10-87933037-A-G

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Very_Strong

The NM_000314.8(PTEN):c.278A>G(p.His93Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H93P) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PTEN NM_000314.8 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:8
• Conservation: PhyloP100: 8.87

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 19 ACMG points.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 14 uncertain in NM_000314.8
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr10-87933037-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 468680.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP2: Missense variant where missense usually causes diseases, PTEN
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.99
• PP5: Variant 10-87933037-A-G is Pathogenic according to our data. Variant chr10-87933037-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 7848.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr10-87933037-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTEN	NM_000314.8	c.278A>G	p.His93Arg	missense_variant	5/9	ENST00000371953.8
PTEN	NM_001304717.5	c.797A>G	p.His266Arg	missense_variant	6/10
PTEN	NM_001304718.2	c.-473A>G		5_prime_UTR_variant	4/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTEN	ENST00000371953.8	c.278A>G	p.His93Arg	missense_variant	5/9	1	NM_000314.8	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: reviewed by expert panel

Submissions by phenotype

PTEN hamartoma tumor syndrome Pathogenic:3

Pathogenic, reviewed by expert panel	curation	Clingen PTEN Variant Curation Expert Panel, Clingen	Nov 28, 2018	PTEN c.278A>G (p.His93Arg) 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). PS2: De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. (internal laboratory contributor(s) ClinVar Organization ID: 26957) PM1: Located at a residue within a catalytic motif as defined by the ClinGen PTEN Expert Panel. 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. PS3_P: Abnormal in vitro cellular assay or transgenic model with phenotype different from wild type that does not meet PS3. (PMID 26579216, 25647146, 20718038, 21828076, 29373119, 29785012, 29706350) PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID 15805158, internal laboratory contributor(s) ClinVar Organization ID: 26957) -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Sep 02, 2021	This sequence change replaces histidine with arginine at codon 93 of the PTEN protein (p.His93Arg). The histidine residue is highly conserved and there is a small physicochemical difference between histidine and arginine. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.His93 amino acid residue in PTEN. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9685848, 10866302, 21828076, 24778394). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Experimental studies have shown that this missense change affects PTEN function (PMID: 20718038, 21828076, 22505997, 25647146, 26579216). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 7848). This missense change has been observed in individuals with clinical features of PTEN hamartoma tumor syndrome (PMID: 15805158, 24345843, 25647146). This variant is not present in population databases (ExAC no frequency). -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 11, 2020	The p.His93Arg variant in PTEN has been reported in 2 individuals with clinical features of PTEN-associated disorders, including 1 de novo case with confirmed maternity and paternity (Butler 2005, Henderson 2014). It was absent from large population studies. Several in vitro and in vivo functional studies support an impact on protein function (Redfern 2010, Rodriguez-Escudero 2011, He 2015, Johnston 2015, Fricano-Kugler 2018, Matreyek 2018). In addition, computational prediction tools and conservation analyses are consistent with pathogenicity. Additionally, this variant was classified as pathogenic on 11/28/18 by the ClinGen-approved PTEN variant expert panel (Variation ID 7848). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant PTEN Hamartoma Tumor Syndrome. ACMG/AMP Criteria applied: PS2, PM2, PP2, PP3, PS3_Supporting, PS4_Supporting. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 09, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -

Cowden syndrome 1 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Sep 26, 2023

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 32350270, 20718038, 25647146]. This variant is expected to disrupt protein structure [Myriad internal data]. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 30, 2022

The p.H93R variant (also known as c.278A>G), located in coding exon 5 of the PTEN gene, results from an A to G substitution at nucleotide position 278. The histidine at codon 93 is replaced by arginine, an amino acid with highly similar properties. In one study, this alteration was detected as a de novo occurrence (paternity confirmed) in an individual with macrocephaly (+8SD), macrosomia, severe speech delay, autistic behavior, adenoidectomy, ear infections, mild bilateral epicanthal folds, and a flattened nasal bridge (Butler MG et al. J. Med. Genet., 2005 Apr;42:318-21). This alteration has also been detected in an individual with PHTS (PTEN hamartoma tumor syndrome) and EGID (eosinophilic gastrointestinal disorders) (Henderson CJ et al. J. Pediatr. Gastroenterol. Nutr., 2014 May;58:553-60). In a massively parallel functional assay using a humanized yeast model, lipid phosphatase activity for this variant was defined as "wild-type like" (Mighell TL et al. Am J Hum Genet, 2018 May;102:943-955), and this variant demonstrated "possibly wild-type like" intracellular protein abundance on one multiplex functional assay (Matreyek KA et al. Nat Genet, 2018 Jun;50:874-882). However, in multiple other functional studies performed on this alteration, authors have found that this alteration reduces phosphatase activity (but does not completely eliminate it), reduces PTEN enzyme activity, and impacts membrane binding (Redfern RE et al. Protein Sci., 2010 Oct;19:1948-56; Rodríguez-Escudero I et al. Hum. Mol. Genet., 2011 Nov;20:4132-42; Johnston SB et al. Biochemistry, 2015 Feb;54:1576-82). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Macrocephaly-autism syndrome Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Apr 01, 2005

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.61
Cadd	Pathogenic	31
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.92	D
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.93	D
M_CAP	Pathogenic	0.85	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.4	M
MutationTaster	Benign	1.0	A
PrimateAI	Pathogenic	0.88	D
PROVEAN	Pathogenic	-7.5	D
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.94
MutPred		0.88		Loss of catalytic residue at D92 (P = 0.1258);
MVP		1.0
MPC		2.5
ClinPred		1.0	D
GERP RS		5.1
Varity_R		0.94
gMVP		0.99

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: rs121909238; hg19: chr10-89692794; COSMIC: COSV64296545;