NM_002834.5(PTPN11):c.923A>C (p.Asn308Thr) AND LEOPARD syndrome 1

Germline classification:: Pathogenic (1 submission)
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:: RCV004795947.2

Allele description [Variation Report for NM_002834.5(PTPN11):c.923A>C (p.Asn308Thr)]

NM_002834.5(PTPN11):c.923A>C (p.Asn308Thr)

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.923A>C (p.Asn308Thr)

Other names:

p.N308T:AAT>ACT

HGVS:

NC_000012.12:g.112477720A>C
NG_007459.1:g.63989A>C
NM_001330437.2:c.923A>C
NM_001374625.1:c.920A>C
NM_002834.5:c.923A>CMANE SELECT
NM_080601.3:c.923A>C
NP_001317366.1:p.Asn308Thr
NP_001361554.1:p.Asn307Thr
NP_002825.3:p.Asn308Thr
NP_542168.1:p.Asn308Thr
LRG_614t1:c.923A>C
LRG_614:g.63989A>C
NC_000012.11:g.112915524A>C
NM_002834.3:c.923A>C
NM_002834.4:c.923A>C
NM_080601.1:c.923A>C
c.923A>C

Protein change:

N307T

Links:

dbSNP: rs121918455

Molecular consequence:

NM_001330437.2:c.923A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.920A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.923A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_080601.3:c.923A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: LEOPARD syndrome 1 (LPRD1)
Synonyms:: LENTIGINOSIS, CARDIOMYOPATHIC; MULTIPLE LENTIGINES SYNDROME; PTPN11-Related LEOPARD Syndrome
Identifiers:: MONDO: MONDO:0100082; MedGen: C4551484; Orphanet: 500; OMIM: 151100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005418654	Juno Genomics, Hangzhou Juno Genomics, Inc	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005418654

Juno Genomics, Hangzhou Juno Genomics, Inc

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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 Juno Genomics, Hangzhou Juno Genomics, Inc, SCV005418654.2

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

Description

Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.;Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc).;Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.;Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 20, 2026

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