ClinVar Genomic variation as it relates to human health
NM_000314.8(PTEN):c.388C>T (p.Arg130Ter)
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.388C>T (p.Arg130Ter)
Variation ID: 7819 Accession: VCV000007819.88
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q23.31 10: 87933147 (GRCh38) [ NCBI UCSC ] 10: 89692904 (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 Oct 19, 2014 Apr 15, 2024 Jan 7, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000314.8:c.388C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000305.3:p.Arg130Ter nonsense NM_000314.5:c.388C>T NM_001304717.5:c.907C>T NP_001291646.4:p.Arg303Ter nonsense NM_001304718.2:c.-363C>T 5 prime UTR NC_000010.11:g.87933147C>T NC_000010.10:g.89692904C>T NG_007466.2:g.74709C>T LRG_311:g.74709C>T LRG_311t1:c.388C>T - Protein change
- R130*, R303*
- Other names
- p.R130X:CGA>TGA
- NM_000314.8(PTEN):c.388C>T
- p.Arg130Ter
- Canonical SPDI
- NC_000010.11:87933146:C:T
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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.
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
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
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
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) |
criteria provided, single submitter
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Jan 25, 2023 | RCV000008265.18 | |
Pathogenic (12) |
criteria provided, multiple submitters, no conflicts
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Jun 22, 2023 | RCV000008263.24 | |
Pathogenic (8) |
criteria provided, multiple submitters, no conflicts
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Nov 1, 2021 | RCV000078615.43 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Jul 8, 2021 | RCV000132187.20 | |
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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Jan 7, 2024 | RCV000199099.27 | |
Pathogenic (2) |
no assertion criteria provided
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Dec 1, 2018 | RCV000424529.12 | |
Likely pathogenic (1) |
no assertion criteria provided
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Jul 14, 2015 | RCV000443514.9 | |
Pathogenic (1) |
no assertion criteria provided
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- | RCV001327978.9 | |
Pathogenic (1) |
no assertion criteria provided
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Sep 1, 2020 | RCV001257555.9 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Dec 9, 2021 | RCV001542771.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 11, 2023 | RCV003326115.6 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 15, 2022 | RCV002476944.8 | |
Pathogenic (1) |
no assertion criteria provided
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Jul 1, 2021 | RCV003162218.8 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 8, 2023 | RCV003934809.1 | |
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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
(Apr 02, 2018)
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criteria provided, single submitter
Method: clinical testing
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PTEN hamartoma tumor syndrome
(Autosomal dominant inheritance)
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000967757.1
First in ClinVar: Aug 26, 2019 Last updated: Aug 26, 2019 |
Comment:
The p.Arg130X variant in PTEN has been reported in at least 10 individuals with Cowden syndrome (a sub-type of PTEN hamartoma tumor syndrome) and segregated … (more)
The p.Arg130X variant in PTEN has been reported in at least 10 individuals with Cowden syndrome (a sub-type of PTEN hamartoma tumor syndrome) and segregated wit h disease in at least 5 affected relatives from 2 families (Nelen 1997, Marsh 19 98, Zori 1998, Kubo 2000, Ngeow 2011). This variant has been identified in 3/246 154 total chromosomes in the Genome Aggregation Database (gnomAD, http://gnomad. broadinstitute.org; dbSNP rs121909224) and in ClinVar (Variation ID# 7819). This nonsense variant leads to a premature termination codon at position 130, which is predicted to lead to a truncated or absent protein. Heterozygous loss of func tion of the PTEN gene is an established disease mechanism in PTEN hamartoma tumo r syndrome. In summary, this variant meets criteria to be classified as pathogen ic for PTEN hamartoma tumor syndrome in an autosomal dominant manner. ACMG/AMP C riteria applied PVS1; PS4; PP1_Moderate. (less)
Number of individuals with the variant: 1
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Pathogenic
(Oct 12, 2017)
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criteria provided, single submitter
Method: clinical testing
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Cowden syndrome 1
Affected status: yes
Allele origin:
germline
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001428573.1
First in ClinVar: Aug 16, 2020 Last updated: Aug 16, 2020 |
Number of individuals with the variant: 1
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Pathogenic
(Oct 23, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
(Unknown mechanism)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001448140.1
