PTP4A3

protein tyrosine phosphatase 4A3, the group of Protein tyrosine phosphatase 4A family

Basic information

Region (hg38): 8:141391995-141432454

Links

ENSG00000184489

∙ NCBI:11156 ∙ OMIM:606449 ∙ HGNC:9636 ∙ Uniprot:O75365 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTP4A3 gene.

not_specified (31 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTP4A3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032611.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			30 clinvar	1 clinvar		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTP4A3	protein_coding	protein_coding	ENST00000521578	5	39528

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0455	0.862	125595	0	7	125602	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	93	127	0.735	0.00000909	1123
Missense in Polyphen		38	59.388	0.63986		503
Synonymous	0.784	47	54.4	0.865	0.00000425	342
Loss of Function	1.38	3	6.91	0.434	2.93e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000509	0.0000462
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Protein tyrosine phosphatase which stimulates progression from G1 into S phase during mitosis. Enhances cell proliferation, cell motility and invasive activity, and promotes cancer metastasis. May be involved in the progression of cardiac hypertrophy by inhibiting intracellular calcium mobilization in response to angiotensin II. {ECO:0000269|PubMed:11355880, ECO:0000269|PubMed:12782572}.;
Pathway: Signaling events mediated by PRL (Consensus)

Recessive Scores

pRec: 0.221

Intolerance Scores

loftool: 0.333
rvis_EVS: -0.32
rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

pHI: 0.219
hipred: Y
hipred_score: 0.714
ghis: 0.576

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.767

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Ptp4a3
Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; neoplasm; 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);

Gene ontology

Biological process: regulation of transcription, DNA-templated;Notch signaling pathway;peptidyl-tyrosine dephosphorylation;positive regulation of vascular permeability;endothelial cell migration;regulation of vascular endothelial growth factor signaling pathway;positive regulation of NIK/NF-kappaB signaling;positive regulation of establishment of protein localization;cellular response to leukemia inhibitory factor
Cellular component: nucleus;cytoplasm;early endosome;plasma membrane
Molecular function: protein tyrosine phosphatase activity;prenylated protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity