ClinVar Genomic variation as it relates to human health
NM_000314.8(PTEN):c.464A>G (p.Tyr155Cys)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000314.8(PTEN):c.464A>G (p.Tyr155Cys)
Variation ID: 404168 Accession: VCV000404168.63
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q23.31 10: 87933223 (GRCh38) [ NCBI UCSC ] 10: 89692980 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 14, 2018 Apr 15, 2024 Nov 22, 2019 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000314.8:c.464A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000305.3:p.Tyr155Cys missense NM_001304717.5:c.983A>G NP_001291646.4:p.Tyr328Cys missense NM_001304718.2:c.-287A>G 5 prime UTR NC_000010.11:g.87933223A>G NC_000010.10:g.89692980A>G NG_007466.2:g.74785A>G LRG_311:g.74785A>G LRG_311t1:c.464A>G - Protein change
- Y155C, Y328C
- Other names
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- Canonical SPDI
- NC_000010.11:87933222:A:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
Trans-Omics for Precision Medicine (TOPMed) 0.00000
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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PTEN | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh38 GRCh37 |
3002 | 3493 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (3) |
reviewed by expert panel
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Nov 22, 2019 | RCV000475421.16 | |
Pathogenic (1) |
criteria provided, single submitter
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Jun 5, 2014 | RCV000491012.5 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Sep 28, 2023 | RCV000656112.8 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 9, 2021 | RCV001022838.4 | |
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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Apr 27, 2023 | RCV001092596.21 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Jan 14, 2019 | RCV001258059.3 | |
Pathogenic (1) |
criteria provided, single submitter
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May 25, 2023 | RCV003326136.2 | |
Pathogenic (1) |
no assertion criteria provided
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Jul 1, 2021 | RCV003168731.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Feb 1, 2024 | RCV003492047.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 12, 2023 | RCV003470396.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Nov 22, 2019)
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reviewed by expert panel
Method: curation
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PTEN hamartoma tumor syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Clingen PTEN Variant Curation Expert Panel, Clingen
Accession: SCV001244247.1
First in ClinVar: May 04, 2020 Last updated: May 04, 2020 |
Comment:
PTEN c.464A>G (p.Tyr155Cys) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID … (more)
PTEN c.464A>G (p.Tyr155Cys) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). PS3: Phosphatase activity <50% of wild type (PMID 21828076, 10866302, 29706350) PS4: Probands with phenotype specificity score of 4-15.5 (PMID 23399955, internal laboratory contributors SCV000579967.3, ClinVar Organization ID: 19864) PM6_S: Two probands with presumed de novo occurrence (maternity/paternity not confirmed) in a patient with the disease and no family history. (internal laboratory contributor ClinVar Organization ID: 26957) PM2: Absent in large sequenced populations (PMID 27535533). PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. (less)
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Uncertain significance
(Sep 01, 2017)
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criteria provided, single submitter
Method: research
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Cowden syndrome 1
(Autosomal dominant inheritance)
Affected status: yes, unknown
Allele origin:
inherited,
unknown
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Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
Accession: SCV000598612.1
First in ClinVar: Jun 02, 2018 Last updated: Jun 02, 2018 |
Comment:
this variant was indentified in an individual with malformations of cortical development
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Abnormality of neuronal migration (present)
Method: WES
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Abnormality of neuronal migration (present)
Method: WES
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Likely pathogenic
(Jan 14, 2019)
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criteria provided, single submitter
Method: clinical testing
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PTEN hamartoma tumor syndromes
Affected status: unknown
Allele origin:
germline
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Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Accession: SCV001434890.1
First in ClinVar: Oct 03, 2020 Last updated: Oct 03, 2020 |
Comment:
The c.464A>G (p.Tyr155Cys) variant in the PTEN gene has been reported in multiple individuals with Cowden's disease or PTEN hamartoma tumor syndrome (PMID 12614768, 17942903, … (more)
The c.464A>G (p.Tyr155Cys) variant in the PTEN gene has been reported in multiple individuals with Cowden's disease or PTEN hamartoma tumor syndrome (PMID 12614768, 17942903, 19265751, 23335809, 23399955, 27531073). This variant is absent from large databases of genetic variation in the general population. In vitro phosphatase activity assay demonstrated that the activity of the mutant protein is equivalent to a null allele (PMID 10866302). Multiple lines of algorithms predict deleterious effect of the p.Tyr155Cys change. Therefore, the c c.464A>G (p.Tyr155Cys) variant in the PTEN gene is classified as likely pathogenic. (less)
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Pathogenic
(Mar 09, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV001184619.3