First in ClinVar: Nov 28, 2020 Last updated: Nov 28, 2020 |
Clinical Features:
Macrocephaly (present) , Global developmental delay (present)
Sex: female
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Pathogenic
(Jan 21, 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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Color Diagnostics, LLC DBA Color Health
Accession: SCV001340966.2
First in ClinVar: Jun 22, 2020 Last updated: Jun 19, 2021 |
Comment:
This variant changes 1 nucleotide in exon 5 of the PTEN gene, creating a premature translation stop signal. This variant is expected to result in … (more)
This variant changes 1 nucleotide in exon 5 of the PTEN gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with Cowden Syndrome (PMID: 9259288, 9467011, 9856571, 10400993, 10848731, 11332402, 11918710, 14566704, 16773562, 17286265, 20600018, 21194675, 21956414, 22266152, 23470840, 23764071, 30659124). It has been shown that this variant segregates with disease (PMID: 9259288, 9856571, 11332402) and has been observed de novo in an individual with Cowden syndrome (PMID: 11918710). This variant has been identified in 3/251384 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of PTEN function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. (less)
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Pathogenic
(Jan 28, 2020)
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criteria provided, single submitter
Method: clinical testing
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PTEN hamartoma tumor syndrome
Affected status: yes
Allele origin:
germline,
somatic
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Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital
Accession: SCV002525581.1
First in ClinVar: Jun 11, 2022 Last updated: Jun 11, 2022 |
Comment:
The p.Arg130* variant replaces the arginine at position 130 with a premature termination codon and is expected to cause a loss of protein function. This … (more)
The p.Arg130* variant replaces the arginine at position 130 with a premature termination codon and is expected to cause a loss of protein function. This variant has previously been reported in several patients with PTEN hamartoma tumor syndrome (PHTS), which includes Cowden syndrome (CS) and Bannayan-Riley-Ruvalcaba syndrome (BRRS) (NBK1488, PMID: 10749983, 28655553, 9856571, and others). The phenotypic spectrum reported in PHTS includes vascular malformations (NBK1488, PMID: 28655553). This variant has been observed in large population studies at an allele frequency of 3/251,384 allele (Genome Aggregation Database). (less)
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Venous malformation (present) , Scoliosis (present) , Tremor (present) , Hemangioma (present)
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Hemihypertrophy (present) , Abnormality of the vasculature (present) , Venous malformation (present)
Observation 3:
Number of individuals with the variant: 1
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Cowden syndrome 1
Affected status: yes
Allele origin:
unknown
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Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV002576484.1
First in ClinVar: Oct 01, 2022 Last updated: Oct 01, 2022 |
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Pathogenic
(Jul 08, 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: SCV000187267.9
First in ClinVar: Aug 06, 2014 Last updated: Nov 29, 2022 |
Comment:
The p.R130* pathogenic mutation (also known as c.388C>T), located in coding exon 5 of the PTEN gene, results from a C to T substitution at … (more)
The p.R130* pathogenic mutation (also known as c.388C>T), located in coding exon 5 of the PTEN gene, results from a C to T substitution at nucleotide position 388. This changes the amino acid from an arginine to a stop codon within coding exon 5. This mutation has been reported in numerous individuals diagnosed with Cowden syndrome, Bannayan-Riley-Ruvalcaba syndrome, breast cancer, thyroid cancer, renal cancer, and/or other clinical features associated with PTEN mutations (Nelen MR et al. Hum. Molec. Genet. 1997 Aug;6:1383-7; Mester JL et al. Urology. 2012 May;79:1187.e1-7; Shuch B et al. J. Urol. 2013 Dec;190:1990-8; Ngeow J et al. J. Clin. Endocrinol. Metab. 2011 Dec;96:E2063-71; Heindl M et al. Gastroenterology. 2012 May;142:1093-6.e6; Busch RM et al Genet. Med. 2013 Jul;15:548-53; Nieuwenhuis MH et al. Fam. Cancer. 2014 Mar;13:57-63; Marsh DJ et al. Hum Mol Genet, 1998 Mar;7:507-15; Zori RT et al. Am J Med Genet, 1998 Dec;80:399-40; Kim RH et al. NPJ Genom Med, 2020 Sep;5:40; Yauy K et al. J Natl Compr Canc Netw, 2019 01;17:7-11; Kubo Y et al. Br J Dermatol, 2000 Jun;142:1100-5; Bouron-Dal Soglio D et al. Eur Thyroid J, 2018 Jan;7:44-50; Hansen-Kiss E et al. J Med Genet, 2017 07;54:471-478). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)
Number of individuals with the variant: 1
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Pathogenic
(Oct 13, 2016)
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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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Counsyl
Accession: SCV000489500.2
