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NM_002834.5(PTPN11):c.171_173del (p.Gln57_Asn58delinsHis) AND RASopathy

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 13, 2022
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:
RCV003041131.3

Allele description [Variation Report for NM_002834.5(PTPN11):c.171_173del (p.Gln57_Asn58delinsHis)]

NM_002834.5(PTPN11):c.171_173del (p.Gln57_Asn58delinsHis)

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.171_173del (p.Gln57_Asn58delinsHis)
HGVS:
  • NC_000012.12:g.112450351_112450353del
  • NG_007459.1:g.36620_36622del
  • NM_001330437.2:c.171_173del
  • NM_001374625.1:c.168_170del
  • NM_002834.5:c.171_173delMANE SELECT
  • NM_080601.3:c.171_173del
  • NP_001317366.1:p.Gln57_Asn58delinsHis
  • NP_001361554.1:p.Gln56_Asn57delinsHis
  • NP_002825.3:p.Gln57_Asn58delinsHis
  • NP_002825.3:p.Gln57_Asn58delinsHis
  • NP_542168.1:p.Gln57_Asn58delinsHis
  • LRG_614t1:c.171_173del
  • LRG_614:g.36620_36622del
  • LRG_614p1:p.Gln57_Asn58delinsHis
  • NC_000012.11:g.112888154_112888156del
  • NC_000012.11:g.112888155_112888157del
  • NM_002834.3:c.171_173delGAA
Molecular consequence:
  • NM_001330437.2:c.171_173del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001374625.1:c.168_170del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_002834.5:c.171_173del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_080601.3:c.171_173del - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

Name:
RASopathy
Synonyms:
rasopathies; Noonan spectrum disorder
Identifiers:
MONDO: MONDO:0021060; MedGen: C5555857

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003354002Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Jun 13, 2022)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003354002.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has been observed in individual(s) with clinical features of Noonan syndrome (Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This variant, c.171_173del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the PTPN11 protein (p.Gln57_Asn58delinsHis).

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

Last Updated: Sep 29, 2024