden syndrome;Proteus-like syndrome;Bannayan-Riley-Ruvalcaba syndrome (1 variants)
• Rhabdomyosarcoma (1 variants)
• Myeloproliferative neoplasm, unclassifiable (1 variants)
• Familial meningioma;Glioma susceptibility 2;Malignant tumor of prostate;Cowden syndrome 1;Macrocephaly-autism syndrome (1 variants)
• Breast cancer, susceptibility to (1 variants)
• Malignant tumor of prostate;Glioma susceptibility 2;Cowden syndrome 1;Macrocephaly-autism syndrome;Familial meningioma (1 variants)
• Cowden syndrome;Macrocephaly-autism syndrome (1 variants)
• Glioma susceptibility 2;Familial meningioma;Malignant tumor of prostate;Cowden syndrome 1;Macrocephaly-autism syndrome (1 variants)
• Epileptic encephalopathy (1 variants)
• Non-small cell lung carcinoma (1 variants)
• Endometrial carcinoma;Endometrial hyperplasia without atypia;Atypical endometrial hyperplasia (1 variants)
• Cowden syndrome 1;Macrocephaly-autism syndrome;VACTERL with hydrocephalus (1 variants)
• Macrocephaly;Autistic behavior;Neurodevelopmental delay (1 variants)
• Autism;Bannayan-Riley-Ruvalcaba syndrome;Macrocephaly;PTEN hamartoma tumor syndrome (1 variants)
• Malignant tumor of floor of mouth (1 variants)
• Familial meningioma;Malignant tumor of prostate;Glioma susceptibility 2;Macrocephaly-autism syndrome;Cowden syndrome 1 (1 variants)
• Malignant tumor of prostate;Macrocephaly-autism syndrome;Familial meningioma;Glioma susceptibility 2;Cowden syndrome 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTEN gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			9	277	1	287
missense	60	137	638	5		840
nonsense	141	15	2			158
start loss	3	3				6
frameshift	457	49	3			509
inframe indel	4	10	25			39
splice donor/acceptor (+/-2bp)	57	66	5	5	1	134
splice region	6	9	53	58	3	129
non coding		4	572	188	56	820
Total	722	284	1254	475	58

Highest pathogenic variant AF is 0.00000667

Variants in PTEN

This is a list of pathogenic ClinVar variants found in the PTEN region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-87863128-G-A			Uncertain significance (Jul 09, 2014)
10-87863131-T-A			Uncertain significance (Aug 30, 2019)
10-87863134-G-A			Uncertain significance (Dec 01, 2015)
10-87863139-A-G		not specified	Uncertain significance (Mar 30, 2015)
10-87863145-C-A			Uncertain significance (Dec 31, 2014)
10-87863148-C-A			Uncertain significance (Jun 21, 2017)
10-87863158-T-C		PTEN hamartoma tumor syndrome	Benign (Jun 02, 2017)
10-87863159-C-T			Uncertain significance (May 12, 2015)
10-87863162-C-T			Uncertain significance (Aug 16, 2016)
10-87863164-T-A		not specified	Uncertain significance (Apr 28, 2017)
10-87863168-T-G			Uncertain significance (Mar 26, 2016)
10-87863171-T-A			Uncertain significance (Oct 11, 2017)
10-87863174-G-T			Uncertain significance (Oct 09, 2017)
10-87863176-C-T			Uncertain significance (Sep 26, 2016)
10-87863179-C-T		not specified	Uncertain significance (Oct 13, 2016)
10-87863181-A-AC		Hereditary cancer-predisposing syndrome	Uncertain significance (Feb 22, 2019)
10-87863182-C-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Sep 07, 2017)
10-87863182-C-T		Hereditary cancer-predisposing syndrome	Uncertain significance (Mar 17, 2018)
10-87863183-C-T		Hereditary cancer-predisposing syndrome	Uncertain significance (Jul 20, 2017)
10-87863184-C-T		Hereditary cancer-predisposing syndrome	Uncertain significance (May 09, 2018)
10-87863185-C-T		Hereditary cancer-predisposing syndrome	Uncertain significance (Jun 07, 2018)
10-87863187-G-GC		Hereditary cancer-predisposing syndrome	Uncertain significance (Nov 01, 2018)
10-87863188-C-T			Uncertain significance (May 02, 2016)
10-87863190-C-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Apr 07, 2016)
10-87863194-A-G		Hereditary cancer-predisposing syndrome	Uncertain significance (May 02, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTEN	protein_coding	protein_coding	ENST00000371953	9	108818

