GeneBe

PTPN14

protein tyrosine phosphatase non-receptor type 14, the group of FERM domain containing|Protein tyrosine phosphatases non-receptor type

Basic information

Region (hg38): 1:214348700-214552449

Links

ENSG00000152104 ∙ NCBI:5784 ∙ OMIM:603155 ∙ HGNC:9647 ∙ Uniprot:Q15678 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • lymphedema-posterior choanal atresia syndrome (Supportive), mode of inheritance: AR
  • lymphedema-posterior choanal atresia syndrome (Strong), mode of inheritance: AR
  • lymphedema-posterior choanal atresia syndrome (Strong), mode of inheritance: AR
  • lymphedema-posterior choanal atresia syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Choanal atresia and lymphedemaARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic; Cardiovascular; Craniofacial7158640; 1872518; 20826270

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTPN14 gene.

  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN14 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
13
clinvar
8
clinvar
 21
missense
79
clinvar
6
clinvar
5
clinvar
 90
nonsense
1
clinvar
1
clinvar
 2
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 1 0 80 19 13

Highest pathogenic variant AF is 0.0000591646

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PTPN14protein_codingprotein_codingENST00000366956 18203754
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.2210.7791257250231257480.0000915
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.685917180.8240.00004407814
Missense in Polyphen2022980.677853210
Synonymous-0.3952992901.030.00001972298
Loss of Function5.501459.90.2340.00000367623

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002180.000213
Ashkenazi Jewish0.000.00
East Asian0.00005500.0000544
Finnish0.0001390.000139
European (Non-Finnish)0.00008840.0000879
Middle Eastern0.00005500.0000544
South Asian0.00009800.0000980
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Protein tyrosine phosphatase which may play a role in the regulation of lymphangiogenesis, cell-cell adhesion, cell- matrix adhesion, cell migration, cell growth and also regulates TGF-beta gene expression, thereby modulating epithelial- mesenchymal transition. Mediates beta-catenin dephosphorylation at adhesion junctions. Acts as a negative regulator of the oncogenic property of YAP, a downstream target of the hippo pathway, in a cell density-dependent manner. May function as a tumor suppressor. {ECO:0000269|PubMed:10934049, ECO:0000269|PubMed:12808048, ECO:0000269|PubMed:17893246, ECO:0000269|PubMed:20826270, ECO:0000269|PubMed:22233626, ECO:0000269|PubMed:22525271, ECO:0000269|PubMed:22948661}.;
Disease
DISEASE: Choanal atresia and lymphedema (CATLPH) [MIM:613611]: A disease characterized by posterior choanal atresia and lymphedema. Additional features are a high-arched palate, hypoplastic nipples, and mild pectus excavatum. {ECO:0000269|PubMed:20826270}. Note=The disease is caused by mutations affecting the gene represented in this entry. A homozygous deletion in PTPN14 predicted to result in frameshift and premature truncation, has been shown to be the cause of choanal atresia and lymphedema in one family.; DISEASE: Note=Influence clinical severity of hereditary haemorragic telagiectasia (HHT). {ECO:0000269|PubMed:22233626}.;

Recessive Scores

pRec
0.283

Intolerance Scores

loftool
0.166
rvis_EVS
-0.3
rvis_percentile_EVS
32.28

Haploinsufficiency Scores

pHI
0.251
hipred
Y
hipred_score
0.563
ghis
0.491

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.902

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ptpn14
Phenotype
growth/size/body region phenotype; homeostasis/metabolism phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype;

Gene ontology

Biological process
lymphangiogenesis;protein dephosphorylation;negative regulation of cell population proliferation;peptidyl-tyrosine dephosphorylation;regulation of protein export from nucleus;cellular response to cytokine stimulus;regulation of nucleic acid-templated transcription
Cellular component
nucleus;nucleoplasm;cytoplasm;cytoskeleton
Molecular function
transcription coregulator activity;protein tyrosine phosphatase activity;protein binding;receptor tyrosine kinase binding