NM_002834.5(PTPN11):c.971A>G (p.Lys324Arg) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 30, 2019
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:: RCV001193712.1

Allele description [Variation Report for NM_002834.5(PTPN11):c.971A>G (p.Lys324Arg)]

NM_002834.5(PTPN11):c.971A>G (p.Lys324Arg)

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.971A>G (p.Lys324Arg)

HGVS:

NC_000012.12:g.112477894A>G
NG_007459.1:g.64163A>G
NM_001330437.2:c.971A>G
NM_001374625.1:c.968A>G
NM_002834.5:c.971A>GMANE SELECT
NM_080601.3:c.971A>G
NP_001317366.1:p.Lys324Arg
NP_001361554.1:p.Lys323Arg
NP_002825.3:p.Lys324Arg
NP_542168.1:p.Lys324Arg
LRG_614t1:c.971A>G
LRG_614:g.64163A>G
NC_000012.11:g.112915698A>G
NM_002834.3:c.971A>G

Protein change:

K323R

Links:

dbSNP: rs772684421

NCBI 1000 Genomes Browser:

rs772684421

Molecular consequence:

NM_001330437.2:c.971A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.968A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.971A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_080601.3:c.971A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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flavanone 3-dioxygenase 3-like [Oryza sativa Japonica Group]
flavanone 3-dioxygenase 3-like [Oryza sativa Japonica Group]
gi|1002258905|ref|XP_015633792.1|

Protein
AAF98317 AND 1[s_discriminator] (0)
dbGaP
AAF98317 (0)
Conserved Domains
dipeptidyl peptidase 8 isoform 2 [Homo sapiens]
dipeptidyl peptidase 8 isoform 2 [Homo sapiens]
gi|18450278|ref|NP_060213.2|

Protein
Chain G, complex I
Chain G, complex I
gi|1109304329|pdb|5LUF|G

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001362751	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Dec 30, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001362751

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Dec 30, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001362751.1

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

Description

Variant summary: PTPN11 c.971A>G (p.Lys324Arg) results in a conservative amino acid change located in the PTP type protein phosphatase (PTPase) domain (IPR000242) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251402 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.971A>G in individuals affected with Noonan Syndrome and Related Conditions and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: Apr 23, 2022

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