Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_002834.5(PTPN11):c.1620C>T (p.His540=)

Help
Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 27, 2018
Accession:
VCV000138842.4
Variation ID:
138842
Description:
single nucleotide variant
Help

NM_002834.5(PTPN11):c.1620C>T (p.His540=)

Allele ID
142545
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q24.13
Genomic location
12: 112502164 (GRCh38) GRCh38 UCSC
12: 112939968 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.112939968C>T
NC_000012.12:g.112502164C>T
NG_007459.1:g.88433C>T
... more HGVS
Protein change
-
Other names
p.H540H:CAC>CAT
Canonical SPDI
NC_000012.12:112502163:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00006
The Genome Aggregation Database (gnomAD), exomes 0.00003
Links
ClinGen: CA273711
dbSNP: rs587781132
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Oct 22, 2013 RCV000127656.2
Likely benign 1 criteria provided, single submitter Dec 27, 2018 RCV000543306.2
Likely benign 1 criteria provided, single submitter Dec 25, 2018 RCV001474997.1
Likely benign 1 no assertion criteria provided Mar 14, 2013 RCV000157005.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PTPN11 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
549 563

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Oct 22, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171235.11
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Dec 27, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000659036.2
Submitted: (Mar 14, 2019)
Evidence details
Likely benign
(Dec 25, 2018)
criteria provided, single submitter
Method: clinical testing
Rasopathy
Allele origin: germline
Invitae
Accession: SCV001679177.1
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Mar 14, 2013)
no assertion criteria provided
Method: clinical testing
Noonan syndrome
Allele origin: unknown
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000206730.1
Submitted: (Jan 27, 2015)
Evidence details

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs587781132...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021