NM_000314.8(PTEN):c.1206A>C (p.Lys402Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Nov 22, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001010303.5

Allele description [Variation Report for NM_000314.8(PTEN):c.1206A>C (p.Lys402Asn)]

NM_000314.8(PTEN):c.1206A>C (p.Lys402Asn)

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.1206A>C (p.Lys402Asn)

HGVS:

NC_000010.11:g.87965466A>C
NG_007466.2:g.107028A>C
NM_000314.8:c.1206A>CMANE SELECT
NM_001304717.5:c.1725A>C
NM_001304718.2:c.615A>C
NP_000305.3:p.Lys402Asn
NP_001291646.4:p.Lys575Asn
NP_001291647.1:p.Lys205Asn
LRG_311t1:c.1206A>C
LRG_311:g.107028A>C
NC_000010.10:g.89725223A>C
NM_000314.4:c.1206A>C
NM_000314.6:c.1206A>C

Protein change:

K205N

Links:

dbSNP: rs1064796017

NCBI 1000 Genomes Browser:

rs1064796017

Molecular consequence:

NM_000314.8:c.1206A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001304717.5:c.1725A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001304718.2:c.615A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001170478	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 22, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29706350, 32350270 Citation Link,
SCV001360136	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 13, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001170478

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 22, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV001360136

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jun 13, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

A Saturation Mutagenesis Approach to Understanding PTEN Lipid Phosphatase Activity and Genotype-Phenotype Relationships.

Mighell TL, Evans-Dutson S, O'Roak BJ.

Am J Hum Genet. 2018 May 3;102(5):943-955. doi: 10.1016/j.ajhg.2018.03.018. Epub 2018 Apr 26.

PubMed [citation]

PMID:: 29706350
PMCID:: PMC5986715

Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction.

Post KL, Belmadani M, Ganguly P, Meili F, Dingwall R, McDiarmid TA, Meyers WM, Herrington C, Young BP, Callaghan DB, Rogic S, Edwards M, Niciforovic A, Cau A, Rankin CH, O'Connor TP, Bamji SX, Loewen CJR, Allan DW, Pavlidis P, Haas K.

Nat Commun. 2020 Apr 29;11(1):2073. doi: 10.1038/s41467-020-15943-0.

PubMed [citation]

PMID:: 32350270
PMCID:: PMC7190743

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV001170478.4

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

Description

The p.K402N variant (also known as c.1206A>C), located in coding exon 9 of the PTEN gene, results from an A to C substitution at nucleotide position 1206. The lysine at codon 402 is replaced by asparagine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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

From Color Diagnostics, LLC DBA Color Health, SCV001360136.1

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

#	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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