First in ClinVar: Oct 19, 2014 Last updated: Dec 24, 2022 |
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Pathogenic
(Feb 23, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cowden syndrome 1
Affected status: yes
Allele origin:
unknown
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3billion
Accession: SCV003841764.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). This variant was predicted to result in … (more)
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been previously reported as assumed (i.e. paternity and maternity not confirmed) de novo in at least one similarly affected unrelated individual (PMID: 11918710). The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000007819 / PMID: 9259288). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Macrocephaly (present) , Mild global developmental delay (present) , Depressed nasal bridge (present) , Hypertelorism (present) , Frontal bossing (present)
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Pathogenic
(Apr 05, 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: SCV004019961.1
First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
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Pathogenic
(Aug 11, 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: SCV004032474.1
First in ClinVar: Sep 09, 2023 Last updated: Sep 09, 2023 |
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Pathogenic
(Jun 22, 2023)
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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:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV004175664.1
First in ClinVar: Dec 17, 2023 Last updated: Dec 17, 2023 |
Comment:
The PTEN c.388C>T missense variant has been classified as Pathogenic (PVS1, PM2, PS4_Moderate). The c.388C>T variant is located in exon 5/9 and introduces a premature … (more)
The PTEN c.388C>T missense variant has been classified as Pathogenic (PVS1, PM2, PS4_Moderate). The c.388C>T variant is located in exon 5/9 and introduces a premature stop codon resulting in a truncated protein (PMID: 11918710) and is predicted to undergo nonsense-mediated decay (PVS1). It is absent in gnomAD (PM2) and prevalent in affected individuals (PS4_moderate). The variant has been reported in PMID: 9259288 in 2 affected individuals within a family. PMID: 11918710 also reports this variant as de novo in an affected individual. This variant has been reported in dbSNP (rs121909224), ClinVar as pathogenic (ClinVar variant ID: 7819) and HGMD as disease causing (CM971273). (less)
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Pathogenic
(Mar 01, 2017)
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criteria provided, single submitter
Method: clinical testing
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PTEN Hamartoma Tumor Syndrome
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
paternal,
de novo
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Herman Laboratory, Nationwide Children's Hospital
Accession: SCV000579271.1
First in ClinVar: Apr 16, 2017 Last updated: Apr 16, 2017 |
Observation 1:
Clinical Features:
Macrocephaly (present) , Speech delay (present) , Autism spectrum disorder (present) , ADHD (present)
Family history: yes
Sex: male
Ethnicity/Population group: Caucasian
Tissue: Blood
Comment on evidence:
Macrocephaly (+3.5 SD)
Observation 2:
Clinical Features:
Macrocephaly (present) , Autism spectrum disorder (present) , Global developmental delay (present) , Patent ductus arteriosus (present) , Melanocytic nevus (present) , Thyroid nodule (present)
Family history: no
Sex: male
Ethnicity/Population group: Caucasian
Tissue: Blood
Comment on evidence:
Macrocephaly (+4.3 SD); Thyroid imaging showed small cystic appearing structures seen in both lobes measuring 2-3mm in diameter. A more prominent nodular appearing structure seen … (more)
Macrocephaly (+4.3 SD); Thyroid imaging showed small cystic appearing structures seen in both lobes measuring 2-3mm in diameter. A more prominent nodular appearing structure seen in the left lobe measuring ~0.8x0.4cm longitudinally and ~0.6x0.4cm transversely (less)
Observation 3:
Clinical Features:
Macrocephaly (present) , Developmental delay (present) , Papillomatosis papules (present) , Tubular adenomas (present)
Family history: no
Sex: male
Ethnicity/Population group: Caucasian
Tissue: Blood
Comment on evidence:
Macrocephaly (+6 SD)
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Pathogenic
(Jun 14, 2019)
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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
|
Knight Diagnostic Laboratories, Oregon Health and Sciences University
Accession: SCV001448935.1
First in ClinVar: Dec 11, 2020 Last updated: Dec 11, 2020 |
Number of individuals with the variant: 1
|
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Pathogenic
(Nov 01, 2019)
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criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000604969.2
First in ClinVar: Sep 30, 2017 Last updated: Jan 26, 2021 |
Comment:
The PTEN c.388C>T; p.Arg130Ter variant (rs121909224) has been reported in multiple individuals diagnosed with Cowden syndrome or PTEN hamartoma tumor syndrome (Busch 2013, Henderson 2014, … (more)
