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NM_005401.5(PTPN14):c.715A>T (p.Ile239Phe) AND Lymphedema-posterior choanal atresia syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 15, 2023
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:
RCV003455870.1

Allele description [Variation Report for NM_005401.5(PTPN14):c.715A>T (p.Ile239Phe)]

NM_005401.5(PTPN14):c.715A>T (p.Ile239Phe)

Gene:
PTPN14:protein tyrosine phosphatase non-receptor type 14 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q32.3
Genomic location:
Preferred name:
NM_005401.5(PTPN14):c.715A>T (p.Ile239Phe)
HGVS:
  • NC_000001.11:g.214397956T>A
  • NG_028036.1:g.158726A>T
  • NM_005401.5:c.715A>TMANE SELECT
  • NP_005392.2:p.Ile239Phe
  • NC_000001.10:g.214571299T>A
Protein change:
I239F
Molecular consequence:
  • NM_005401.5:c.715A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Lymphedema-posterior choanal atresia syndrome
Synonyms:
Choanal atresia and lymphedema
Identifiers:
MONDO: MONDO:0013324; MedGen: C3150875; OMIM: 613611

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004177040Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 15, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Clinical Genomics Laboratory, Washington University in St. Louis, SCV004177040.1

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

Description

The PTPN14 c.715A>T (p.Ile239Phe) variant was identified at a near-heterozygous allelic fraction. This variant, to our knowledge, has not been reported in the medical literature. This variant is only observed on 1/152106 alleles in the general population (gnomAD v.3.1.2), indicating it is not a common variant. Computational predictors indicate that the variant is damaging; however, functional evidence that correlates with impact on PTPN14 function is lacking. Due to limited information and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time.

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

Last Updated: Dec 30, 2023