NM_000314.8(PTEN):c.1212A>C (p.Ter404Cys) AND PTEN hamartoma tumor syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 21, 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:: RCV002523438.3

Allele description [Variation Report for NM_000314.8(PTEN):c.1212A>C (p.Ter404Cys)]

NM_000314.8(PTEN):c.1212A>C (p.Ter404Cys)

Gene:

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.8(PTEN):c.1212A>C (p.Ter404Cys)

Other names:

*404C; *577C; *207C

HGVS:

NC_000010.11:g.87965472A>C
NG_007466.2:g.107034A>C
NM_000314.8:c.1212A>CMANE SELECT
NM_001304717.5:c.1731A>C
NM_001304718.2:c.621A>C
NP_000305.3:p.Ter404Cys
NP_001291646.4:p.Ter577Cys
NP_001291647.1:p.Ter207Cys
LRG_311t1:c.1212A>C
LRG_311:g.107034A>C
NC_000010.10:g.89725229A>C
NM_000314.4:c.1212A>C

Links:

dbSNP: rs876660879

NCBI 1000 Genomes Browser:

rs876660879

Molecular consequence:

NM_000314.8:c.1212A>C - stop lost - [Sequence Ontology: SO:0001578]
NM_001304717.5:c.1731A>C - stop lost - [Sequence Ontology: SO:0001578]
NM_001304718.2:c.621A>C - stop lost - [Sequence Ontology: SO:0001578]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003223136	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 21, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31594918, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003223136

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 21, 2022)

germline

clinical testing

PubMed (2)
[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

Neurobehavioral phenotype of autism spectrum disorder associated with germline heterozygous mutations in PTEN.

Busch RM, Srivastava S, Hogue O, Frazier TW, Klaas P, Hardan A, Martinez-Agosto JA, Sahin M, Eng C; Developmental Synaptopathies Consortium..

Transl Psychiatry. 2019 Oct 8;9(1):253. doi: 10.1038/s41398-019-0588-1.

PubMed [citation]

PMID:: 31594918
PMCID:: PMC6783427

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003223136.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 428265). This protein extension has been observed in individual(s) with autism spectrum disorder (PMID: 31594918). This variant is not present in population databases (gnomAD no frequency). This sequence change disrupts the translational stop signal of the PTEN mRNA. It is expected to extend the length of the PTEN protein by 8 additional amino acid residues.

#	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: Sep 29, 2024

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