NC_000010.11:g.(?_87863161)_(88948936_?)del AND PTEN hamartoma tumor syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 7, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001032107.2

Allele description [Variation Report for NC_000010.11:g.(?_87863161)_(88948936_?)del]

NC_000010.11:g.(?_87863161)_(88948936_?)del

Genes:

STAMBPL1:STAM binding protein like 1 [Gene - OMIM - HGNC]
ACTA2:actin alpha 2, smooth muscle [Gene - OMIM - HGNC]
ANKRD22:ankyrin repeat domain 22 [Gene - HGNC]
KLLN:killin, p53 regulated DNA replication inhibitor [Gene - OMIM - HGNC]
LIPF:lipase F, gastric type [Gene - OMIM - HGNC]
LIPJ:lipase family member J [Gene - OMIM - HGNC]
LIPK:lipase family member K [Gene - OMIM - HGNC]
LIPM:lipase family member M [Gene - OMIM - HGNC]
LIPN:lipase family member N [Gene - OMIM - HGNC]
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
RNLS:renalase, FAD dependent amine oxidase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q23.31

Genomic location:

Chr10: 89622918 - 90708693 (on Assembly GRCh37)

Preferred name:

NC_000010.11:g.(?_87863161)_(88948936_?)del

HGVS:

NC_000010.11:g.(?_87863161)_(88948936_?)del
NC_000010.10:g.(?_89622918)_(90708693_?)del

Condition(s)

Name:: PTEN hamartoma tumor syndrome (PHTS)
Synonyms:: PTEN Hamartomatous Tumour Syndrome; PTEN-related disorders
Identifiers:: MONDO: MONDO:0017623; MeSH: D006223; MedGen: C1959582

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001195414	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 7, 2022)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 9467011, 21194675, 18456716, 21926107, 22382802, 23132533, 23335809, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001195414

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 7, 2022)

germline

clinical testing

PubMed (8)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation.

Marsh DJ, Coulon V, Lunetta KL, Rocca-Serra P, Dahia PL, Zheng Z, Liaw D, Caron S, Duboué B, Lin AY, Richardson AL, Bonnetblanc JM, Bressieux JM, Cabarrot-Moreau A, Chompret A, Demange L, Eeles RA, Yahanda AM, Fearon ER, Fricker JP, Gorlin RJ, Hodgson SV, et al.

Hum Mol Genet. 1998 Mar;7(3):507-15.

PubMed [citation]

PMID:: 9467011

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, Mester J, Peterson C, Yang Y, Chen JL, Rybicki LA, Milas K, Pederson H, Remzi B, Orloff MS, Eng C.

Am J Hum Genet. 2011 Jan 7;88(1):42-56. doi: 10.1016/j.ajhg.2010.11.013. Epub 2010 Dec 30.

PubMed [citation]

PMID:: 21194675
PMCID:: PMC3014373

See all PubMed Citations (8)

Details of each submission

From Invitae, SCV001195414.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the PTEN gene has been identified. Loss-of-function variants in PTEN are known to be pathogenic (PMID: 9467011, 21194675). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. A similar copy number variant has been observed in individual(s) with PTEN hamartoma tumor syndrome (PMID: 18456716, 21926107, 22382802, 23132533, 23335809). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 21, 2023

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