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.

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.

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						0
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	22	2	0

Variants in PTP4A3

This is a list of pathogenic ClinVar variants found in the PTP4A3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-141422238-G-T			Likely benign (Jan 01, 2023)
8-141422248-G-A		not specified	Uncertain significance (May 23, 2024)
8-141422257-G-A		not specified	Uncertain significance (Nov 21, 2024)
8-141422260-C-A		not specified	Uncertain significance (Aug 14, 2024)
8-141422260-C-T		not specified	Uncertain significance (Dec 23, 2024)
8-141422278-G-C		not specified	Uncertain significance (Aug 07, 2024)
8-141422320-A-C		not specified	Uncertain significance (Oct 09, 2024)
8-141422322-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-141425059-G-T		not specified	Uncertain significance (Dec 18, 2023)
8-141425103-A-G		not specified	Uncertain significance (Oct 11, 2024)
8-141425109-C-T		not specified	Uncertain significance (Nov 02, 2023)
8-141426934-C-T			Benign (Apr 10, 2018)
8-141426976-A-G		not specified	Uncertain significance (Jan 18, 2023)
8-141427002-G-C		not specified	Likely benign (Oct 17, 2024)
8-141427029-G-A		not specified	Uncertain significance (Dec 20, 2023)
8-141427047-C-T		not specified	Uncertain significance (Jan 23, 2023)
8-141427053-G-A		not specified	Uncertain significance (Jul 02, 2024)
8-141427805-G-A		not specified	Uncertain significance (Jan 03, 2022)
8-141430934-C-T		not specified	Uncertain significance (Dec 28, 2022)
8-141430935-G-A		not specified	Uncertain significance (Dec 05, 2024)
8-141430961-A-G		not specified	Uncertain significance (Aug 12, 2024)
8-141430998-G-A		not specified	Uncertain significance (Jul 12, 2023)
8-141431009-C-T		not specified	Uncertain significance (Aug 10, 2021)
8-141431015-A-C		not specified	Uncertain significance (Dec 03, 2021)
8-141431016-C-T		not specified	Uncertain significance (Dec 17, 2023)

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