The PTEN c.388C>T; p.Arg130Ter variant (rs121909224) has been reported in multiple individuals diagnosed with Cowden syndrome or PTEN hamartoma tumor syndrome (Busch 2013, Henderson 2014, Kubo 2000, Nelen 1997). The variant is reported in the ClinVar database (Variation ID: 7819) and in the general population with an allele frequency of 0.001% (3/251384 alleles) in the Genome Aggregation Database. This variant induces an early termination codon and is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered to be pathogenic. References: Busch R et al. Cognitive characteristics of PTEN hamartoma tumor syndromes. Genet Med. 2013; 15(7):548-53. Henderson C et al. Increased prevalence of eosinophilic gastrointestinal disorders in pediatric PTEN hamartoma tumor syndromes. J Pediatr Gastroenterol Nutr. 2014; 58(5):553-60. Kubo Y et al. A novel PTEN mutation in a Japanese patient with Cowden disease. Br J Dermatol. 2000; 142(6):1100-5. Nelen M et al. Germline mutations in the PTEN/MMAC1 gene in patients with Cowden disease. Hum Mol Genet. 1997; 6(8):1383-7. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Glioma susceptibility 2
Affected status: yes
Allele origin:
germline
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Genomics England Pilot Project, Genomics England
Accession: SCV001760260.1
First in ClinVar: Jul 27, 2021 Last updated: Jul 27, 2021 |
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Pathogenic
(Oct 07, 2021)
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criteria provided, single submitter
Method: clinical testing
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Cowden syndrome 1
Affected status: yes
Allele origin:
de novo
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Centogene AG - the Rare Disease Company
Accession: SCV002059850.1
First in ClinVar: Jan 15, 2022 Last updated: Jan 15, 2022 |
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Pathogenic
(Jan 05, 2022)
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criteria provided, single submitter
Method: clinical testing
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Cowden syndrome 1
Affected status: yes
Allele origin:
germline
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DASA
Accession: SCV002061182.1
First in ClinVar: Jan 15, 2022 Last updated: Jan 15, 2022 |
Comment:
The c.388C>T;p.(Arg130*) variant creates a premature translational stop signal in the PTEN gene. It is expected to result in an absent or disrupted protein product … (more)
The c.388C>T;p.(Arg130*) variant creates a premature translational stop signal in the PTEN gene. It is expected to result in an absent or disrupted protein product -PVS1.This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant(ClinVar ID: 7819; OMIM: 601728.0007; PMID: 9259288; 21956414; 22266152; 23470840; 16773562; 24345843; 28655553) - PS4. The variant is present at low allele frequencies population databases (rs121909224 – gnomAD 0.001193%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The variant was assumed de novo, but without confirmation of paternity and maternity(PMID: 11918710) - PM6. The variant co-segregated with disease in multiple affected family members (PMID: 9259288; 9856571; 11332402) - PP1_strong. In summary, the currently available evidence indicates that the variant is pathogenic. (less)
Number of individuals with the variant: 1
Sex: female
Geographic origin: Brazil
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Pathogenic
(Aug 09, 2021)
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criteria provided, single submitter
Method: clinical testing
|
Cowden syndrome 1
Affected status: yes
Allele origin:
germline
|
MGZ Medical Genetics Center
Accession: SCV002580289.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022 |
Number of individuals with the variant: 1
Sex: female
|
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Pathogenic
(Mar 15, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Cowden syndrome 1
Malignant tumor of prostate Macrocephaly-autism syndrome Familial meningioma Glioma susceptibility 2
Affected status: unknown
Allele origin:
unknown
|
Fulgent Genetics, Fulgent Genetics
Accession: SCV002793214.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Jan 25, 2023)
|
criteria provided, single submitter
Method: curation
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Macrocephaly-autism syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
|
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV003761297.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
The heterozygous p.Arg130Ter variant in PTEN was identified by our study in one individual with macrocephaly-autism syndrome (PMID: 32959437). Trio exome analysis showed this variant … (more)
