10-87933147-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000314.8(PTEN):c.388C>T(p.Arg130Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000274 in 1,461,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. R130R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: PTEN NM_000314.8 stop_gained
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:41 O:1
• Conservation: PhyloP100: 5.57

Genes affected

PTEN (HGNC:9588): (phosphatase and tensin homolog) This gene was identified as a tumor suppressor that is mutated in a large number of cancers at high frequency. The protein encoded by this gene is a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It contains a tensin like domain as well as a catalytic domain similar to that of the dual specificity protein tyrosine phosphatases. Unlike most of the protein tyrosine phosphatases, this protein preferentially dephosphorylates phosphoinositide substrates. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/PKB signaling pathway. The use of a non-canonical (CUG) upstream initiation site produces a longer isoform that initiates translation with a leucine, and is thought to be preferentially associated with the mitochondrial inner membrane. This longer isoform may help regulate energy metabolism in the mitochondria. A pseudogene of this gene is found on chromosome 9. Alternative splicing and the use of multiple translation start codons results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 10-87933147-C-T is Pathogenic according to our data. Variant chr10-87933147-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 7819.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-87933147-C-T is described in Lovd as [Likely_pathogenic]. Variant chr10-87933147-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTEN	NM_000314.8	c.388C>T	p.Arg130Ter	stop_gained	5/9	ENST00000371953.8
PTEN	NM_001304717.5	c.907C>T	p.Arg303Ter	stop_gained	6/10
PTEN	NM_001304718.2	c.-363C>T		5_prime_UTR_variant	4/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTEN	ENST00000371953.8	c.388C>T	p.Arg130Ter	stop_gained	5/9	1	NM_000314.8	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.0000119 AC: 3 AN: 251384 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135856

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461670 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727136

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:41 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cowden syndrome 1 Pathogenic:11 Other:1

Pathogenic, no assertion criteria provided	clinical testing	Pathway Genomics	Jul 24, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Oct 12, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Oct 13, 2016	- -
not provided, no classification provided	literature only	GeneReviews	-	Recurrent pathogenic variants -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Aug 09, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jun 22, 2023	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). -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Apr 05, 2023	This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	Oct 07, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	DASA	Jan 05, 2022	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. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 15, 2007	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Feb 23, 2023	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. -

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 01, 2019	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. -
Likely pathogenic, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 26, 2019	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 18, 2021	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) -

PTEN hamartoma tumor syndrome Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Herman Laboratory, Nationwide Children's Hospital	Mar 01, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 02, 2018	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 07, 2024	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital	Jan 28, 2020	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). -
Pathogenic, no assertion criteria provided	clinical testing	University Health Network, Princess Margaret Cancer Centre	-	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). -

Macrocephaly-autism syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 25, 2023	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). -
Pathogenic, no assertion criteria provided	clinical testing	Center for Molecular Medicine, Children’s Hospital of Fudan University	Feb 08, 2022	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 15, 2007	- -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 21, 2021	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 08, 2021	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Jun 14, 2019	- -

Glioma susceptibility 2 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Genomics England Pilot Project, Genomics England	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 09, 2021	- -

Neoplasm of ovary Pathogenic:2

Pathogenic, no assertion criteria provided	research	German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne	Dec 01, 2018	- -
Pathogenic, no assertion criteria provided	literature only	Database of Curated Mutations (DoCM)	Oct 02, 2014	- -

PTEN-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 08, 2023

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. -

Rhabdomyosarcoma Pathogenic:1

Pathogenic, no assertion criteria provided

provider interpretation

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Sep 01, 2020

- -

Gastric cancer Pathogenic:1

Pathogenic, no assertion criteria provided

research

Laboratory for Genotyping Development, RIKEN

Jul 01, 2021

- -

Malignant tumor of prostate;C1854416:Macrocephaly-autism syndrome;C2751642:Glioma susceptibility 2;C3551915:Familial meningioma;CN072330:Cowden syndrome 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Mar 15, 2022

- -

Macrocephaly-autism syndrome;CN072330:Cowden syndrome 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn

Aug 11, 2023

- -

Abnormal cardiovascular system morphology Pathogenic:1

Pathogenic, no assertion criteria provided

provider interpretation

MAGI's Lab - Research, MAGI Group

-

- -

Neoplasm of brain Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Database of Curated Mutations (DoCM)

Jul 14, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.63
Cadd	Pathogenic	42
Dann	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.95
FATHMM_MKL	Uncertain	0.95	D
MutationTaster	Benign	1.0	A
Vest4		0.97
GERP RS		5.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs121909224; hg19: chr10-89692904; COSMIC: COSV64288463;