NM_002834.5(PTPN11):c.179_181del (p.Gly60del) AND Noonan syndrome 1

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jul 1, 2004
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:: RCV000014274.6

Allele description [Variation Report for NM_002834.5(PTPN11):c.179_181del (p.Gly60del)]

NM_002834.5(PTPN11):c.179_181del (p.Gly60del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

12q24.13

Genomic location:

Preferred name:

NM_002834.5(PTPN11):c.179_181del (p.Gly60del)

HGVS:

NC_000012.12:g.112450359_112450361del
NG_007459.1:g.36628_36630del
NM_001330437.2:c.179_181del
NM_001374625.1:c.176_178del
NM_002834.5:c.179_181delMANE SELECT
NM_080601.3:c.179_181del
NP_001317366.1:p.Gly60del
NP_001361554.1:p.Gly59del
NP_002825.3:p.Gly60del
NP_542168.1:p.Gly60del
LRG_614t1:c.179_181del
LRG_614:g.36628_36630del
NC_000012.11:g.112888161_112888163del
NC_000012.11:g.112888163_112888165del
NM_002834.3:c.179_181delGTG

Protein change:

G59del

Links:

OMIM: 176876.0024; dbSNP: rs80338836

NCBI 1000 Genomes Browser:

rs80338836

Molecular consequence:

NM_001330437.2:c.179_181del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374625.1:c.176_178del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_002834.5:c.179_181del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_080601.3:c.179_181del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Noonan syndrome 1 (NS1)
Synonyms:: Turner Syndrome, Male; Turner phenotype with normal karyotype; Female pseudo-Turner 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
SCV000034523	OMIM	no assertion criteria provided	Pathogenic (Jul 1, 2004)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000040936	GeneReviews	no classification provided	not provided	unknown	literature only	PubMed (2) [See all records that cite these PMIDs] 15240615, 20301303

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000034523

OMIM

no assertion criteria provided

Pathogenic
(Jul 1, 2004)

germline

literature only

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

SCV000040936

GeneReviews

no classification provided

not provided

unknown

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Protein-tyrosine phosphatase, nonreceptor type 11 mutation analysis and clinical assessment in 45 patients with Noonan syndrome.

Yoshida R, Hasegawa T, Hasegawa Y, Nagai T, Kinoshita E, Tanaka Y, Kanegane H, Ohyama K, Onishi T, Hanew K, Okuyama T, Horikawa R, Tanaka T, Ogata T.

J Clin Endocrinol Metab. 2004 Jul;89(7):3359-64.

PubMed [citation]

PMID:: 15240615

Noonan Syndrome.

Roberts AE.

2001 Nov 15 [updated 2022 Feb 17]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 20301303

Details of each submission

From OMIM, SCV000034523.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a Japanese patient with Noonan syndrome (NS1; 163950), Yoshida et al. (2004) identified a 3-bp deletion in exon 3 of the PTPN11 gene, 181delGTG, that resulted in deletion of the gly60 codon in the N-SH2 domain of the protein. Because gly60 is directly involved in the N-SH2/PTP interaction, loss of this residue was predicted to disrupt N-SH2/PTP binding, activating the phosphatase function. Yoshida et al. (2004) stated that 181delGTG was the sole deletion mutation identified in the PTPN11 gene to that time.

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

From GeneReviews, SCV000040936.3

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

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

Last Updated: Sep 29, 2024

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