The heterozygous p.Arg130Ter variant in PTEN was identified by our study in one individual with macrocephaly-autism syndrome (PMID: 32959437). Trio exome analysis showed this variant to be de novo. The p.Arg130Ter variant in PTEN has been previously reported in over 30 unrelated individuals with PTEN-associated disease (PMID: 29594054, PMID: 33083010, PMID: 24345843, PMID: 28655553, PMID: 28526761, PMID: 10400993, PMID: 14566704, PMID: 16773562, PMID: 11332402, PMID: 17286265, PMID: 20600018, PMID: 21194675, PMID: 23470840, PMID: 30659124, PMID: 23764071, PMID: 1191871, PMID: 10848731, PMID: 9467011, PMID: 9856571, PMID: 9259288, PMID: 21956414, SCV002059850.1) and segregated with disease in 17 affected relatives from 6 families (PMID: 28655553, PMID: 17286265, PMID: 30659124, PMID: 11332402, PMID: 9259288, PMID: 9856571), but has been identified in 0.003% (1/30614) of South Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs121909224). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. Pathogenic variants may be present at a low frequency in the general population, for diseases with clinical variability, or reduced penetrance. The number of reported affected individuals with this variant is greater than expected compared to non-affected individuals with this variant. This variant was found to be de novo in 5 individuals with confirmed paternity and maternity (PMID: 28526761, PMID: 11918710, PMID: 32959437, PMID: 28526761, SCV002059850.1). This variant has also been reported in ClinVar (Variation ID: 7819) and has been interpreted as pathogenic by multiple submitters. This nonsense variant leads to a premature termination codon at position 130, which is predicted to lead to a truncated or absent protein. Heterozygous loss of function of the PTEN gene is an established disease mechanism in autosomal dominant PTEN-associated disease, including autosomal dominant macrocephaly-autism syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant macrocephaly-autism syndrome. ACMG/AMP Criteria applied: PVS1, PS2_VeryStrong, PS4, PP1_Strong (Richards 2015). (less)
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Pathogenic
(Oct 18, 2021)
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criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000222110.15
First in ClinVar: Mar 24, 2015 Last updated: Mar 04, 2023 |
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more)
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 25525159, 10400993, 9259288, 24345843, 27168869, 24375884, 28315634, 10749983, 22266152, 23470840, 10848731, 21956414, 9467011, 9856571, 23335809, 22252256, 22595938, 17526801, 22446940, 17526800, 11918710, 19265751, 17286265, 27477328, 27157322, 26786923, 27553368, 26976419, 16773562, 29594054, 28152038, 28655553, 30287823, 30720243, 31166879, 30306255, 32369273, 33509259, 33083010) (less)
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Pathogenic
(Dec 09, 2021)
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criteria provided, single submitter
Method: clinical testing
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Glioma susceptibility 2
Affected status: unknown
Allele origin:
unknown
|
Baylor Genetics
Accession: SCV004207132.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Aug 26, 2019)
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criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001134775.4
First in ClinVar: Jan 05, 2020 Last updated: Jan 06, 2024 |
Comment:
This nonsense variant causes the premature termination of PTEN protein synthesis. In addition, it has been reported in individuals with PTEN hamartoma tumor syndrome (PHTS) … (more)
This nonsense variant causes the premature termination of PTEN protein synthesis. In addition, it has been reported in individuals with PTEN hamartoma tumor syndrome (PHTS) in the published literature (PMID: 9259288 (1997), 21956414 (2011), 23934601 (2014), 24345843 (2014), 28526761 (2017)). Based on the available information, this variant is classified as pathogenic. (less)
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Pathogenic
(Jan 07, 2024)
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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
|
Invitae
Accession: SCV000253832.13
First in ClinVar: Oct 11, 2015 Last updated: Feb 28, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg130*) in the PTEN gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Arg130*) in the PTEN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PTEN are known to be pathogenic (PMID: 9467011, 21194675). This variant is present in population databases (rs121909224, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with PTEN hamartoma tumor syndrome (PMID: 9259288, 16773562, 21956414, 22266152, 23470840, 24345843, 28655553). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 7819). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Dec 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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PTEN-related condition
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV004749777.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
The PTEN c.388C>T variant is predicted to result in premature protein termination (p.Arg130*). This variant has previously been reported to be causative for PTEN Hamartoma … (more)
The PTEN c.388C>T variant is predicted to result in premature protein termination (p.Arg130*). This variant has previously been reported to be causative for PTEN Hamartoma Tumor Syndrome (Heindl et al. 2012. PubMed ID: 22266152; Ngeow et al. 2011. PubMed ID: 21956414; Sarquis et al. 2006. PubMed ID: 16773562). This variant is reported in 3 of ~251,000 alleles in gnomAD and interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/7819/). Nonsense variants in PTEN are expected to be pathogenic. This variant is interpreted as pathogenic. (less)