First in ClinVar: Mar 16, 2020 Last updated: Nov 29, 2022 |
Comment:
The p.Y155C pathogenic mutation (also known as c.464A>G), located in coding exon 5 of the PTEN gene, results from an A to G substitution at … (more)
The p.Y155C pathogenic mutation (also known as c.464A>G), located in coding exon 5 of the PTEN gene, results from an A to G substitution at nucleotide position 464. The tyrosine at codon 155 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant has been reported in numerous individuals with personal and/or family history consistent with PTEN Hamartoma Tumor Syndrome (Tan MH et al. Am. J. Hum. Genet. 2011 Jan; 88(1):42-56; Gicquel JJ et al. Am. J. Ophthalmol. 2003 Mar; 135(3):400-2; Bubien V et al. J. Med. Genet., 2013 Apr;50:255-63; Ngeow J et al. Gastroenterology, 2013 Jun;144:1402-9, 1409.e1-5; Nizialek E et al. Eur. J. Hum. Genet. 2015 Nov;23(11):1538-43; Driessen GJ et al. J. Allergy Clin. Immunol., 2016 12;138:1744-1747.e5; Wiszniewski W et al. Eur J Hum Genet, 2018 08;26:1121-1131; Szabo Yamashita T et al. Eur Thyroid J, 2020 Sep;9:243-246; Plamper M et al. Cells, 2020 07;9; Kim RH et al. NPJ Genom Med, 2020 Sep;5:40; Ambry internal data). In a yeast functional assay, this variant demonstrated loss of in vivo phosphatase activity (Rodríguez-Escudero I et al. Hum. Mol. Genet. 2011 Nov; 20(21):4132-42). This missense alteration is located in a region that has a low rate of benign missense variation (Lek M et al. Nature. 2016 Aug 18;536(7616):285-91; DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth H.V. et al. 2009. Am.J.Hum.Genet. 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
Number of individuals with the variant: 1
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Pathogenic
(Jun 02, 2021)
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criteria provided, single submitter
Method: clinical testing
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Cowden syndrome 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
Accession: SCV002764845.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Number of individuals with the variant: 1
Clinical Features:
Hydrocephalus (present) , Macrocephaly (present) , Migraine (present) , Hypoglycemia (present) , Global developmental delay (present)
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Pathogenic
(Jun 05, 2014)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: yes
Allele origin:
germline
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Ambry Genetics
Accession: SCV000579967.5
First in ClinVar: Jun 25, 2017 Last updated: Jan 07, 2023 |
Number of individuals with the variant: 1
Sex: male
Ethnicity/Population group: Asian/Caucasian
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Pathogenic
(May 25, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cowden syndrome 1
Macrocephaly-autism syndrome
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: yes
Allele origin:
germline
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Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn
Accession: SCV004032469.1
First in ClinVar: Sep 09, 2023 Last updated: Sep 09, 2023 |
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Likely pathogenic
(Sep 28, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cowden syndrome 1
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004188743.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 10866302, 11051241, 27829222]. This variant is expected to disrupt protein … (more)
This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 10866302, 11051241, 27829222]. This variant is expected to disrupt protein structure [Myriad internal data]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 12614768]. (less)
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Pathogenic
(Sep 12, 2023)
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criteria provided, single submitter
Method: clinical testing
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Glioma susceptibility 2
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004206667.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Apr 27, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV004219136.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in individuals with conditions … (more)
This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in individuals with conditions associated with PTEN-hamartoma tumor syndrome (PMID: 23399955 (2013), 21194675 (2011), 27531073 (2016), 29706646 (2018), 32664367 (2020), 33083010 (2020), 33088792 (2020), 12614768 (2003), 23335809 (2013)). Published functional studies showed that this variant causes reduced phosphatase activity compared to the wild type protein (PMID: 10866302 (2000), 21828076 (2011)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic. (less)
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Pathogenic
(Feb 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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Papillary tumor of the pineal region
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV004240770.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
Clinical Features:
Pinealoma (present) , Pediatric onset (present)
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Pathogenic
(Dec 19, 2023)
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criteria provided, single submitter
Method: clinical testing
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PTEN hamartoma tumor syndrome
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000541626.10
First in ClinVar: Apr 17, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 155 of the PTEN protein … (more)