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.257	0.743	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.49	72	216	0.333	0.0000106	2705
Missense in Polyphen		5	50.786	0.098453		669
Synonymous	-0.123	74	72.7	1.02	0.00000360	691
Loss of Function	3.20	5	20.8	0.241	0.00000115	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tumor suppressor. Acts as a dual-specificity protein phosphatase, dephosphorylating tyrosine-, serine- and threonine- phosphorylated proteins. Also acts as a lipid phosphatase, removing the phosphate in the D3 position of the inositol ring from phosphatidylinositol 3,4,5-trisphosphate, phosphatidylinositol 3,4-diphosphate, phosphatidylinositol 3- phosphate and inositol 1,3,4,5-tetrakisphosphate with order of substrate preference in vitro PtdIns(3,4,5)P3 > PtdIns(3,4)P2 > PtdIns3P > Ins(1,3,4,5)P4 (PubMed:26504226). The lipid phosphatase activity is critical for its tumor suppressor function. Antagonizes the PI3K-AKT/PKB signaling pathway by dephosphorylating phosphoinositides and thereby modulating cell cycle progression and cell survival. The unphosphorylated form cooperates with AIP1 to suppress AKT1 activation. Dephosphorylates tyrosine-phosphorylated focal adhesion kinase and inhibits cell migration and integrin-mediated cell spreading and focal adhesion formation. Plays a role as a 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. May be a negative regulator of insulin signaling and glucose metabolism in adipose tissue. The nuclear monoubiquitinated form possesses greater apoptotic potential, whereas the cytoplasmic nonubiquitinated form induces less tumor suppressive ability. In motile cells, suppresses the formation of lateral pseudopods and thereby promotes cell polarization and directed movement. {ECO:0000269|PubMed:26504226}.
• Disease: DISEASE: Cowden syndrome 1 (CWS1) [MIM:158350]: An autosomal dominant 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:10051160, ECO:0000269|PubMed:10234502, ECO:0000269|PubMed:10400993, ECO:0000269|PubMed:10866302, ECO:0000269|PubMed:11230179, ECO:0000269|PubMed:11494117, ECO:0000269|PubMed:15355975, ECO:0000269|PubMed:18716620, ECO:0000269|PubMed:9140396, ECO:0000269|PubMed:9241266, ECO:0000269|PubMed:9259288, ECO:0000269|PubMed:9345101, ECO:0000269|PubMed:9399897, ECO:0000269|PubMed:9425889, ECO:0000269|PubMed:9467011, ECO:0000269|PubMed:9600246, ECO:0000269|PubMed:9735393, ECO:0000269|PubMed:9797362, ECO:0000269|PubMed:9811831, ECO:0000269|PubMed:9832031, ECO:0000269|PubMed:9915974}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Lhermitte-Duclos disease (LDD) [MIM:158350]: A rare disease characterized by the occurrence of a slowly enlarging mass within the cerebellar cortex corresponding histologically to a cerebellar hamartoma. It manifests, most commonly in the third and fourth decades of life, with increased intracranial pressure, headache, nausea, cerebellar dysfunction, occlusive hydrocephalus, ataxia, visual disturbances and other cranial nerve palsies. Various associated abnormalities may be present such as megalencephaly, microgyria, hydromyelia, polydactyly, partial gigantism, macroglossia. LDD is part of the PTEN hamartoma tumor syndromes spectrum that also includes Cowden syndrome. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. {ECO:0000269|PubMed:11801303}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Endometrial cancer (ENDMC) [MIM:608089]: A malignancy of endometrium, the mucous lining of the uterus. Most endometrial cancers are adenocarcinomas, cancers that begin in cells that make and release mucus and other fluids. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Note=PTEN mutations are found in a subset of patients with Proteus syndrome, a genetically heterogeneous condition. The molecular diagnosis of PTEN mutation positive cases classifies Proteus syndrome patients as part of the PTEN hamartoma syndrome spectrum. As such, patients surviving the early years of Proteus syndrome are likely at a greater risk of developing malignancies.; DISEASE: Glioma 2 (GLM2) [MIM:613028]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. {ECO:0000269|PubMed:12085208}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Prostate cancer (PC) [MIM:176807]: A malignancy originating in tissues of the prostate. Most prostate cancers are adenocarcinomas that develop in the acini of the prostatic ducts. Other rare histopathologic types of prostate cancer that occur in approximately 5% of patients include small cell carcinoma, mucinous carcinoma, prostatic ductal carcinoma, transitional cell carcinoma, squamous cell carcinoma, basal cell carcinoma, adenoid cystic carcinoma (basaloid), signet-ring cell carcinoma and neuroendocrine carcinoma. {ECO:0000269|PubMed:26504226, ECO:0000269|PubMed:9072974}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Macrocephaly/autism syndrome (MCEPHAS) [MIM:605309]: Patients have autism spectrum disorders and macrocephaly, with head circumferences ranging from +2.5 to +8 SD for age and sex (average head circumference +4.0 SD). {ECO:0000269|PubMed:15805158, ECO:0000269|PubMed:23160955, ECO:0000269|PubMed:26637798}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A microdeletion of chromosome 10q23 involving BMPR1A and PTEN is a cause of chromosome 10q23 deletion syndrome, which shows overlapping features of the following three disorders: Bannayan-Zonana syndrome, Cowden disease and juvenile polyposis syndrome.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Focal adhesion - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Inositol phosphate metabolism - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);Melanoma - Homo sapiens (human);Insulin resistance - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Breast cancer - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Phosphatidylinositol Phosphate Metabolism;Joubert syndrome;IGF-Ncore;EGF-Ncore;Androgen receptor signaling pathway;Leptin signaling pathway;Regulation of Microtubule Cytoskeleton;Signaling Pathways in Glioblastoma;Androgen Receptor Network in Prostate Cancer;T-Cell Receptor and Co-stimulatory Signaling;PIP3 activates AKT signaling;Focal Adhesion;Signaling of Hepatocyte Growth Factor Receptor;Copper homeostasis;TP53 Regulates Metabolic Genes;Pathways Affected in Adenoid Cystic Carcinoma;Hematopoietic Stem Cell Gene Regulation by GABP alpha-beta Complex;PI3K-AKT-mTOR signaling pathway and therapeutic opportunities;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;miRNA regulation of p53 pathway in prostate cancer;Pathways in clear cell renal cell carcinoma;PTEN Regulation;Endometrial cancer;PI3K-Akt Signaling Pathway;Somatroph axis (GH) and its relationship to dietary restriction and aging;EGF-EGFR Signaling Pathway;Insulin Signaling;Senescence and Autophagy in Cancer;DNA Damage Response (only ATM dependent);Signal Transduction;Gene expression (Transcription);D-<i>myo</i>-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;mtor signaling pathway;regulation of eif-4e and p70s6 kinase;pten dependent cell cycle arrest and apoptosis;Regulation of PTEN localization;skeletal muscle hypertrophy is regulated via akt-mtor pathway;ctcf: first multivalent nuclear factor;Generic Transcription Pathway;Regulation of PTEN stability and activity;Metabolism of lipids;Downstream TCR signaling;TCR signaling;Post-translational protein modification;Metabolism of proteins;Inositol phosphate metabolism;RNA Polymerase II Transcription;3-phosphoinositide degradation;Immune System;Metabolism;Adaptive Immune System;superpathway of inositol phosphate compounds;insulin Mam;AndrogenReceptor;TP53 Regulates Metabolic Genes;EGFR1;Synthesis of IP3 and IP4 in the cytosol;CXCR4-mediated signaling events;Regulation of PTEN gene transcription;Ub-specific processing proteases;BCR signaling pathway;PTEN Regulation;PIP3 activates AKT signaling;Inositol phosphate metabolism;Ovarian tumor domain proteases;Deubiquitination;Synthesis of PIPs at the plasma membrane;Class I PI3K signaling events;Transcriptional Regulation by TP53;Negative regulation of the PI3K/AKT network;Direct p53 effectors;PI Metabolism;Phospholipid metabolism;Intracellular signaling by second messengers;AP-1 transcription factor network;Signaling events mediated by Stem cell factor receptor (c-Kit);PDGFR-beta signaling pathway;TCR signaling in na&#xef;ve CD4+ T cells;RhoA signaling pathway;insulin (Consensus)