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Pathogenic
(Nov 01, 2021)
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criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001249159.20
First in ClinVar: May 09, 2020 Last updated: Apr 15, 2024 |
Number of individuals with the variant: 5
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Pathogenic
(Mar 15, 2007)
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no assertion criteria provided
Method: literature only
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MACROCEPHALY/AUTISM SYNDROME
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000028472.5
First in ClinVar: Apr 04, 2013 Last updated: Dec 15, 2018 |
Comment on evidence:
Cowden Syndrome 1 In a study of Cowden disease (CWS1; 158350), Nelen et al. (1997) found 2 independent occurrences of an arg130-to-ter (R130X) mutation in … (more)
Cowden Syndrome 1 In a study of Cowden disease (CWS1; 158350), Nelen et al. (1997) found 2 independent occurrences of an arg130-to-ter (R130X) mutation in the PTEN gene. The mutation involved a CpG dinucleotide. Zori et al. (1998) described a family in which a mother had Cowden disease and her son had been diagnosed with Bannayan-Riley-Ruvalcaba syndrome. Both were heterozygous for the R130X mutation. The son had been seen at the age of 11 years for severe developmental delay and autistic behavior. In early childhood, rectal bleeding led to removal of a few rectal polyps; the pathology showed benign pseudopolyp with telangiectatic vessels in an inflamed myxoid stroma. His verbal and performance IQs were 40 at 11 years. He developed a goiter at 18 years for which left hemithyroidectomy was performed, and a tumor was also excised from the right side of the thyroid. The left lobe contained insular (follicular) carcinoma while the right showed nodular hyperplasia with a focus of papillary microcarcinoma. At the age of 11 years, the son had multiple pigmented macules on the glands and shaft of the penis. He lacked the second toes. The mother of the patient reported by Zori et al. (1998) had a large head (59.5 cm) and multiple small papules on her tongue and oral mucosa. She had polyposis of the entire gastrointestinal tract. Mammogram showed bilateral fibroglandular tissue with single well-defined benign nodules in each breast with mild dysplasia. Macrocephaly/Autism Syndrome In a 4-year-old boy with macrocephaly/autism syndrome (605309), Herman et al. (2007) identified a heterozygous R130X substitution. The substitution occurs in exon 5 of the PTEN gene within the core phosphatase domain of the protein. The child inherited the mutation from his unaffected father. Herman et al. (2007) noted that the boy may develop further clinical manifestations of other PTEN-associated syndromes and emphasized that the family was counseled on the possibility of increased tumor risk in the boy and the mutation-carrying father. (less)
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Pathogenic
(Mar 15, 2007)
|
no assertion criteria provided
Method: literature only
|
COWDEN SYNDROME 1
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000028470.5
First in ClinVar: Apr 04, 2013 Last updated: Dec 15, 2018 |
Comment on evidence:
Cowden Syndrome 1 In a study of Cowden disease (CWS1; 158350), Nelen et al. (1997) found 2 independent occurrences of an arg130-to-ter (R130X) mutation in … (more)
Cowden Syndrome 1 In a study of Cowden disease (CWS1; 158350), Nelen et al. (1997) found 2 independent occurrences of an arg130-to-ter (R130X) mutation in the PTEN gene. The mutation involved a CpG dinucleotide. Zori et al. (1998) described a family in which a mother had Cowden disease and her son had been diagnosed with Bannayan-Riley-Ruvalcaba syndrome. Both were heterozygous for the R130X mutation. The son had been seen at the age of 11 years for severe developmental delay and autistic behavior. In early childhood, rectal bleeding led to removal of a few rectal polyps; the pathology showed benign pseudopolyp with telangiectatic vessels in an inflamed myxoid stroma. His verbal and performance IQs were 40 at 11 years. He developed a goiter at 18 years for which left hemithyroidectomy was performed, and a tumor was also excised from the right side of the thyroid. The left lobe contained insular (follicular) carcinoma while the right showed nodular hyperplasia with a focus of papillary microcarcinoma. At the age of 11 years, the son had multiple pigmented macules on the glands and shaft of the penis. He lacked the second toes. The mother of the patient reported by Zori et al. (1998) had a large head (59.5 cm) and multiple small papules on her tongue and oral mucosa. She had polyposis of the entire gastrointestinal tract. Mammogram showed bilateral fibroglandular tissue with single well-defined benign nodules in each breast with mild dysplasia. Macrocephaly/Autism Syndrome In a 4-year-old boy with macrocephaly/autism syndrome (605309), Herman et al. (2007) identified a heterozygous R130X substitution. The substitution occurs in exon 5 of the PTEN gene within the core phosphatase domain of the protein. The child inherited the mutation from his unaffected father. Herman et al. (2007) noted that the boy may develop further clinical manifestations of other PTEN-associated syndromes and emphasized that the family was counseled on the possibility of increased tumor risk in the boy and the mutation-carrying father. (less)