This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 155 of the PTEN protein (p.Tyr155Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Cowden syndrome or PTEN hamartoma tumor syndrome (PMID: 12614768, 17942903, 23335809, 23399955, 27531073). ClinVar contains an entry for this variant (Variation ID: 404168). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is expected to disrupt PTEN function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects PTEN function (PMID: 10866302, 17942903, 21828076). This variant disrupts the p.Tyr155 amino acid residue in PTEN. Other variant(s) that disrupt this residue have been observed in individuals with PTEN-related conditions (PMID: 30181857), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Apr 01, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001249160.20
First in ClinVar: May 12, 2020 Last updated: Apr 15, 2024 |
Number of individuals with the variant: 1
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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PTEN hamartoma tumor syndrome
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
unknown
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University Health Network, Princess Margaret Cancer Centre
Accession: SCV001430889.1
First in ClinVar: Aug 29, 2020 Last updated: Aug 29, 2020 |
Comment:
This variant c.464 A>G is not present in population databases. It has been reported in individuals affected with PHTS (Bubien 2013, Gicquel 2003, Ngeow 2013, … (more)
This variant c.464 A>G is not present in population databases. It has been reported in individuals affected with PHTS (Bubien 2013, Gicquel 2003, Ngeow 2013, Andres-Pons 2007). (less)
Clinical Features:
Renal cell carcinoma (present) , Macrocephaly (present) , Verrucous papule (present) , Hemihyperplasia (present) , Vascular malformations (present)
Age: 20-29 years
Sex: female
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001920709.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001951497.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001963428.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
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Pathogenic
(Jul 01, 2021)
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no assertion criteria provided
Method: research
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Gastric cancer
Affected status: unknown
Allele origin:
germline
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Laboratory for Genotyping Development, RIKEN
Accession: SCV002758069.1
First in ClinVar: Apr 15, 2023 Last updated: Apr 15, 2023 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Helicobacter pylori, Homologous-Recombination Genes, and Gastric Cancer. | Usui Y | The New England journal of medicine | 2023 | PMID: 36988593 |
Occurrence and Natural History of Thyroid Cancer in Patients with Cowden Syndrome. | Szabo Yamashita T | European thyroid journal | 2020 | PMID: 33088792 |
Early-onset renal cell carcinoma in PTEN harmatoma tumour syndrome. | Kim RH | NPJ genomic medicine | 2020 | PMID: 33083010 |
Cerebral MRI and Clinical Findings in Children with PTEN Hamartoma Tumor Syndrome: Can Cerebral MRI Scan Help to Establish an Earlier Diagnosis of PHTS in Children? | Plamper M | Cells | 2020 | PMID: 32664367 |
Posterior Neocortex-Specific Regulation of Neuronal Migration by CEP85L Identifies Maternal Centriole-Dependent Activation of CDK5. | Kodani A | Neuron | 2020 | PMID: 32097629 |
Considerations for total thyroidectomy in an adolescent with PTEN mutation. | Tosur M | Therapeutic advances in endocrinology and metabolism | 2018 | PMID: 30181857 |
Comprehensive genomic analysis of patients with disorders of cerebral cortical development. | Wiszniewski W | European journal of human genetics : EJHG | 2018 | PMID: 29706646 |
A Saturation Mutagenesis Approach to Understanding PTEN Lipid Phosphatase Activity and Genotype-Phenotype Relationships. | Mighell TL | American journal of human genetics | 2018 | PMID: 29706350 |
PTEN dephosphorylates AKT to prevent the expression of GLUT1 on plasmamembrane and to limit glucose consumption in cancer cells. | Phadngam S | Oncotarget | 2016 | PMID: 27829222 |
Analysis of protein-coding genetic variation in 60,706 humans. | Lek M | Nature | 2016 | PMID: 27535533 |
Increased PI3K/Akt activity and deregulated humoral immune response in human PTEN deficiency. | Driessen GJ | The Journal of allergy and clinical immunology | 2016 | PMID: 27531073 |
Prevalence of germline PTEN, BMPR1A, SMAD4, STK11, and ENG mutations in patients with moderate-load colorectal polyps. | Ngeow J | Gastroenterology | 2013 | PMID: 23399955 |
High cumulative risks of cancer in patients with PTEN hamartoma tumour syndrome. | Bubien V | Journal of medical genetics | 2013 | PMID: 23335809 |
A comprehensive functional analysis of PTEN mutations: implications in tumor- and autism-related syndromes. | Rodríguez-Escudero I | Human molecular genetics | 2011 | PMID: 21828076 |
A clinical scoring system for selection of patients for PTEN mutation testing is proposed on the basis of a prospective study of 3042 probands. | Tan MH | American journal of human genetics | 2011 | PMID: 21194675 |
In vivo functional analysis of the counterbalance of hyperactive phosphatidylinositol 3-kinase p110 catalytic oncoproteins by the tumor suppressor PTEN. | Andrés-Pons A | Cancer research | 2007 | PMID: 17942903 |
Retinal angioma in a patient with Cowden disease. | Gicquel JJ | American journal of ophthalmology | 2003 | PMID: 12614768 |
Functional evaluation of p53 and PTEN gene mutations in gliomas. | Kato H | Clinical cancer research : an official journal of the American Association for Cancer Research | 2000 | PMID: 11051241 |
Functional evaluation of PTEN missense mutations using in vitro phosphoinositide phosphatase assay. | Han SY | Cancer research | 2000 | PMID: 10866302 |
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/dab6b7c8-ee3d-4d08-bdd5-ffb0fee948cd | - | - | - | - |
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Text-mined citations for rs1060500126 ...
HelpRecord last updated Apr 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.