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encyclopedia of Rare Disease Annotation for Precision Medicine



   pten hamartoma tumor syndrome
  

Disease ID 1793
Disease pten hamartoma tumor syndrome
Definition
The primary findings in PHTS include increased risk for certain types of cancer, benign tumors and tumor-like malformations (hamartomas), and neurodevelopmental disorders. The symptoms of PHTS vary greatly from person to person and can develop at any age.Cancer in PHTSPrevious data, which focused only on patients with a clinical diagnosis of Cowden syndrome without understanding whether an underlying PTEN mutation was present estimated lifetime breast cancer risk to be 25-50% and risk for non-medullary thyroid cancer to be 10%. Risks for endometrial (uterine) and renal cell (kidney) cancer were thought to be increased, but an exact risk level was undetermined.Current data focusing on patients known to have PHTS provide the following lifetime risk estimates, with the majority of diagnoses occurring after age 30:·Breast cancer: 85%·Thyroid cancer: 35%·Renal cell cancer: 34%·Endometrial cancer: 28%·Colorectal cancer: 9%·Melanoma: 6%.Benign tumors in PHTSBenign skin or oral lesions are very common and most commonly appear in adulthood. The most common types of benign skin lesions seen in PHTS include:.·Lipomas – benign fatty tumors which can appear just under the skin or elsewhere (breast area, GI tract)·Acral keratosis – rough patches of skin most often seen on the extremities (arms, hands, legs, feet)·Papillomatous skin papules – wart-like lesions which can appear anywhere, with feet and hands commonly being affected·Mucosal papillomas – Benign overgrowth of tissue affecting the tongue, gums, or inside the nose·Trichilemmomas – Benign tumor of the hair follicle·Fibromas – another kind of overgrowth involving the skin and other connective tissue; may also affect tissue covering organs, such as the ovaries.Gastrointestinal polyps are very common in adults with PHTS. Among patients who had undergone endoscopy, 93% were found to have polyps. The kinds of polyps found most often were hyperplastic or hamartomatous, which rarely develop into malignancy; however adenomas, which may develop into a cancer, were also identified. Many polyps were very small and did not cause symptoms to make their presence known such as pain or rectal bleeding.Benign breast, thyroid, and uterine lesions are also common in persons with PHTS. Some women have severe fibrocystic disease or changes which lead to multiple breast biopsies and complications with imaging. Multinodular goiter and Hashimoto’s thyroiditis may develop in children and adults. Uterine fibroids may appear and cause bleeding or discomfort to the extent that hysterectomy is indicated without an underlying cancer diagnosis.Vascular tumors, including hemangiomas, arteriovenous malformations, and developmental venous anomalies, have also been observed in patients with PHTS. Treatment of some lesions has been complicated by tendency for regrowth.A minority of adults develop a rare tumor known as a cerebellar dysplastic gangliocytoma (Lhermitte-Duclos syndrome). Symptoms of Lhermitte-Duclos syndrome include increased intracranial pressure, impaired ability to coordinate voluntary movements (ataxia), and seizures. It is rare when a person with adult-onset Lhermitte-Duclos does not have an underlying PTEN mutation, and observing this tumor type is an automatic indicator of need for PTEN testing.Neurodevelopmental concerns in PHTSMacrocephaly (large head size) is found in 94% measured patients with PHTS and can be a helpful screening tool to identify patients at increased risk for PTEN mutation. In most patients large head size is caused by overgrowth of brain tissue as opposed to hydrocephalus. The head shape also tends to be longer than wide (dolicocephaly).Autism and other developmental disorders, such as mental retardation and developmental delays, have been observed in patients with PHTS. In previous case series, up to 12% of children presenting with macrocephaly and an autism spectrum disorder alone were found to have an underlying PTEN mutation. - NORD
Reference: NORD
Synonym
pten hamartoma tumor syndrome (disorder)
pten hamartoma tumour syndrome
Orphanet
UMLS
C1959582
Comorbidity
UMLS | Disease | Sentences' Count(Total Sentences:6)
Curated Gene
Entrez_id | Symbol | Resource(Total Genes:1)
5728  |  PTEN  |  CLINVAR
Inferring Gene(Waiting for update.)
Text Mined Gene(Waiting for update.)