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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:
germline
|
University Health Network, Princess Margaret Cancer Centre
Accession: SCV001430888.1
First in ClinVar: Aug 29, 2020 Last updated: Aug 29, 2020 |
Comment:
The variant c.388C>T has rarely been reported in general population databases, however, it has been reported as pathogenic in ClinVar by multiple laboratories. It is … (more)
The variant c.388C>T has rarely been reported in general population databases, however, it has been reported as pathogenic in ClinVar by multiple laboratories. It is a loss of function variant that was reported in ClinVar to be associated with Cowden Syndrome (RCV000008263.6) and PTEN hamartoma syndrome (RCV000199099.8). (less)
Clinical Features:
Renal cell carcinoma (present) , Macrocephaly (present) , Thyroid lesions (present)
Age: 20-29 years
Sex: male
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Pathogenic
(Sep 01, 2020)
|
no assertion criteria provided
Method: provider interpretation
|
Rhabdomyosarcoma
Affected status: yes
Allele origin:
germline
|
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Accession: SCV001434381.1
First in ClinVar: Oct 02, 2020 Last updated: Oct 02, 2020 |
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Pathogenic
(-)
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no assertion criteria provided
Method: provider interpretation
|
Abnormal cardiovascular system morphology
Affected status: yes
Allele origin:
somatic
|
MAGI's Lab - Research, MAGI Group
Accession: SCV001437654.1
First in ClinVar: Mar 18, 2021 Last updated: Mar 18, 2021 |
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Likely pathogenic
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001799589.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
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Pathogenic
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
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: SCV001956019.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(Feb 08, 2022)
|
no assertion criteria provided
Method: clinical testing
|
Macrocephaly-autism syndrome
Affected status: yes
Allele origin:
de novo
|
Center for Molecular Medicine, Children’s Hospital of Fudan University
Accession: SCV002073923.1
First in ClinVar: Feb 13, 2022 Last updated: Feb 13, 2022 |
Sex: male
|
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Pathogenic
(Jul 24, 2014)
|
no assertion criteria provided
Method: clinical testing
|
Cowden syndrome
Affected status: unknown
Allele origin:
germline
|
Pathway Genomics
Accession: SCV000189986.1
First in ClinVar: Oct 19, 2014 Last updated: Oct 19, 2014 |
|
|
Likely pathogenic
(Jul 14, 2015)
|
no assertion criteria provided
Method: literature only
|
Neoplasm of brain
(Somatic mutation)
Affected status: yes
Allele origin:
somatic
|
Database of Curated Mutations (DoCM)
Accession: SCV000504380.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
|
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Pathogenic
(Oct 02, 2014)
|
no assertion criteria provided
Method: literature only
|
Neoplasm of ovary
(Somatic mutation)
Affected status: yes
Allele origin:
somatic
|
Database of Curated Mutations (DoCM)
Accession: SCV000504381.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
|
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Pathogenic
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000692010.1
First in ClinVar: Feb 19, 2018 Last updated: Feb 19, 2018 |
|
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Pathogenic
(Dec 01, 2018)
|
no assertion criteria provided
Method: research
|
Neoplasm of ovary
Affected status: yes
Allele origin:
somatic
|
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne
Accession: SCV000923927.1
First in ClinVar: Jun 17, 2019 Last updated: Jun 17, 2019 |
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Pathogenic
(Jul 01, 2021)
|
no assertion criteria provided
Method: research
|
Gastric cancer
Affected status: unknown
Allele origin:
germline
|
Laboratory for Genotyping Development, RIKEN
Accession: SCV002758067.1
First in ClinVar: Apr 15, 2023 Last updated: Apr 15, 2023 |
|
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not provided
(-)
|
no classification provided
Method: literature only
|
Cowden syndrome 1
Affected status: unknown
Allele origin:
germline
|
GeneReviews
Accession: SCV002034735.2
First in ClinVar: Dec 18, 2021 Last updated: Oct 01, 2022 |
Comment:
Recurrent pathogenic variants
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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 |
---|---|---|---|---|
Helicobacter pylori, Homologous-Recombination Genes, and Gastric Cancer. | Usui Y | The New England journal of medicine | 2023 | PMID: 36988593 |
