NM_002834.5(PTPN11):c.1381G>T (p.Ala461Ser) AND LEOPARD syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 1, 2021
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:: RCV001729356.1

Allele description [Variation Report for NM_002834.5(PTPN11):c.1381G>T (p.Ala461Ser)]

NM_002834.5(PTPN11):c.1381G>T (p.Ala461Ser)

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.1381G>T (p.Ala461Ser)

Other names:

p.A461S:GCT>TCT

HGVS:

NC_000012.12:g.112488444G>T
NG_007459.1:g.74713G>T
NM_001330437.2:c.1393G>T
NM_001374625.1:c.1378G>T
NM_002834.5:c.1381G>TMANE SELECT
NP_001317366.1:p.Ala465Ser
NP_001361554.1:p.Ala460Ser
NP_002825.3:p.Ala461Ser
LRG_614t1:c.1381G>T
LRG_614:g.74713G>T
NC_000012.11:g.112926248G>T
NM_002834.3:c.1381G>T
NM_002834.4:c.1381G>T
c.1381G>T

Protein change:

A460S

Links:

dbSNP: rs121918468

NCBI 1000 Genomes Browser:

rs121918468

Molecular consequence:

NM_001330437.2:c.1393G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.1378G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.1381G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: LEOPARD syndrome 1 (LPRD1)
Synonyms:: LENTIGINOSIS, CARDIOMYOPATHIC; MULTIPLE LENTIGINES 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
SCV001976665	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 1, 2021)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34008892, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001976665

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 1, 2021)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Phenotype-driven variant filtration strategy in exome sequencing toward a high diagnostic yield and identification of 85 novel variants in 400 patients with rare Mendelian disorders.

Marinakis NM, Svingou M, Veltra D, Kekou K, Sofocleous C, Tilemis FN, Kosma K, Tsoutsou E, Fryssira H, Traeger-Synodinos J.

Am J Med Genet A. 2021 Aug;185(8):2561-2571. doi: 10.1002/ajmg.a.62338. Epub 2021 May 19.

PubMed [citation]

PMID:: 34008892

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 Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV001976665.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

PM1, PM2, PM5, PP2, PP3, PP5

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

Last Updated: Feb 20, 2024

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