NM_002834.5(PTPN11):c.990A>C (p.Thr330=) AND not specified

Germline classification:: Likely benign (4 submissions)
Last evaluated:: Aug 30, 2020
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:: RCV000220386.22

Allele description [Variation Report for NM_002834.5(PTPN11):c.990A>C (p.Thr330=)]

NM_002834.5(PTPN11):c.990A>C (p.Thr330=)

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.990A>C (p.Thr330=)

Other names:

p.T330T

HGVS:

NC_000012.12:g.112477913A>C
NG_007459.1:g.64182A>C
NM_001330437.2:c.990A>C
NM_001374625.1:c.987A>C
NM_002834.5:c.990A>CMANE SELECT
NM_080601.3:c.990A>C
NP_001317366.1:p.Thr330=
NP_001361554.1:p.Thr329=
NP_002825.3:p.Thr330=
NP_542168.1:p.Thr330=
LRG_614t1:c.990A>C
LRG_614:g.64182A>C
NC_000012.11:g.112915717A>C
NM_002834.3:c.990A>C
NM_002834.4:c.990A>C
p.Thr330Thr

Links:

dbSNP: rs369739920

NCBI 1000 Genomes Browser:

rs369739920

Molecular consequence:

NM_001330437.2:c.990A>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001374625.1:c.987A>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_002834.5:c.990A>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_080601.3:c.990A>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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RecName: Full=Initiator protein NS1; Short=NS1; AltName: Full=NCVP1; AltName: Fu...
RecName: Full=Initiator protein NS1; Short=NS1; AltName: Full=NCVP1; AltName: Full=Non-capsid protein NS-1; AltName: Full=Non-structural protein 1; AltName: Full=Non-structural protein NS1
gi|138881|sp|P07298.1|NS1_PAVHU

Protein
Papilionoidea
Papilionoidea
ButterflyNet

BioProject
BioProject Links for Nucleotide (Select 2569174934) (1)
BioProject
mct-1 protein, partial [Eroessa chiliensis]
mct-1 protein, partial [Eroessa chiliensis]
gi|2569178155|gb|WMI16998.1|

Protein
Eroessa chiliensis voucher CCNY:HB-18-C009 ras-related GTP binding protein gene,...
Eroessa chiliensis voucher CCNY:HB-18-C009 ras-related GTP binding protein gene, partial cds
gi|2569164964|gb|OL150143.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000270777	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Jan 29, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000309218	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000698088	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Aug 30, 2020)	germline	clinical testing	Citation Link,
SCV002068880	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 4, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	1	1	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

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000270777.3

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

Description

p.Thr330Thr in exon 9 of PTPN11: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 2/11546 Latino an d 2/8650 East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http: //exac.broadinstitute.org; dbSNP rs369739920).

#	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		1	not provided	1	not provided

From PreventionGenetics, part of Exact Sciences, SCV000309218.1

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698088.3

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

#	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 Genetic Services Laboratory, University of Chicago, SCV002068880.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 25, 2024

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