Germline Cancer Predisposition Variants in Pediatric Rhabdomyosarcoma: A Report From the Children's Oncology Group. | Li H | Journal of the National Cancer Institute | 2021 | PMID: 33372952 |
PTEN Hamartoma Tumor Syndrome. | Adam MP | - | 2021 | PMID: 20301661 |
Early-onset renal cell carcinoma in PTEN harmatoma tumour syndrome. | Kim RH | NPJ genomic medicine | 2020 | PMID: 33083010 |
Ovarian Clear Cell Carcinoma in Cowden Syndrome. | Yauy K | Journal of the National Comprehensive Cancer Network : JNCCN | 2019 | PMID: 30659124 |
PTEN-opathies: from biological insights to evidence-based precision medicine. | Yehia L | The Journal of clinical investigation | 2019 | PMID: 30614812 |
A Case Report of Syndromic Multinodular Goitre in Adolescence: Exploring the Phenotype Overlap between Cowden and DICER1 Syndromes. | Bouron-Dal Soglio D | European thyroid journal | 2018 | PMID: 29594054 |
Variant discovery in patients with Mendelian vascular anomalies by next-generation sequencing and their use in patient clinical management. | Mattassi R | Journal of vascular surgery | 2018 | PMID: 28655553 |
A retrospective chart review of the features of PTEN hamartoma tumour syndrome in children. | Hansen-Kiss E | Journal of medical genetics | 2017 | PMID: 28526761 |
Prospective enterprise-level molecular genotyping of a cohort of cancer patients. | MacConaill LE | The Journal of molecular diagnostics : JMD | 2014 | PMID: 25157968 |
Increased prevalence of eosinophilic gastrointestinal disorders in pediatric PTEN hamartoma tumor syndromes. | Henderson CJ | Journal of pediatric gastroenterology and nutrition | 2014 | PMID: 24345843 |
Cancer risk and genotype-phenotype correlations in PTEN hamartoma tumor syndrome. | Nieuwenhuis MH | Familial cancer | 2014 | PMID: 23934601 |
Germline PTEN mutation Cowden syndrome: an underappreciated form of hereditary kidney cancer. | Shuch B | The Journal of urology | 2013 | PMID: 23764071 |
Cognitive characteristics of PTEN hamartoma tumor syndromes. | Busch RM | Genetics in medicine : official journal of the American College of Medical Genetics | 2013 | PMID: 23470840 |
High cumulative risks of cancer in patients with PTEN hamartoma tumour syndrome. | Bubien V | Journal of medical genetics | 2013 | PMID: 23335809 |
Papillary renal cell carcinoma is associated with PTEN hamartoma tumor syndrome. | Mester JL | Urology | 2012 | PMID: 22381246 |
Autoimmunity, intestinal lymphoid hyperplasia, and defects in mucosal B-cell homeostasis in patients with PTEN hamartoma tumor syndrome. | Heindl M | Gastroenterology | 2012 | PMID: 22266152 |
Incidence and clinical characteristics of thyroid cancer in prospective series of individuals with Cowden and Cowden-like syndrome characterized by germline PTEN, SDH, or KLLN alterations. | Ngeow J | The Journal of clinical endocrinology and metabolism | 2011 | PMID: 21956414 |
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 |
The PI3K pathway as drug target in human cancer. | Courtney KD | Journal of clinical oncology : official journal of the American Society of Clinical Oncology | 2010 | PMID: 20085938 |
PTEN and the PI3-kinase pathway in cancer. | Chalhoub N | Annual review of pathology | 2009 | PMID: 18767981 |
Increasing knowledge of PTEN germline mutations: Two additional patients with autism and macrocephaly. | Herman GE | American journal of medical genetics. Part A | 2007 | PMID: 17286265 |
Distinct expression profiles for PTEN transcript and its splice variants in Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome. | Sarquis MS | American journal of human genetics | 2006 | PMID: 16773562 |
PTEN mutations in eight Spanish families and one Brazilian family with Cowden syndrome. | Bussaglia E | The Journal of investigative dermatology | 2002 | PMID: 11918710 |
Enhanced sensitivity of PTEN-deficient tumors to inhibition of FRAP/mTOR. | Neshat MS | Proceedings of the National Academy of Sciences of the United States of America | 2001 | PMID: 11504908 |
The spectrum and evolution of phenotypic findings in PTEN mutation positive cases of Bannayan-Riley-Ruvalcaba syndrome. | Parisi MA | Journal of medical genetics | 2001 | PMID: 11332402 |
PTEN controls tumor-induced angiogenesis. | Wen S | Proceedings of the National Academy of Sciences of the United States of America | 2001 | PMID: 11274365 |
Mutations of the human PTEN gene. | Bonneau D | Human mutation | 2000 | PMID: 10923032 |
A novel PTEN mutation in a Japanese patient with Cowden disease. | Kubo Y | The British journal of dermatology | 2000 | PMID: 10848731 |
Germline PTEN mutation in a family with Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome. | Zori RT | American journal of medical genetics | 1998 | PMID: 9856571 |
Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation. | Marsh DJ | Human molecular genetics | 1998 | PMID: 9467011 |
Germline mutations in the PTEN/MMAC1 gene in patients with Cowden disease. | Nelen MR | Human molecular genetics | 1997 | PMID: 9259288 |
http://docm.genome.wustl.edu/variants/ENST00000371953:c.388C>T | - | - | - | - |
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Text-mined citations for rs121909224 ...
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.