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NM_002834.5(PTPN11):c.1379+6A>G AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 24, 2017
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:
RCV000590231.1

Allele description [Variation Report for NM_002834.5(PTPN11):c.1379+6A>G]

NM_002834.5(PTPN11):c.1379+6A>G

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.1379+6A>G
HGVS:
  • NC_000012.12:g.112486635A>G
  • NG_007459.1:g.72904A>G
  • NM_001330437.2:c.1391+6A>G
  • NM_001374625.1:c.1376+6A>G
  • NM_002834.5:c.1379+6A>GMANE SELECT
  • NM_080601.3:c.*2A>G
  • LRG_614t1:c.1379+6A>G
  • LRG_614:g.72904A>G
  • NC_000012.11:g.112924439A>G
  • NM_002834.3:c.1379+6A>G
Links:
dbSNP: rs746958309
NCBI 1000 Genomes Browser:
rs746958309
Molecular consequence:
  • NM_080601.3:c.*2A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001330437.2:c.1391+6A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374625.1:c.1376+6A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_002834.5:c.1379+6A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000698053Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Jul 24, 2017) 		germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698053.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The PTPN11 c.1379+6A>G variant involves the alteration of a non-conserved intronic nucleotide and 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 3/274018 control chromosomes at a frequency of 0.0000109, which does not exceed the estimated maximal expected allele frequency of a pathogenic PTPN11 variant (0.0000625). The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a "Variant of Uncertain Significance (VUS)," until additional information becomes available.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 16, 2025