Locus(Waiting for update.)
Disease ID 1793
Disease pten hamartoma tumor syndrome
Integrated Phenotype
HPO | Name(Total Integrated Phenotypes:24)
HP:0012740  |  Papilloma
HP:0012480  |  Abnormality of cerebral veins
HP:0005987  |  Multinodular goiter
HP:0045059  |  Hyperkeratotic papule
HP:0001480  |  Freckling
HP:0008046  |  Abnormality of the retinal vasculature
HP:0012032  |  Lipoma
HP:0012846  |  Multiple trichilemmomata
HP:0003005  |  Ganglioneuroma
HP:0012114  |  Endometrial carcinoma
HP:0005584  |  Renal cell carcinoma
HP:0010612  |  Plantar pits
HP:0003003  |  Colon cancer
HP:0001028  |  Hemangioma
HP:0000729  |  Autistic behavior
HP:0002664  |  Neoplasm
HP:0000256  |  Macrocephaly
HP:0000077  |  Abnormality of the kidney
HP:0002597  |  Abnormality of the vasculature
HP:0001249  |  Intellectual disability
HP:0002890  |  Thyroid carcinoma
HP:0200034  |  Papule
HP:0000854  |  Thyroid adenoma
HP:0003002  |  Breast carcinoma
Text Mined Phenotype
HPO | Name | Sentences' Count(Total Phenotypes:4)
Disease ID 1793
Disease pten hamartoma tumor syndrome
Manually Symptom(Waiting for update.)
Text Mined Symptom(Waiting for update.)
Manually Genotype(Total Manually Genotypes:19)
Gene Mutation DOI Article Title
PTENc.287C>G (Pro96Arg)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.389G>A (Arg130Gln)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.44ins16doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.734del4doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.1003C>T (Arg335Ter)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.376G>C (Ala126Pro)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.76A>C (Thr26Pro)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENWhole gene deletiondoi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.737C>T (Pro246Leu)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.486C>G (Asp162Glu)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.75G>T (Leu25Phe)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.511C>T (Gln171Ter)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.420_421insAdoi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.401T>G (Met134Arg)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.388C>T (Arg130Ter)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.209+5G>Adoi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENc.263A>G (Tyr88Cys)doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTENDuplication of promoter, exon 1doi:10.1038/gim.2012.51Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome
PTEN-doi:10.1038/gim.2015.51Clinical performance of the CytoScan Dx Assay in diagnosing developmental delay/intellectual disability
Text Mining Genotype(Total Genotypes:0)
(Waiting for update.)
All Snps(Total Genotypes:10)
snpId pubmedId geneId geneSymbol diseaseId sourceId sentence score Year geneSymbol_dbSNP CHROMOSOME POS REF ALT
rs121909219NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087957915CT
rs121909224NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087933147CG,T
rs121909229NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087933148GA,C
rs121909231NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087961095CT
rs121909241NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087933154GA,T
rs587776673NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087952132C-
rs587781254NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087933097GT
rs587781255NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087933138GA
rs730882131NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087957999CT
rs786204933NA5728PTENumls:C1959582CLINVARNA0.125971721NAPTEN1087933196TA
GWASdb Annotation(Total Genotypes:0)
(Waiting for update.)
GWASdb Snp Trait(Total Genotypes:0)
(Waiting for update.)
