NM_002834.5(PTPN11):c.1678C>T (p.Leu560Phe) AND Noonan syndrome and Noonan-related syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 12, 2016
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:: RCV001813327.3

Allele description [Variation Report for NM_002834.5(PTPN11):c.1678C>T (p.Leu560Phe)]

NM_002834.5(PTPN11):c.1678C>T (p.Leu560Phe)

Gene:

PTPN11:protein tyrosine phosphatase non-receptor type 11 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q24.13

Genomic location:

Preferred name:

NM_002834.5(PTPN11):c.1678C>T (p.Leu560Phe)

Other names:

p.L560F:CTC>TTC; NM_002834.4(PTPN11):c.1678C>T

HGVS:

NC_000012.12:g.112502222C>T
NG_007459.1:g.88491C>T
NM_001330437.2:c.1690C>T
NM_001374625.1:c.1675C>T
NM_002834.5:c.1678C>TMANE SELECT
NP_001317366.1:p.Leu564Phe
NP_001361554.1:p.Leu559Phe
NP_002825.3:p.Leu560Phe
LRG_614t1:c.1678C>T
LRG_614:g.88491C>T
NC_000012.11:g.112940026C>T
NM_002834.3:c.1678C>T
NM_002834.4:c.1678C>T
c.1678C>T

Protein change:

L559F

Links:

dbSNP: rs397516797

Molecular consequence:

NM_001330437.2:c.1690C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.1675C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.1678C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Noonan syndrome and Noonan-related syndrome
Identifiers:: MONDO: MONDO:0020297; MedGen: C5681679; Orphanet: 98733

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002060838	Genome Diagnostics Laboratory, The Hospital for Sick Children	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 12, 2016)	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

SCV002060838

Genome Diagnostics Laboratory, The Hospital for Sick Children

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 12, 2016)

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genome Diagnostics Laboratory, The Hospital for Sick Children, SCV002060838.1

#	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: Apr 12, 2026

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