NM_000314.8(PTEN):c.-910T>C AND PTEN hamartoma tumor syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jul 25, 2018
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000758225.9

Allele description [Variation Report for NM_000314.8(PTEN):c.-910T>C]

NM_000314.8(PTEN):c.-910T>C

Genes:

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
LOC130004273:ATAC-STARR-seq lymphoblastoid silent region 2585 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.8(PTEN):c.-910T>C

HGVS:

NC_000010.11:g.87863560T>C
NG_007466.2:g.5123T>C
NG_033079.1:g.4878A>G
NG_183718.1:g.281T>C
NM_000314.4:c.-909T>C
NM_000314.6:c.-909T>C
NM_001304717.4:c.-390T>C
NM_001304718.1:c.-1614T>C
LRG_311t1:c.-909T>C
LRG_1087:g.4878A>G
LRG_311:g.5123T>C
NC_000010.10:g.89623317T>C
NM_000314.8:c.-910T>CMANE SELECT
c.-910T>C[hg19]

Links:

dbSNP: rs550385924

NCBI 1000 Genomes Browser:

rs550385924

Condition(s)

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

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putative sugar porter [[Candida] hispaniensis]
putative sugar porter [[Candida] hispaniensis]
gi|1119198162|emb|SIP56070.1|

Protein
protein canopy homolog 2 precursor [Mus musculus]
protein canopy homolog 2 precursor [Mus musculus]
gi|2716983413|ref|NP_001416159.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000886860	Clingen PTEN Variant Curation Expert Panel, Clingen	reviewed by expert panel (ClinGen PTEN ACMG Specifications v1)	Likely benign (Jul 25, 2018)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000886860

Clingen PTEN Variant Curation Expert Panel, Clingen

reviewed by expert panel

(ClinGen PTEN ACMG Specifications v1)

Likely benign
(Jul 25, 2018)

germline

curation

Citation Link

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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	curation

Details of each submission

From Clingen PTEN Variant Curation Expert Panel, Clingen, SCV000886860.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

PTEN c.-909T>C (NC_000010.10:g.87863560T>C) meets criteria to be classified as likely benign 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). BP2: Observed in trans with a pathogenic or likely pathogenic PTEN variant. (internal laboratory contributor ClinVar Organization ID 19864) BP5: Variant found in multiple cases with alternate molecular basis for disease. (internal laboratory contributors SCV000185347.1, SCV000149485.5)

#	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: Nov 3, 2024

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