Recessive Scores

• pRec: 0.946

Intolerance Scores

• loftool: 0.0929
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.210
• hipred: Y
• hipred_score: 0.783
• ghis: 0.672

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Low	Medium

Mouse Genome Informatics

• Gene name: Pten
• Phenotype: muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; taste/olfaction phenotype; pigmentation phenotype; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; embryo phenotype; neoplasm

Zebrafish Information Network

• Gene name: ptenb
• Affected structure: myeloid lineage restricted progenitor cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;angiogenesis;negative regulation of protein phosphorylation;regulation of B cell apoptotic process;transcription initiation from RNA polymerase II promoter;protein dephosphorylation;phosphatidylinositol biosynthetic process;apoptotic process;neuron-neuron synaptic transmission;synapse assembly;central nervous system development;heart development;aging;learning or memory;memory;locomotory behavior;cell population proliferation;positive regulation of cell population proliferation;negative regulation of cell population proliferation;response to glucose;response to zinc ion;positive regulation of gene expression;positive regulation of cardiac muscle cell apoptotic process;negative regulation of epithelial to mesenchymal transition;regulation of neuron projection development;negative regulation of phosphatidylinositol 3-kinase signaling;response to activity;cell migration;protein deubiquitination;dentate gyrus development;central nervous system neuron axonogenesis;negative regulation of cell migration;adult behavior;negative regulation of myelination;regulation of protein stability;regulation of synaptic transmission, GABAergic;central nervous system myelin maintenance;response to estradiol;regulation of cellular component size;cellular response to insulin stimulus;regulation of myeloid cell apoptotic process;response to ATP;multicellular organismal response to stress;social behavior;peptidyl-tyrosine dephosphorylation;maternal behavior;negative regulation of apoptotic process;protein kinase B signaling;endothelial cell migration;inositol phosphate metabolic process;cellular response to leptin stimulus;locomotor rhythm;positive regulation of neuron differentiation;negative regulation of cell size;negative regulation of organ growth;response to arsenic-containing substance;inositol phosphate dephosphorylation;phosphatidylinositol dephosphorylation;platelet-derived growth factor receptor signaling pathway;negative regulation of axon regeneration;cardiac muscle tissue development;forebrain morphogenesis;brain morphogenesis;negative regulation of epithelial cell proliferation;negative regulation of phagocytosis;negative regulation of axonogenesis;protein stabilization;positive regulation of DNA-binding transcription factor activity;negative regulation of keratinocyte migration;negative regulation of focal adhesion assembly;negative regulation of protein kinase B signaling;rhythmic synaptic transmission;negative regulation of cardiac muscle cell proliferation;canonical Wnt signaling pathway;synapse maturation;prepulse inhibition;male mating behavior;long-term synaptic potentiation;long-term synaptic depression;prostate gland growth;dendritic spine morphogenesis;negative regulation of dendritic spine morphogenesis;negative regulation of ERK1 and ERK2 cascade;positive regulation of ERK1 and ERK2 cascade;cellular response to electrical stimulus;cellular response to ethanol;cellular response to hypoxia;negative regulation of ribosome biogenesis;negative regulation of cell aging;negative regulation of excitatory postsynaptic potential;presynaptic membrane assembly;postsynaptic density assembly;negative regulation of potassium ion transmembrane transporter activity;negative regulation of wound healing, spreading of epidermal cells;positive regulation of TRAIL-activated apoptotic signaling pathway;positive regulation of ubiquitin protein ligase activity;negative regulation of vascular smooth muscle cell proliferation;cellular response to nerve growth factor stimulus;cellular response to insulin-like growth factor stimulus;positive regulation of ubiquitin-dependent protein catabolic process;negative regulation of G1/S transition of mitotic cell cycle;negative regulation of signaling receptor activity;positive regulation of excitatory postsynaptic potential;negative regulation of synaptic vesicle clustering
• Cellular component: extracellular region;nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol;plasma membrane;cytoplasmic side of plasma membrane;apical plasma membrane;PML body;myelin sheath adaxonal region;cell projection;neuron projection;dendritic spine;Schmidt-Lanterman incisure;postsynaptic membrane;postsynaptic cytosol
• Molecular function: phosphatidylinositol-3-phosphatase activity;phosphoprotein phosphatase activity;protein serine/threonine phosphatase activity;protein tyrosine phosphatase activity;platelet-derived growth factor receptor binding;protein binding;protein tyrosine/serine/threonine phosphatase activity;lipid binding;anaphase-promoting complex binding;phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity;enzyme binding;PDZ domain binding;ionotropic glutamate receptor binding;identical protein binding;inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity;phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity;ubiquitin-specific protease binding;protein tyrosine kinase binding