NM_002834.5(PTPN11):c.762ACA[2] (p.Gln257del) AND Noonan syndrome 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 19, 2019
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000991102.1

Allele description [Variation Report for NM_002834.5(PTPN11):c.762ACA[2] (p.Gln257del)]

NM_002834.5(PTPN11):c.762ACA[2] (p.Gln257del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

12q24.13

Genomic location:

Preferred name:

NM_002834.5(PTPN11):c.762ACA[2] (p.Gln257del)

HGVS:

NC_000012.12:g.112472949ACA[2]
NC_000012.12:g.112472949_112472951ACA[2]
NG_007459.1:g.59218ACA[2]
NM_001330437.2:c.762ACA[2]
NM_001374625.1:c.759ACA[2]
NM_002834.3:c.768_770del
NM_002834.5:c.762ACA[2]MANE SELECT
NM_080601.3:c.762ACA[2]
NP_001317366.1:p.Gln257del
NP_001361554.1:p.Gln256del
NP_002825.3:p.Gln257del
NP_542168.1:p.Gln257del
LRG_614t1:c.768_770del
LRG_614:g.59218ACA[2]
NC_000012.11:g.112910753ACA[2]
NC_000012.11:g.112910753_112910755del
NM_002834.4:c.768_770delACA
NM_002834.5:c.768_770delMANE SELECT

Protein change:

Q256del

Links:

dbSNP: rs397507524

Molecular consequence:

NM_001330437.2:c.762ACA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374625.1:c.759ACA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_002834.5:c.762ACA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_080601.3:c.762ACA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]

Observations:

Condition(s)

Name:: Noonan syndrome 1 (NS1)
Synonyms:: FEMALE PSEUDO-TURNER SYNDROME; TURNER PHENOTYPE WITH NORMAL KARYOTYPE; PTPN11-Related Noonan Syndrome
Identifiers:: MONDO: MONDO:0008104; MedGen: C4551602; Orphanet: 648; OMIM: 163950

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001132049	Department of Human Genetics, University Hospital Magdeburg	no assertion criteria provided	Uncertain significance (Dec 19, 2019)	paternal	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001132049

Department of Human Genetics, University Hospital Magdeburg

no assertion criteria provided

Uncertain significance
(Dec 19, 2019)

paternal

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	paternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Department of Human Genetics, University Hospital Magdeburg, SCV001132049.1

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

Description

We found the variant in an affected girl. Her father also carries the variant, but is not affected. However, Noonan syndrome may be subtle in adults and clinical variation within families has been described. Two alleles were reported in gnomAD (AF 8.081e-6). Biochemical and functional studies show an activating effect, but not as strongly as for the Q257dup mutation.

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

Last Updated: Apr 12, 2026

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