Mapped by lexical matching(Total Items:8)
HP ID HP Name MP ID MP Name Annotation
HP:0005584Renal cell carcinomaMP:0013774decreased KLRG1-positive T-helper cell numberreduction in the number of CD4-positive alpha-beta T-helper cells expressing KLRG1, a marker associated with activation
HP:0000729Autistic behaviorMP:0009848increased horizontal stereotypic behaviorincrease in the frequency of repetitive rearings (greater than one per second)
HP:0008046Abnormality of the retinal vasculatureMP:0004686decreased length of long bonesreduced end-to-end length of the several elongated bones of the extremities
HP:0012114Endometrial carcinomaMP:0010346increased thyroid carcinoma incidencegreater than the expected number of a malignant epithelial neoplasms of the thyroid gland, occurring in a specific population in a given time period
HP:0000854Thyroid adenomaMP:0003496increased thyroid adenoma incidencegreater than the expected number of a benign epithelial neoplasm with a glandular organization arising in the thyroid gland, occurring in a specific population in a given time period
HP:0002890Thyroid carcinomaMP:0003331increased hepatocellular carcinoma incidencegreater than the expected number of a malignant neoplasm arising from liver cells, usually in adults and caused by liver trauma due to disease or injury, occurring in a specific population in a given time period
HP:0003002Breast carcinomaMP:0010367increased spindle cell carcinoma incidencegreater than the expected number of a highly malignant variant of squamous cell carcinoma, occurring in a specific population in a given time period; spindle cell carcinoma shows biphasic proliferation of conventional SCC component and malignant spindle s
HP:0000077Abnormality of the kidneyMP:0011665d-loop transposition of the great arteriescomplete transposition of the great arteries; the d- refers to the dextroposition of the bulboventricular loop (ie, the position of the right ventricle, which is on the right side); in addition, the aorta also tends to be on the right and anterior, and th
Mapped by homologous gene(Total Items:19)
HP ID HP Name MP ID MP Name Annotation
HP:0200034PapuleMP:0013745abnormal eyelid margin morphologyany structural anomaly of the confluence of the mucosal surface of the conjunctiva, the edge of the orbicularis, and the cutaneous epithelium
HP:0005987Multinodular goiterMP:0013293embryonic lethality prior to tooth bud stagedeath prior to the appearance of tooth buds (Mus: E12-E12.5)
HP:0008046Abnormality of the retinal vasculatureMP:0014059abnormal photoreceptor connecting cilium morphologyany structural anomaly of the nonmotile primary cilium that has a 9+0 microtubule array and forms the portion of the axoneme traversing the boundary between the retinal photoreceptor inner and outer segments
HP:0003003Colon cancerMP:0020039increased bone ossificationincrease in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance
HP:0001028HemangiomaMP:0014171increased fatty acid oxidationincreased rate or incidence of the process of removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydr
HP:0003005GanglioneuromaMP:0013795abnormal colon goblet cell morphologyany structural anomaly of the glandular simple columnar epithelial cell found in the mucosal lining of the colon, whose primary function is to secrete gel-forming mucins, the major components of mucus
HP:0005584Renal cell carcinomaMP:0020039increased bone ossificationincrease in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance
HP:0002664NeoplasmMP:0020154impaired humoral immune responseimpaired response of the immune system that mediates secreted antibodies produced in B cells
HP:0012114Endometrial carcinomaMP:0014171increased fatty acid oxidationincreased rate or incidence of the process of removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydr
HP:0001249Intellectual disabilityMP:0020316decreased vascular endothelial cell proliferationdecrease in the expansion rate of any vascular endothelial cell population by cell division
HP:0000256MacrocephalyMP:0020309increased creatine kinase activityincreased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+).
HP:0001480FrecklingMP:0013787photophobia abnormal aversion or avoidance behavior in response to light; photophobia is symptom of abnormal intolerance to visual perception of light; as a medical symptom, photophobia is not a morbid fear or phobia, but an experience of discomfort or pain to the e
HP:0002890Thyroid carcinomaMP:0013618decreased areal bone mineral densityreduction of the mineral mass per unit area of bone, the hard, rigid form of connective tissue constituting most of the skeleton of vertebrates and composed chiefly of calcium salts; expressed as the amount of mineral per area cm^2 of bone (usually in g/c
HP:0000854Thyroid adenomaMP:0014171increased fatty acid oxidationincreased rate or incidence of the process of removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydr
HP:0012032LipomaMP:0014171increased fatty acid oxidationincreased rate or incidence of the process of removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydr
HP:0003002Breast carcinomaMP:0020039increased bone ossificationincrease in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance
HP:0000077Abnormality of the kidneyMP:0013294prenatal lethality prior to heart atrial septationdeath prior to the completion of heart atrial septation (Mus: E14.5-15.5)
HP:0010612Plantar pitsMP:0013293embryonic lethality prior to tooth bud stagedeath prior to the appearance of tooth buds (Mus: E12-E12.5)
HP:0000729Autistic behaviorMP:0020157abnormal behavioral response to alcoholany anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior
Disease ID 1793
Disease pten hamartoma tumor syndrome
Case(Waiting for update.)