NM_002834.5(PTPN11):c.226G>C (p.Glu76Gln) AND Noonan syndrome 1

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Mar 26, 2024
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:: RCV002288669.4

Allele description [Variation Report for NM_002834.5(PTPN11):c.226G>C (p.Glu76Gln)]

NM_002834.5(PTPN11):c.226G>C (p.Glu76Gln)

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.226G>C (p.Glu76Gln)

Other names:

p.E76Q:GAG>CAG

HGVS:

NC_000012.12:g.112450406G>C
NG_007459.1:g.36675G>C
NM_001330437.2:c.226G>C
NM_001374625.1:c.223G>C
NM_002834.5:c.226G>CMANE SELECT
NM_080601.3:c.226G>C
NP_001317366.1:p.Glu76Gln
NP_001361554.1:p.Glu75Gln
NP_002825.3:p.Glu76Gln
NP_542168.1:p.Glu76Gln
LRG_614t1:c.226G>C
LRG_614:g.36675G>C
NC_000012.11:g.112888210G>C
NM_002834.3:c.226G>C
NM_002834.4:c.226G>C
NM_002834.5:c.226G>C

Protein change:

E75Q

Links:

dbSNP: rs121918464

NCBI 1000 Genomes Browser:

rs121918464

Molecular consequence:

NM_001330437.2:c.226G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.223G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.226G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_080601.3:c.226G>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV002581080	MGZ Medical Genetics Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 7, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004806648	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 26, 2024)	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

SCV002581080

MGZ Medical Genetics Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 7, 2022)

germline

clinical testing

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

SCV004806648

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 26, 2024)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing
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 MGZ Medical Genetics Center, SCV002581080.1

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

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004806648.1

#	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: Aug 4, 2024

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